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A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule


Authors: K. Meyer, O. Ostrenko, G. Bourantas, H. Morales-Navarrete, N. Porat-Shliom, F. Segovia-Miranda, H. Nonaka, A. Ghaemi, J. M. Verbavatz, L. Brusch, I. Sbalzarini, Y. Kalaidzidis, R. Weigert, M. Zerial

PubMed ID: 28330614

Date Published: 24th Mar 2017

Projects: Showcase LIAM (Liver Image Analysis Based Model)

Journal: Cell Syst

Citation: Cell Syst. 2017 Mar 15. pii: S2405-4712(17)30052-2. doi: 10.1016/j.cels.2017.02.008.

Scales: Liver lobule

Abstract (Expand)

Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its ...

Created: 25th Jul 2017 at 13:19


 

Use of Fibonacci numbers in lipidomics - Enumerating various classes of fatty acids


Authors: S. Schuster, M. Fichtner, S. Sasso

PubMed ID: 28071669

Date Published: 11th Jan 2017

Projects: Showcase Steatosis

Journal: Sci Rep

Citation: Sci Rep. 2017 Jan 10;7:39821. doi: 10.1038/srep39821.

Scales: Cell

Abstract (Expand)

In lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when ...

Created: 24th Jun 2017 at 17:16


 

Quantification of Hepatic Vascular and Parenchymal Regeneration in Mice


Authors: Chichi Xie, Lars Ole Schwen, Weiwei Wei, Andrea Schenk, Sara Zafarnia, Felix Gremse, Uta Dahmen

DOI: 10.1371/journal.pone.0160581

Date Published: 5th Aug 2016

Projects: D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale

Journal: PLoS ONE

Citation: PLoS ONE 11(8) : e0160581

Scales: Liver

Abstract (Expand)

Background. Liver regeneration consists of cellular proliferation leading to parenchymal and vascular growth. This study complements previous studies on cellular proliferation and weight recovery by ...

Created: 26th May 2017 at 09:10   Last updated: 26th May 2017 at 09:12


 

Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages


Authors: Julia Rex, Ute Albrecht, Christian Ehlting, Maria Thomas, Ulrich M. Zanger, Oliver Sawodny, Dieter Häussinger, Michael Ederer, Ronny Feuer, Johannes G. Bode

DOI: 10.1371/journal.pcbi.1005018

Date Published: 27th Jul 2016

Projects: B1: Intercellular communication of hepatocytes and macrophages

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 12(7) : e1005018

Scales: Cell and Intercellular

Abstract (Expand)

Macrophages are cells with remarkable plasticity. They integrate signals from their microenvironment leading to context-dependent polarization into classically (M1) or alternatively (M2) activated ...

Created: 23rd Nov 2016 at 13:29   Last updated: 23rd Nov 2016 at 13:32


 

Intrahepatic Size Regulation in a Surgical Model: Liver Resection-Induced Liver Regeneration Counteracts the Local Atrophy following Simultaneous Portal Vein Ligation


Authors: Weiwei Wei, Tianjiao Zhang, Haoshu Fang, Olaf Dirsch, Andrea Schenk, André Homeyer, Felix Gremse, Sara Zafarnia, Utz Settmacher, Uta Dahmen

DOI: 10.1159/000446875

Date Published: 5th Jul 2016

Projects: D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale

Journal: Eur Surg Res

Citation: Eur Surg Res 57(1-2) : 125

Scales: Liver

Abstract (Expand)

Background/Aim: Liver size regulation is based on the balance between hepatic regeneration and atrophy. To achieve a better understanding of intrahepatic size regulation, we explored the size regulation ...

Created: 26th May 2017 at 10:43   Last updated: 26th May 2017 at 10:45


 

Establishment of a rat model: Associating liver partition with portal vein ligation for staged hepatectomy


Authors: Weiwei Wei, Tianjiao Zhang, Sara Zafarnia, Andrea Schenk, Chichi Xie, Chunyi Kan, Olaf Dirsch, Utz Settmacher, Uta Dahmen

DOI: 10.1016/j.surg.2015.12.005

Date Published: 1st May 2016

Projects: D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale

Journal: Surgery

Citation: Surgery 159(5) : 1299

Scales: Liver

Abstract (Expand)

BACKGROUND: We adapted the anatomically oriented parenchyma-preserving resection technique for associating liver partition with portal vein ligation (PVL) for staged hepatectomy (ALPPS) in rats and ...

Created: 26th May 2017 at 10:46   Last updated: 26th May 2017 at 10:47


 

Mechanistically linked serum miRNAs distinguish between drug induced and fatty liver disease of different grades


Authors: Z. Liu, Y. Wang, J. Borlak, W. Tong

PubMed ID: 27045805

Date Published: 6th Apr 2016

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Sci Rep

Citation: Sci Rep. 2016 Apr 5;6:23709. doi: 10.1038/srep23709.

Scales: Liver

Abstract (Expand)

Hepatic steatosis is characterised by excessive triglyceride accumulation in the form of lipid droplets (LD); however, mechanisms differ in drug induced (DIS) and/or non-alcoholic fatty liver disease ...

Created: 18th May 2016 at 10:50


 

Zonated Quantification of Steatosis in an Entire Mouse Liver


Authors: Lars Ole Schwen, André Homeyer, Michael Schwier, Uta Dahmen, Olaf Dirsch, Arne Schenk, Lars Kuepfer, Tobias Preusser, Andrea Schenk

DOI: 10.1016/j.compbiomed.2016.04.004

Date Published: 1st Apr 2016

Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, Showcase Steatosis

Journal: Computers in Biology and Medicine

Citation: Computers in Biology and Medicine

Scales: Cell, Liver lobule, Liver and Organism

Abstract (Expand)

Many physiological processes and pathological conditions in livers are spatially heterogeneous, forming patterns at the lobular length scale or varying across the organ. Steatosis, a common liver disease ...

Created: 13th Apr 2016 at 15:13   Last updated: 13th Apr 2016 at 15:16


 

Inhibition of bile salt transport by drugs associated with liver injury in primary hepatocytes from human, monkey, dog, rat, and mouse


Authors: J. Zhang, K. He, L. Cai, Y. C. Chen, Y. Yang, Q. Shi, T. F. Woolf, W. Ge, L. Guo, J. Borlak, W. Tong

PubMed ID: 27000539

Date Published: 24th Mar 2016

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Chem Biol Interact

Citation: Chem Biol Interact. 2016 Mar 19. pii: S0009-2797(16)30089-8. doi: 10.1016/j.cbi.2016.03.019.

Scales: Cell

Abstract (Expand)

Interference of bile salt transport is one of the underlying mechanisms for drug-induced liver injury (DILI). We developed a novel bile salt transport activity assay involving in situ biosynthesis of ...

Created: 18th May 2016 at 10:56


 

Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice


Authors: E. H. Lee, J. H. Oh, S. Selvaraj, S. M. Park, M. S. Choi, R. Spanel, S. Yoon, J. Borlak

PubMed ID: 26934552

Date Published: 5th Mar 2016

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Oncotarget

Citation: Oncotarget. 2016 Feb 25. doi: 10.18632/oncotarget.7698.

Scales: Liver

Abstract (Expand)

Diclofenac is a non-steroidal anti-inflammatory drug and its use can be associated with severe adverse reactions, notably myocardial infarction, stroke and drug-induced liver injury (DILI). In pursue ...

Created: 18th May 2016 at 10:52


 

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling


Authors: Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger

DOI: 10.1371/journal.pcbi.1004431

Date Published: 4th Jan 2016

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 12(1) : e1004431

Scales: Cell

Abstract (Expand)

During various inflammatory processes circulating cytokines including IL-6, IL-1β, and TNFα elicit a broad and clinically relevant impairment of hepatic detoxification that is based on the downregulation ...

Created: 7th Jan 2016 at 15:20   Last updated: 7th Jan 2016 at 15:24


 

Visualization of Vascular and Parenchymal Regeneration after 70% Partial Hepatectomy in Normal Mice


Authors: Chichi Xie, Weiwei Wei, Andrea Schenk, Lars Ole Schwen, Sara Zafarnia, Michael Schwier, Felix Gremse, Isabel Jank, Olaf Dirsch, Uta Dahmen

DOI: 10.3791/53935

Date Published: 2016

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: JoVE

Citation: JoVE (115)

Scales: Liver

Abstract (Expand)

A modified silicone injection procedure was used for visualization of the hepatic vascular tree. This procedure consisted of in-vivo injection of the silicone compound, via a 26 G catheter, into the ...

Created: 14th Sep 2016 at 10:17   Last updated: 14th Sep 2016 at 10:20


 

The evolution of standards and data management practices in systems biology


Authors: N. J. Stanford, K. Wolstencroft, M. Golebiewski, R. Kania, N. Juty, C. Tomlinson, S. Owen, S. Butcher, H. Hermjakob, N. Le Novere, W. Mueller, J. Snoep, C. Goble

PubMed ID: 26700851

Date Published: 25th Dec 2015

Projects: F1: The data management system, Virtual Liver

Journal: Mol Syst Biol

Citation: Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053.

Scales: Not specified

Abstract:

Not specified

Created: 8th Jan 2016 at 09:38


 

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks


Authors: Andreas Dräger, Daniel C Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O Palsson, Andreas Zell

DOI: 10.1186/s12918-015-0212-9

Date Published: 1st Dec 2015

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 9(1) : 389

Scales: Cell and Intercellular

Abstract (Expand)

Background: The size and complexity of published biochemical network reconstructions are steadily increasing, expanding the potential scale of derived computational models. However, the construction ...

Created: 16th Nov 2015 at 15:27   Last updated: 16th Nov 2015 at 15:29


 

Intrahepatic Vascular Anatomy in Rats and Mice—Variations and Surgical Implications


Authors: Constanze Sänger, Andrea Schenk, Lars Ole Schwen, Lei Wang, Felix Gremse, Sara Zafarnia, Fabian Kiessling, Chichi Xie, Weiwei Wei, Beate Richter, Olaf Dirsch, Uta Dahmen

DOI: 10.1371/journal.pone.0141798

Date Published: 30th Nov 2015

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: PLoS ONE

Citation: PLoS ONE 10(11) : e0141798

Scales: Liver

Abstract (Expand)

Introduction The intra-hepatic vascular anatomy in rodents, its variations and corresponding supplying and draining territories in respect to the lobar structure of the liver have not been described. ...

Created: 13th Jan 2016 at 08:00   Last updated: 13th Jan 2016 at 08:03


 

Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice


Authors: K. Abshagen, M. Konig, A. Hoppe, I. Muller, M. Ebert, H. Weng, H. G. Holzhutter, U. M. Zanger, J. Bode, B. Vollmar, M. Thomas, S. Dooley

PubMed ID: 26589287

Date Published: 20th Nov 2015

Projects: A1: Cellular metabolism, A2: Integration of Signalling Pathways in Hepatocellular Response, A3: Crosslinking signalling metabolism and hepatocyte polarisation, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells, C: Liver lobule level, D: Whole organ level

Journal: BMC Syst Biol

Citation: BMC Syst Biol. 2015 Nov 20;9(1):83.

Scales: Cell, Liver lobule and Liver

Abstract (Expand)

BACKGROUND: Disrupted bile secretion leads to liver damage characterized by inflammation, fibrosis, eventually cirrhosis, and hepatocellular cancer. As obstructive cholestasis often progresses insidiously, ...

Created: 23rd Nov 2015 at 07:41


 

Evaluation of multiple mechanism-based toxicity endpoints in primary cultured human hepatocytes for the identification of drugs with clinical hepatotoxicity: Results from 152 marketed drugs with known liver injury profiles


Authors: J. Zhang, U. Doshi, A. Suzuki, C. W. Chang, J. Borlak, A. P. Li, W. Tong

PubMed ID: 26581450

Date Published: 20th Nov 2015

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Chem Biol Interact

Citation: Chem Biol Interact. 2015 Nov 12. pii: S0009-2797(15)30110-1. doi: 10.1016/j.cbi.2015.11.008.

Scales: Cell

Abstract (Expand)

We report here the results of a collaborative research program to develop a robust and reliable in vitro system to allow an accurate definition of the drug-induced liver injury (DILI) potential of new ...

Created: 30th Dec 2015 at 10:41


 

The Therapeutic Promise of Mesenchymal Stem Cells for Liver Restoration


Authors: B. Christ, S. Bruckner, S. Winkler

PubMed ID: 26476857

Date Published: 22nd Oct 2015

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Trends Mol Med

Citation: Trends Mol Med. 2015 Nov;21(11):673-86. doi: 10.1016/j.molmed.2015.09.004. Epub 2015 Oct 22.

Scales: Liver

Abstract (Expand)

Hepatocyte transplantation aims to provide a functional substitution of liver tissue lost due to trauma or toxins. Chronic liver diseases are associated with inflammation, deterioration of tissue ...

Created: 11th Nov 2015 at 11:21


 

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways


Authors: M. Garmhausen, F. Hofmann, V. Senderov, M. Thomas, B. A. Kandel, B. H. Habermann

PubMed ID: 26467653

Date Published: 14th Oct 2015

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: BMC Genomics

Citation: BMC Genomics. 2015 Oct 14;16(1):790. doi: 10.1186/s12864-015-2017-z.

Scales: Not specified

Abstract (Expand)

BACKGROUND: Interpreting large-scale studies from microarrays or next-generation sequencing for further experimental testing remains one of the major challenges in quantitative biology. Combining ...

Created: 18th Dec 2015 at 12:55


 

Optimality in the zonation of ammonia detoxification in rodent liver


Authors: M. Bartl, M. Pfaff, A. Ghallab, D. Driesch, S. G. Henkel, J. G. Hengstler, S. Schuster, C. Kaleta, R. Gebhardt, S. Zellmer, P. Li

PubMed ID: 26438405

Date Published: 5th Oct 2015

Projects: C3: Zonation of metabolism and its regulation

Journal: Arch Toxicol

Citation: Arch Toxicol. 2015 Nov;89(11):2069-78. doi: 10.1007/s00204-015-1596-4. Epub 2015 Oct 5.

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

The rodent liver eliminates toxic ammonia. In mammals, three enzymes (or enzyme systems) are involved in this process: glutaminase, glutamine synthetase and the urea cycle enzymes, represented by ...

Created: 11th Dec 2015 at 09:07


 

Development of Human Membrane Transporters: Drug Disposition and Pharmacogenetics


Authors: M. G. Mooij, A. T. Nies, C. A. Knibbe, E. Schaeffeler, D. Tibboel, M. Schwab, S. N. de Wildt

PubMed ID: 26410689

Date Published: 28th Sep 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin Pharmacokinet

Citation: Clin Pharmacokinet. 2015 Sep 26.

Scales: Not specified

Abstract (Expand)

Membrane transporters play an essential role in the transport of endogenous and exogenous compounds, and consequently they mediate the uptake, distribution, and excretion of many drugs. The clinical ...

Created: 17th Dec 2015 at 11:53


 

Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types


Authors: H. Stark, M. Fichtner, R. Konig, S. Lorkowski, S. Schuster

PubMed ID: 26382968

Date Published: 14th Sep 2015

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Biochimie

Citation: Biochimie. 2015 Nov;118:185-94. doi: 10.1016/j.biochi.2015.09.017. Epub 2015 Sep 14.

Scales: Cell

Abstract (Expand)

In this review, we revisit the metabolic shift from respiration to glycolysis in lymphocytes upon activation, which is known as the Warburg effect in tumour cells. We compare the situation in lymphocytes ...

Created: 11th Dec 2015 at 16:06


 

Heritability of metoprolol and torsemide pharmacokinetics


Authors: J. Matthaei, J. Brockmoller, M. V. Tzvetkov, D. Sehrt, C. Sachse-Seeboth, J. B. Hjelmborg, S. Moller, U. Halekoh, U. Hofmann, M. Schwab, R. Kerb

PubMed ID: 26344676

Date Published: 8th Sep 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin Pharmacol Ther

Citation: Clin Pharmacol Ther. 2015 Sep 7. doi: 10.1002/cpt.258.

Scales: Not specified

Abstract (Expand)

Genetic variation in the pharmacokinetics of metoprolol and torsemide due to polymorphisms in CYP2D6, CYP2C9, and OATP1B1 has been extensively studied. However, it is still unknown how much of the ...

Created: 17th Dec 2015 at 11:46


 

Specifications of Standards in Systems and Synthetic Biology


Authors: F. Schreiber, G. D. Bader, M. Golebiewski, M. Hucka, B. Kormeier, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Waltemath, S. Weise

PubMed ID: 26528556

Date Published: 4th Sep 2015

Projects: F1: The data management system, Virtual Liver

Journal: J Integr Bioinform

Citation: J Integr Bioinform. 2015 Sep 4;12(2):258. doi: 10.2390/biecoll-jib-2015-258.

Scales: Not specified

Abstract (Expand)

Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic ...

Created: 17th Dec 2015 at 09:15


 

LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods


Authors: R. Feuer, S. Vlaic, J. Arlt, O. Sawodny, U. Dahmen, U. M. Zanger, M. Thomas

PubMed ID: 26325269

Date Published: 1st Sep 2015

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase LPS and Inflammation

Journal: PLoS One

Citation: PLoS One. 2015 Sep 1;10(9):e0135852. doi: 10.1371/journal.pone.0135852. eCollection 2015.

Scales: Cell

Abstract (Expand)

BACKGROUND: Gene expression analysis is an essential part of biological and medical investigations. Quantitative real-time PCR (qPCR) is characterized with excellent sensitivity, dynamic range, ...

Created: 17th Sep 2015 at 10:13


 

Comparative Analysis and Functional Characterization of HC-AFW1 Hepatocarcinoma Cells: CYP Expression and Induction by Nuclear Receptor Agonists


Authors: A. Braeuning, M. Thomas, U. Hofmann, S. Vetter, E. Zeller, B. Petzuch, J. Johanning, W. Schroth, T. S. Weiss, U. M. Zanger, M. Schwarz

PubMed ID: 26310804

Date Published: 28th Aug 2015

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Drug Metab Dispos

Citation: Drug Metab Dispos. 2015 Aug 26. pii: dmd.115.064667.

Scales: Cell

Abstract (Expand)

Enzymatic conversion of most xenobiotic compounds is accomplished by hepatocytes in the liver, which are also an important target for the manifestation of the toxic effects of foreign compounds. Most ...

Created: 17th Sep 2015 at 10:17


 

Mouse white adipose tissue-derived mesenchymal stem cells gain pericentral and periportal hepatocyte features after differentiation in vitro, which are preserved in vivo after hepatic transplantation


Authors: S. Winkler, M. Hempel, S. Bruckner, F. Mallek, A. Weise, T. Liehr, H. M. Tautenhahn, M. Bartels, B. Christ

PubMed ID: 26235702

Date Published: 19th Aug 2015

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Acta Physiol (Oxf)

Citation: Acta Physiol (Oxf). 2015 Oct;215(2):89-104. doi: 10.1111/apha.12560. Epub 2015 Aug 19.

Scales: Liver lobule

Abstract (Expand)

AIM: Mesenchymal stem cells may differentiate into hepatocyte-like cells in vitro and in vivo. Therefore, they are considered a novel cell resource for the treatment of various liver diseases. Here, ...

Created: 11th Nov 2015 at 11:22


 

SDA 7: A modular and parallel implementation of the simulation of diffusional association software


Authors: Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter, Rebecca C. Wade

DOI: 10.1002/jcc.23971

Date Published: 5th Aug 2015

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: J. Comput. Chem.

Citation: J. Comput. Chem. 36(21) : 1631

Scales: Cell

Abstract (Expand)

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular ...

Created: 18th Sep 2015 at 11:12   Last updated: 18th Sep 2015 at 12:36


 

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation


Authors: Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer, Bernd Bukau

DOI: 10.1038/nature14884

Date Published: 5th Aug 2015

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Nature

Citation: Nature 524(7564) : 247

Scales: Organism

Abstract (Expand)

Protein aggregates are the hallmark of stressed and ageing cells, and characterize several pathophysiological states. Healthy metazoan cells effectively eliminate intracellular protein aggregates, ...

Created: 18th Sep 2015 at 13:35   Last updated: 18th Sep 2015 at 13:41


 

Variability in hepatic expression of organic anion transporter 7/SLC22A9, a novel pravastatin uptake transporter: impact of genetic and regulatory factors


Authors: A. Emami Riedmaier, O. Burk, B. A. van Eijck, E. Schaeffeler, K. Klein, S. Fehr, S. Biskup, S. Muller, S. Winter, U. M. Zanger, M. Schwab, A. T. Nies

PubMed ID: 26239079

Date Published: 5th Aug 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Pharmacogenomics J

Citation: Pharmacogenomics J. 2015 Aug 4. doi: 10.1038/tpj.2015.55.

Scales: Not specified

Abstract (Expand)

Human organic anion transporter 7 (OAT7, SLC22A9) is a hepatic transport protein poorly characterized so far. We therefore sought to identify novel OAT7 substrates and factors contributing to variable ...

Created: 17th Dec 2015 at 11:49


 

Representative Sinusoids for Hepatic Four-Scale Pharmacokinetics Simulations


Authors: Lars Ole Schwen, Arne Schenk, Clemens Kreutz, Jens Timmer, María Matilde Bartolomé Rodríguez, Lars Kuepfer, Tobias Preusser

DOI: 10.1371/journal.pone.0133653

Date Published: 29th Jul 2015

Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: PLoS ONE

Citation: PLoS ONE 10(7) : e0133653

Scales: Cell, Liver lobule, Liver and Organism

Abstract (Expand)

The mammalian liver plays a key role for metabolism and detoxification of xenobiotics in the body. The corresponding biochemical processes are typically subject to spatial variations at different length ...

Created: 30th Jul 2015 at 09:09   Last updated: 30th Jul 2015 at 09:13


 

SEEK: a systems biology data and model management platform


Authors: K. Wolstencroft, S. Owen, O. Krebs, Q. Nguyen, N. J. Stanford, M. Golebiewski, A. Weidemann, M. Bittkowski, L. An, D. Shockley, J. L. Snoep, W. Mueller, C. Goble

PubMed ID: 26160520

Date Published: 11th Jul 2015

Projects: F1: The data management system, Virtual Liver

Journal: BMC Syst Biol

Citation: BMC Syst Biol. 2015 Jul 11;9:33. doi: 10.1186/s12918-015-0174-y.

Scales: Not specified

Abstract (Expand)

BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools ...

Created: 7th Aug 2015 at 11:48


 

The truncated splice variant of peroxisome proliferator-activated receptor alpha, PPARalpha-tr, autonomously regulates proliferative and pro-inflammatory genes


Authors: M. Thomas, C. Bayha, K. Klein, S. Muller, T. S. Weiss, M. Schwab, U. M. Zanger

PubMed ID: 26122096

Date Published: 30th Jun 2015

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Cancer

Citation: BMC Cancer. 2015 Jun 30;15:488. doi: 10.1186/s12885-015-1500-x.

Scales: Not specified

Abstract (Expand)

BACKGROUND: The peroxisome proliferator-activated receptor alpha (PPARalpha) controls lipid/energy homeostasis and inflammatory responses. The truncated splice variant PPARalpha-tr was suggested to ...

Created: 17th Sep 2015 at 10:19


 

webSDA: a web server to simulate macromolecular diffusional association


Authors: Xiaofeng Yu, Michael Martinez, Annika L. Gable, Jonathan C. Fuller, Neil J. Bruce, Stefan Richter, Rebecca C. Wade

DOI: 10.1093/nar/gkv335

Date Published: 30th Jun 2015

Projects: F3: Kinetic data handling

Journal: Nucleic Acids Res

Citation: Nucleic Acids Res 43(W1) : W220

Scales: Cell

Abstract (Expand)

Macromolecular interactions play a crucial role in biological systems. Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study ...

Created: 18th Sep 2015 at 13:33   Last updated: 18th Sep 2015 at 13:34


 

libRoadRunner: A High Performance SBML Simulation and Analysis Library


Authors: Endre T Somogyi, Jean-Marie Bouteiller, James A Glazier, Matthias König, J Kyle Medley, Maciej H Swat, Herbert M Sauro

PubMed ID: 26085503

Date Published: 19th Jun 2015

Projects: No Projects

Journal: Bioinformatics

Citation: Bioinformatics :

Scales: Not specified

Abstract (Expand)

This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language ...

Created: 1st Jul 2015 at 16:00


 

JSBML 1.0: providing a smorgasbord of options to encode systems biology models


Authors: N. Rodriguez, A. Thomas, L. Watanabe, I. Y. Vazirabad, V. Kofia, H. F. Gomez, F. Mittag, J. Matthes, J. Rudolph, F. Wrzodek, E. Netz, A. Diamantikos, J. Eichner, R. Keller, C. Wrzodek, S. Frohlich, N. E. Lewis, C. J. Myers, N. Le Novere, B. O. Palsson, M. Hucka, A. Drager

PubMed ID: 26079347

Date Published: 17th Jun 2015

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Bioinformatics

Citation: Bioinformatics :

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

Abstract (Expand)

JSBML, the official pure Java programming library for the SBML format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented ...

Created: 22nd Jun 2015 at 17:56


 

Is laboratory medicine ready for the era of personalized medicine? A survey addressed to laboratory directors of hospitals/academic schools of medicine in Europe


Authors: F. Malentacchi, I. Mancini, I. Brandslund, P. Vermeersch, M. Schwab, J. Marc, R. H. van Schaik, G. Siest, E. Theodorsson, M. Pazzagli, C. Di Resta

PubMed ID: 26036226

Date Published: 4th Jun 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Drug Metabol Personal Ther

Citation: Drug Metabol Personal Ther. 2015 Jun;30(2):121-8. doi: 10.1515/dmdi-2015-0012.

Scales: Not specified

Abstract (Expand)

Developments in "-omics" are creating a paradigm shift in laboratory medicine leading to personalized medicine. This allows the increase in diagnostics and therapeutics focused on individuals ...

Created: 17th Dec 2015 at 11:44


 

Tools for visualization and analysis of molecular networks, pathways, and -omics data


Authors: J. M. Villaveces, P. Koti, B. H. Habermann

PubMed ID: 26082651

Date Published: 4th Jun 2015

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Adv Appl Bioinform Chem

Citation: Adv Appl Bioinform Chem. 2015 Jun 4;8:11-22. doi: 10.2147/AABC.S63534. eCollection 2015.

Scales: Not specified

Abstract (Expand)

Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological ...

Created: 18th Dec 2015 at 12:57


 

Fast and accurate identification of fat droplets in histological images


Authors: André Homeyer, Andrea Schenk, Janine Arlt, Uta Dahmen, Olaf Dirsch, Horst K. Hahn

DOI: 10.1016/j.cmpb.2015.05.009

Date Published: 1st Jun 2015

Projects: D4: Regeneration and Liver Size, Showcase Steatosis

Journal: Computer Methods and Programs in Biomedicine

Citation: Computer Methods and Programs in Biomedicine

Scales: Cell, Liver lobule and Liver

Abstract (Expand)

Background and objective: The accurate identification of fat droplets is a prerequisite for the automatic quantification of steatosis in histological images. A major challenge in this regard is the ...

Created: 25th Jun 2015 at 09:02   Last updated: 29th Jun 2015 at 09:38


 

Hepatocyte fate upon TGF-β challenge is determined by the matrix environment


Authors: Christoph Meyer, Roman Liebe, Katja Breitkopf-Heinlein, Yan Liu, Alexandra Müller, Pia Rakoczy, Maria Thomas, Honglei Weng, Anastasia Bachmann, Matthias Ebert, Steven Dooley

PubMed ID: 25982745

Date Published: 20th May 2015

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., A3.3: Hepatocyte polarity

Journal: Differentiation

Citation: Differentiation :

Scales: Cell

Abstract (Expand)

Primary hepatocytes are a versatile tool to investigate all aspects of liver function, and frequently used in drug development and testing. Upon TGF-β challenge, hepatocytes either undergo an epithelial ...

Created: 17th Jun 2015 at 09:09


 

Computational Approaches for Studying Drug Binding Kinetics


Authors: Julia Romanowska, Daria B. Kokh, Jonathan C. Fuller, Rebecca C. Wade

DOI: 10.1002/9783527673025.ch11

Date Published: 11th May 2015

Projects: F3: Kinetic data handling

Book: Thermodynamics and Kinetics of Drug Binding

Citation: Methods and Principles in Medicinal Chemistry : 211

Scales: Cell

Abstract (Expand)

The binding kinetics of a drug to its macromolecular receptor can be of key importance for its overall efficacy. Thus, there is a need for methods to compute and predict kinetic parameters for drug-receptor ...

Created: 18th Sep 2015 at 13:23   Last updated: 18th Sep 2015 at 13:26


 

Drug-Induced liver injury: interactions between drug properties and host factors


Authors: Minjun Chen, Ayako Suzuki, Jürgen Borlak, Raúl J Andrade, M Isabel Lucena

PubMed ID: 25912521

Date Published: 29th Apr 2015

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: J. Hepatol.

Citation: J. Hepatol. :

Scales: Not specified

Abstract (Expand)

Idiosyncratic drug-induced liver injury (DILI) is a common cause for drug withdrawal from the market and although infrequent, DILI can result in serious clinical outcomes including acute liver failure ...

Created: 5th May 2015 at 09:06


 

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling


Authors: Lorenza A. D’Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller

DOI: 10.1371/journal.pcbi.1004192

Date Published: 23rd Apr 2015

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., A2: Integration of Signalling Pathways in Hepatocellular Response, A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.4: Linking signalling to metabolic functions, E1: Integration on the cellular level, Showcase HGF and Regeneration

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 11(4) : e1004192

Scales: Cell

Abstract (Expand)

Signaling pathways are characterized by crosstalk, feedback and feedforward mechanisms giving rise to highly complex and cell-context specific signaling networks. Dissecting the underlying relations ...

Created: 5th May 2015 at 13:29   Last updated: 22nd May 2015 at 08:57


 

Regulation of Liver Enriched Transcription Factors in Rat Hepatocytes Cultures on Collagen and EHS Sarcoma Matrices


Authors: Jürgen Borlak, Prafull Kumar Singh, Ina Rittelmeyer

PubMed ID: 25901575

Date Published: 22nd Apr 2015

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: PLoS ONE

Citation: PLoS ONE 10(4): e0124867

Scales: Cell

Abstract (Expand)

Liver-enriched transcription factors (LETF) play a crucial role in the control of liver-specific gene expression and for hepatocytes to retain their molecular and cellular functions complex interactions ...

Created: 5th May 2015 at 13:28


 

Functional characterization of common protein variants in the efflux transporter ABCC11 and identification of T546M as functionally damaging variant


Authors: R. Arlanov, T. Lang, G. Jedlitschky, E. Schaeffeler, T. Ishikawa, M. Schwab, A. T. Nies

PubMed ID: 25896536

Date Published: 22nd Apr 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Pharmacogenomics J

Citation: Pharmacogenomics J. 2015 Apr 21. doi: 10.1038/tpj.2015.27.

Scales: Not specified

Abstract (Expand)

Multidrug resistance protein 8 (ABCC11) is an efflux transporter for anionic lipophilic compounds, conferring resistance to antiviral and anticancer agents like 5-fluorouracil (5-FU). ABCC11 missense ...

Created: 17th Dec 2015 at 11:41


 

Impact of Genetic Polymorphisms of ABCB1 (MDR1, P-Glycoprotein) on Drug Disposition and Potential Clinical Implications: Update of the Literature


Authors: S. Wolking, E. Schaeffeler, H. Lerche, M. Schwab, A. T. Nies

PubMed ID: 25860377

Date Published: 11th Apr 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin Pharmacokinet

Citation: Clin Pharmacokinet. 2015 Jul;54(7):709-35. doi: 10.1007/s40262-015-0267-1.

Scales: Not specified

Abstract (Expand)

ATP-binding cassette transporter B1 (ABCB1; P-glycoprotein; multidrug resistance protein 1) is an adenosine triphosphate (ATP)-dependent efflux transporter located in the plasma membrane of many different ...

Created: 17th Dec 2015 at 11:51


 

Activating and Inhibitory Functions of WNT/β-catenin in the Induction of Cytochromes P450 by Nuclear Receptors in HepaRG Cells


Authors: Maria Thomas, Christine Bayha, Silvia Vetter, Ute Hofmann, Michael Schwarz, Ulrich M Zanger, Albert Braeuning

PubMed ID: 25824487

Date Published: 1st Apr 2015

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase Steatosis

Journal: Mol. Pharmacol.

Citation: Mol. Pharmacol. :

Scales: Cell

Abstract (Expand)

The WNT/β-catenin signaling pathway has been identified as an important endogenous regulator of hepatic cytochrome P450 (CYP) expression in mouse liver. In particular, it is involved in the regulation ...

Created: 7th Apr 2015 at 14:00


 

Mathematical modelling of fluid transport and its regulation at multiple scales


Authors: Osvaldo Chara, Lutz Brusch

DOI: 10.1016/j.biosystems.2015.02.004

Date Published: 1st Apr 2015

Projects: A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., Showcase LIAM (Liver Image Analysis Based Model)

Journal: Biosystems

Citation: Biosystems 130 : 1

Scales: Cell and Liver lobule

Abstract (Expand)

Living matter equals water, to a first approximation, and water transport across barriers such as membranes and epithelia is vital. Water serves two competing functions. On the one hand, it is the ...

Created: 30th Apr 2015 at 15:04   Last updated: 30th Apr 2015 at 15:08


 

Dysregulated serum response factor triggers formation of hepatocellular carcinoma


Authors: Stefan Ohrnberger, Abhishek Thavamani, Albert Braeuning, Daniel B. Lipka, Milen Kirilov, Robert Geffers, Stella E. Authenrieth, Michael Römer, Andreas Zell, Michael Bonin, Michael Schwarz, Günther Schütz, Peter Schirmacher, Christoph Plass, Thomas Longerich, Alfred Nordheim

DOI: 10.1002/hep.27539

Date Published: 1st Mar 2015

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Hepatology

Citation: Hepatology 61(3) : 979

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

The ubiquitously expressed transcriptional regulator serum response factor (SRF) is controlled by both Ras/MAPK (mitogen-activated protein kinase) and Rho/actin signaling pathways, which are frequently ...

Created: 14th Dec 2015 at 15:12   Last updated: 14th Dec 2015 at 15:15


 

Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events


Authors: Jürgen Borlak, Prashant Singh, Giuseppe Gazzana

PubMed ID: 25872475

Date Published: 25th Feb 2015

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: BMC Genomics

Citation: BMC Genomics 16: 124

Scales: Cell

Abstract (Expand)

Hepatocellular carcinoma (HCC) is on the rise and the sixth most common cancer worldwide. To combat HCC effectively research is directed towards its early detection and the development of targeted ...

Created: 5th May 2015 at 13:29


 

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative


Authors: Michael Hucka, David P. Nickerson, Gary D. Bader, Frank T. Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J. Myers, Falk Schreiber, Dagmar Waltemath, Nicolas Le Novère

DOI: 10.3389/fbioe.2015.00019

Date Published: 24th Feb 2015

Projects: F1: The data management system, Virtual Liver

Journal: Front. Bioeng. Biotechnol.

Citation: Front. Bioeng. Biotechnol. 3

Scales: Not specified

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s ...

Created: 25th Feb 2015 at 12:58   Last updated: 25th Feb 2015 at 13:01


 

Pathological implications of cadherin zonation in mouse liver


Authors: M. Hempel, A. Schmitz, S. Winkler, O. Kucukoglu, S. Bruckner, C. Niessen, B. Christ

PubMed ID: 25687506

Date Published: 17th Feb 2015

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Cell Mol Life Sci

Citation: Cell Mol Life Sci. 2015 Jul;72(13):2599-612. doi: 10.1007/s00018-015-1861-y. Epub 2015 Feb 17.

Scales: Liver lobule

Abstract (Expand)

Both acute and chronic liver diseases are associated with ample re-modeling of the liver parenchyma leading to functional impairment, which is thus obviously the cause or the consequence of the disruption ...

Created: 11th Nov 2015 at 11:12


 

Zonation of hepatic fatty acid metabolism - The diversity of its regulation and the benefit of modeling


Authors: J Schleicher, C Tokarski, E Marbach, M Matz-Soja, S Zellmer, R Gebhardt, S Schuster

PubMed ID: 25677822

Date Published: 14th Feb 2015

Projects: C3: Zonation of metabolism and its regulation

Journal: Biochim. Biophys. Acta

Citation: Biochim. Biophys. Acta :

Scales: Intercellular and Liver lobule

Abstract (Expand)

A pronounced heterogeneity between hepatocytes in subcellular structure and enzyme activities was discovered more than 50years ago and initiated the idea of metabolic zonation. In the last decades ...

Created: 26th Feb 2015 at 09:40


 

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data


Authors: Sylvie Schulze, Sebastian G. Henkel, Dominik Driesch, Reinhard Guthke, Jörg Linde

DOI: 10.3389/fmicb.2015.00065

Date Published: 6th Feb 2015

Projects: Virtual Liver

Journal: Front. Microbiol.

Citation: Front. Microbiol. 6

Scales: Cell and Intercellular

Abstract:

Not specified

Created: 11th Feb 2015 at 08:18   Last updated: 11th Feb 2015 at 08:24


 

A Quick Guide for Building a Successful Bioinformatics Community


Authors: Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg

DOI: 10.1371/journal.pcbi.1003972

Date Published: 5th Feb 2015

Projects: No Projects

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 11(2) : e1003972

Scales: Not specified

Abstract (Expand)

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role ...

Created: 9th Feb 2015 at 13:55   Last updated: 9th Feb 2015 at 14:06


 

Submassive hepatic necrosis distinguishes HBV-associated acute on chronic liver failure from cirrhotic patients with acute decompensation


Authors: Hai Li, Qiang Xia, Bo Zeng, Shu-Ting Li, Heng Liu, Qi Li, Jun Li, Shu-Yin Yang, Xiao-Jun Dong, Ting Gao, Stefan Munker, Yan Liu, Roman Liebe, Feng Xue, Qi-Gen Li, Xiao-Song Chen, Qiang Liu, Hui Zeng, Ji-Yao Wang, Qing Xie, Qin-Hua Meng, Jie-Fei Wang, Peter R Mertens, Frank Lammert, Manfred V Singer, Steven Dooley, Matthias P A Ebert, De-Kai Qiu, Tai-Ling Wang, Hong-Lei Weng

PubMed ID: 25646889

Date Published: 4th Feb 2015

Projects: C5: Structural changes and functional consequences of the liver lobular/...

Journal: J. Hepatol.

Citation: J. Hepatol. :

Scales: Liver and Organism

Abstract:

Distinguishing between acute on chronic liver failure (ACLF) and decompensated liver cirrhosis is difficult due to a lack of pathological evidence.

Created: 17th Jun 2015 at 09:18


 

Human sterol regulatory element-binding protein 1a contributes significantly to hepatic lipogenic gene expression


Authors: Andreas Bitter, Andreas K Nüssler, Wolfgang E Thasler, Kathrin Klein, Ulrich M Zanger, Matthias Schwab, Oliver Burk

PubMed ID: 25634759

Date Published: 30th Jan 2015

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, Showcase Steatosis

Journal: Cell. Physiol. Biochem.

Citation: Cell. Physiol. Biochem. 35(2): 803-15

Scales: Not specified

Abstract (Expand)

Sterol regulatory element-binding protein (SREBP) 1, the master regulator of lipogenesis, was shown to be associated with non-alcoholic fatty liver disease, which is attributed to its major isoform ...

Created: 7th Apr 2015 at 14:59


 

Ten Simple Rules for Organizing an Unconference


Authors: Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood

DOI: 10.1371/journal.pcbi.1003905

Date Published: 29th Jan 2015

Projects: No Projects

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 11(1) : e1003905

Scales: Not specified

Abstract:

Not specified

Created: 2nd Feb 2015 at 14:43   Last updated: 2nd Feb 2015 at 14:47


 

Smad7 regulates compensatory hepatocyte proliferation in damaged mouse liver and positively relates to better clinical outcome in human hepatocellular carcinoma


Authors: Teng Feng, Johanna Dzieran, Xing Gu, Silke Marhenke, Arndt Vogel, Keigo Machida, Thomas S Weiss, Petra Ruemmele, Otto Kollmar, Patrick Hoffmann, Friedrich Grässer, Heike Allgayer, Jasmin Fabian, Hong Lei Weng, Andreas Teufel, Thorsten Maass, Christoph Meyer, Ulrich Lehmann, Cheng Zhu, Peter R Mertens, Chun Fang Gao, Steven Dooley, Nadja M Meindl-Beinker

PubMed ID: 25602745

Date Published: 21st Jan 2015

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd...

Journal: Clin. Sci.

Citation: Clin. Sci. 128(11): 761-74

Scales: Liver

Abstract (Expand)

Transforming growth factor β (TGF-β) is cytostatic towards damage-induced compensatory hepatocyte proliferation. This function is frequently lost during hepatocarcinogenesis, thereby switching the TGF-β ...

Created: 17th Jun 2015 at 11:08


 

GPU-Accelerated Sparse Matrix-Matrix Multiplication by Iterative Row Merging


Authors: Felix Gremse, Andreas Höfter, Lars Ole Schwen, Fabian Kiessling, Uwe Naumann

DOI: 10.1137/130948811

Date Published: 8th Jan 2015

Projects: D3: Inflammation and Regeneration: the whole organ

Journal: SIAM J. Sci. Comput.

Citation: SIAM J. Sci. Comput. 37(1) : C54

Scales: Organism

Abstract (Expand)

We present an algorithm for general sparse matrix-matrix multiplication (SpGEMM) on many-core architectures, such as GPUs. SpGEMM is implemented by iterative row merging, similar to merge sort, except ...

Created: 26th Jan 2015 at 16:56   Last updated: 26th Jan 2015 at 17:01


 

Role of ABC transporters in fluoropyrimidine-based chemotherapy response


Authors: Anne T Nies, Tarek Magdy, Matthias Schwab, Ulrich M Zanger

PubMed ID: 25640272

Date Published: 8th Jan 2015

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Adv. Cancer Res.

Citation: Adv. Cancer Res. 125: 217-43

Scales: Not specified

Abstract (Expand)

Since over 50 years, 5-fluorouracil (5-FU) is in use as backbone of chemotherapy treatment regimens for a wide range of cancers including colon, breast, and head and neck carcinomas. However, drug ...

Created: 7th Apr 2015 at 14:52


 

Oncostatin M regulates SOCS3 mRNA stability via the MEK-ERK1/2-pathway independent of p38(MAPK)/MK2


Authors: Christian Ehlting, Oliver Böhmer, Maximilian J Hahnel, Maria Thomas, Ulrich M Zanger, Matthias Gaestel, Wolfram T Knoefel, Jan Schulte Am Esch, Dieter Häussinger, Johannes G Bode

PubMed ID: 25562430

Date Published: 7th Jan 2015

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A2.1: Multi-level regulation of signalling pathways important for primin..., A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., A: Cellular level

Journal: Cell. Signal.

Citation: Cell. Signal. :

Scales: Not specified

Abstract (Expand)

The induction of suppressor of cytokine signalling (SOCS)3 expression context dependently involves regulation of SOCS3 transcript stability as previously demonstrated for MAPK activated protein kinase ...

Created: 7th Jan 2015 at 14:25


 

Mathematical Modelling suggests Differential Impact of β-TrCP Paralogues on Wnt/β-catenin Signalling Dynamics


Authors: Uwe Benary, Bente Kofahl, Andreas Hecht, Jana Wolf

DOI: 10.1111/febs.13204

Date Published: 2015

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, B2.2: Importance of Wnt- and Hedgehog factors for hepatic stellate cells...

Journal: FEBS J

Citation: FEBS J : n/a

Scales: Cell

Abstract (Expand)

The Wnt/β-catenin signalling pathway is involved in the regulation of a multitude of cellular processes by controlling the concentration of the transcriptional regulator β-catenin. Proteasomal degradation ...

Created: 20th Jan 2015 at 07:51   Last updated: 20th Jan 2015 at 07:52


 

Implementation of systems theory in liver cancer research


Authors: Federico Pinna, Kai Breuhahn

DOI: 10.2217/hep.14.29

Date Published: 2015

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., A2.4: Linking signalling pathways regulating liver regeneration and orga...

Journal: Hepatic Oncology

Citation: Hepatic Oncology 2(1) : 9

Scales: Cell and Intercellular

Abstract:

Not specified

Created: 20th Jan 2015 at 13:49   Last updated: 20th Jan 2015 at 13:52


 

Unraveling liver complexity from molecular to organ level: Challenges and perspectives


Authors: L.A. D'Alessandro, S. Hoehme, A. Henney, D. Drasdo, U. Klingmüller

DOI: 10.1016/j.pbiomolbio.2014.11.005

Date Published: 2015

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., C5: Structural changes and functional consequences of the liver lobular/..., E1: Integration on the cellular level, Interleukin-6 signalling, Showcase HGF and Regeneration

Journal: Progress in Biophysics and Molecular Biology

Citation: Progress in Biophysics and Molecular Biology 117(1) : 78

Scales: Not specified

Abstract (Expand)

Biological responses are determined by information processing at multiple and highly interconnected scales. Within a tissue the individual cells respond to extracellular stimuli by regulating intracellular ...

Created: 6th Apr 2015 at 12:17   Last updated: 9th Jun 2015 at 10:40


 

Multi-bio and multi-scale systems biology


Authors: Adriano Henney, Peter Hunter, Andrew McCulloch, Denis Noble

DOI: 10.1016/j.pbiomolbio.2015.03.001

Date Published: 2015

Projects: No Projects

Journal: Progress in Biophysics and Molecular Biology

Citation: Progress in Biophysics and Molecular Biology 117(1) : 1

Scales: Not specified

Abstract:

Not specified

Created: 6th Apr 2015 at 12:20   Last updated: 6th Apr 2015 at 12:21


 

Interleukin-1β Enhances FasL-Induced Caspase-3/-7 Activity without Increasing Apoptosis in Primary Mouse Hepatocytes


Authors: Anna Lutz, Julia Sanwald, Maria Thomas, Ronny Feuer, Oliver Sawodny, Michael Ederer, Christoph Borner, Matjaz Humar, Irmgard Merfort

DOI: 10.1371/journal.pone.0115603

Date Published: 31st Dec 2014

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...

Journal: PLoS ONE

Citation: PLoS ONE 9(12) : e115603

Scales: Cell

Abstract (Expand)

Sustained inflammation may increase the susceptibility of hepatocytes to apoptotic cell death and therefore exacerbate liver damage. Here we report that the pro-inflammatory cytokine IL-1β sensitizes ...

Created: 23rd Jan 2015 at 09:58   Last updated: 23rd Jan 2015 at 10:00


 

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project


Authors: Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

PubMed ID: 25494900

Date Published: 14th Dec 2014

Projects: F1: The data management system

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 15(1): 369

Scales: Not specified

Abstract (Expand)

BackgroundWith the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more ...

Created: 9th Jan 2015 at 15:06


 

A Systematic Comparison of the Impact of Inflammatory Signaling on ADME Gene Expression and Activity in Primary Human Hepatocytes and HepaRG Cells


Authors: Marcus Klein, Maria Thomas, Ute Hofmann, Daniel Seehofer, Georg Damm, Ulrich M Zanger

PubMed ID: 25480923

Date Published: 7th Dec 2014

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase LPS and Inflammation, Showcase Steatosis

Journal: Drug Metab. Dispos.

Citation: Drug Metab. Dispos. :

Scales: Not specified

Abstract (Expand)

Inflammatory processes are associated with compromised metabolism and elimination of drugs in the liver, largely mediated by proinflammatory cytokines, such as interleukin-6 (IL-6). The HepaRG cell ...

Created: 7th Dec 2014 at 10:17


 

Whole genome transcript profiling of drug induced steatosis in rats reveals a gene signature predictive of outcome


Authors: Nishika Sahini, Saravanakumar Selvaraj, Jürgen Borlak

PubMed ID: 25470483

Date Published: 3rd Dec 2014

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: PLoS ONE

Citation: PLoS ONE 9(12): e114085

Scales: Liver

Abstract (Expand)

Drug induced steatosis (DIS) is characterised by excess triglyceride accumulation in the form of lipid droplets (LD) in liver cells. To explore mechanisms underlying DIS we interrogated the publically ...

Created: 29th Jan 2015 at 14:53


 

Data collection as a barrier to personalized medicine


Authors: David Zakim, Matthias Schwab

PubMed ID: 25479798

Date Published: 2nd Dec 2014

Projects: G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Trends Pharmacol. Sci.

Citation: Trends Pharmacol. Sci. 36(2): 68-71

Scales: Not specified

Abstract (Expand)

Basic life science research holds the promise of personalizing medical care. However, translation steps from the laboratory to the bedside are not trivial. Results from clinical research are difficult ...

Created: 7th Apr 2015 at 14:54


 

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology


Authors: Alexander Dörr, Roland Keller, Andreas Zell, Andreas Dräger

DOI: 10.3390/computation2040246

Date Published: 1st Dec 2014

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Computation

Citation: Computation 2(4) : 246

Scales: Cell and Intercellular

Abstract (Expand)

The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be ...

Created: 14th Jan 2015 at 15:05   Last updated: 10th Jun 2015 at 18:36


 

LigDig: a web server for querying ligand-protein interactions


Authors: J. C. Fuller, M. Martinez, S. Henrich, A. Stank, S. Richter, R. C. Wade

DOI: 10.1093/bioinformatics/btu784

Date Published: 29th Nov 2014

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., F3: Kinetic data handling

Journal: Bioinformatics

Citation: Bioinformatics

Scales: Cell

Abstract (Expand)

Summary: LigDig is a webserver designed to answer questions that previously required several independent queries to diverse data-sources. It also performs basic manipulations and analyses of the ...

Created: 6th Dec 2014 at 18:03   Last updated: 6th Dec 2014 at 18:07


 

Fluorescence based cell counting in collagen monolayer cultures of primary hepatocytes


Authors: C Priesnitz, S Sperber, R Garg, M Orsini, F Noor

PubMed ID: 25424145

Date Published: 26th Nov 2014

Projects: A1: Cellular metabolism, C3: Zonation of metabolism and its regulation

Journal: Cytotechnology

Citation: Cytotechnology :

Scales: Cell

Abstract (Expand)

Accurate determination of cell number is essential for the quantitative description of biological processes. The changes should be related to a measurable reference e.g. in the case of cell culture, ...

Created: 14th Jan 2015 at 16:17


 

Stratified medicine for the use of antidiabetic medication in treatment of type II diabetes and cancer: where do we go from here


Authors: A Emami-Riedmaier, E Schaeffeler, A T Nies, K Mörike, M Schwab

PubMed ID: 25418285

Date Published: 25th Nov 2014

Projects: G3: Clinical Translation to Pharmaceutical Drug Development

Journal: J. Intern. Med.

Citation: J. Intern. Med. 277(2): 235-47

Scales: Not specified

Abstract (Expand)

At present, the global diabetes epidemic is affecting 347 million individuals, 90% of whom are diagnosed with type II diabetes mellitus (T2DM). T2DM is commonly treated with more than one type of ...

Created: 7th Apr 2015 at 14:50


 

Isolation, characterization, and cultivation of human hepatocytes and non-parenchymal liver cells


Authors: Elisa Pfeiffer, Victoria Kegel, Katrin Zeilinger, Jan G Hengstler, Andreas K Nüssler, Daniel Seehofer, Georg Damm

PubMed ID: 25394621

Date Published: 15th Nov 2014

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., CTU Liver bank

Journal: Exp. Biol. Med. (Maywood)

Citation: Exp. Biol. Med. (Maywood) :

Scales: Cell and Intercellular

Abstract (Expand)

Primary human hepatocytes (PHH) are considered to be the gold standard for in vitro testing of xenobiotic metabolism and hepatotoxicity. However, PHH cultivation in 2D mono-cultures leads to dedifferentiation ...

Created: 5th Jan 2015 at 13:19


 

Algorithmically generated rodent hepatic vascular trees in arbitrary detail


Authors: Lars Ole Schwen, Weiwei Wei, Felix Gremse, Josef Ehling, Lei Wang, Uta Dahmen, Tobias Preusser

DOI: 10.1016/j.jtbi.2014.10.026

Date Published: 1st Nov 2014

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: Journal of Theoretical Biology

Citation: Journal of Theoretical Biology

Scales: Liver

Abstract (Expand)

Physiologically realistic geometric models of the vasculature in the liver are indispensable for modelling hepatic blood flow, the main connection between the liver and the organism. Current in vivo ...

Created: 17th Nov 2014 at 10:07   Last updated: 17th Nov 2014 at 10:12


 

The virtual liver: state of the art and future perspectives


Authors: Dirk Drasdo, Johannes Bode, Uta Dahmen, Olaf Dirsch, Steven Dooley, Rolf Gebhardt, Ahmed Ghallab, Patricio Godoy, Dieter Häussinger, Seddik Hammad, Stefan Hoehme, Hermann-Georg Holzhütter, Ursula Klingmüller, Lars Kuepfer, Jens Timmer, Marino Zerial, Jan G. Hengstler

DOI: 10.1007/s00204-014-1384-6

Date Published: 21st Oct 2014

Projects: No Projects

Journal: Arch Toxicol

Citation: Arch Toxicol

Scales: Not specified

Abstract:

Not specified

Created: 7th Nov 2014 at 15:06   Last updated: 7th Nov 2014 at 15:06


 

Nuclear Expression of the Deubiquitinase CYLD Is Associated with Improved Survival in Human Hepatocellular Carcinoma


Authors: Stefan Welte, Toni Urbanik, Christin Elßner, Nicole Kautz, Bruno Christian Koehler, Nina Waldburger, Justo Lorenzo Bermejo, Federico Pinna, Karl-Heinz Weiss, Peter Schemmer, Dirk Jaeger, Thomas Longerich, Kai Breuhahn, Henning Schulze-Bergkamen

DOI: 10.1371/journal.pone.0110591

Date Published: 16th Oct 2014

Projects: A2.1: Multi-level regulation of signalling pathways important for primin...

Journal: PLoS ONE

Citation: PLoS ONE 9(10) : e110591

Scales: Cell

Abstract:

Not specified

Created: 20th Jan 2015 at 13:44   Last updated: 20th Jan 2015 at 13:46


 

WISP1 is a novel adipokine linked to inflammation in obesity


Authors: Veronica Murahovschi, Olga Pivovarova, Iryna Ilkavets, Renata M Dmitrieva, Stephanie Döcke, Farnaz Keyhani-Nejad, Özlem Gögebakan, Martin Osterhoff, Margrit Kemper, Silke Hornemann, Mariya Markova, Nora Klöting, Martin Stockmann, Martin O Weickert, Valeria Lamounier-Zepter, Peter Neuhaus, Alexandra Konradi, Steven Dooley, Christian von Loeffelholz, Matthias Blüher, Andreas F H Pfeiffer, Natalia Rudovich

PubMed ID: 25281430

Date Published: 3rd Oct 2014

Projects: C5: Structural changes and functional consequences of the liver lobular/...

Journal: Diabetes

Citation: Diabetes 64(3): 856-66

Scales: Organism

Abstract (Expand)

WISP1 (Wnt1-inducible signaling pathway protein-1, also known as CCN4) is a member of the secreted extracellular matrix-associated proteins of the CCN family and a target gene of the Wingless-type (WNT) ...

Created: 17th Jun 2015 at 09:29


 

Evolutionary game theory: cells as players


Authors: Sabine Hummert, Katrin Bohl, David Basanta, Andreas Deutsch, Sarah Werner, Günter Theißen, Anja Schroeter, Stefan Schuster

PubMed ID: 25270362

Date Published: 2nd Oct 2014

Projects: No Projects

Journal: Mol Biosyst

Citation: Mol Biosyst 10(12): 3044-65

Scales: Not specified

Abstract (Expand)

In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors ...

Created: 3rd Dec 2014 at 20:25


 

How predictive quantitative modelling of tissue organisation can inform liver disease pathogenesis


Authors: Dirk Drasdo, Stefan Hoehme, Jan G. Hengstler

DOI: 10.1016/j.jhep.2014.06.013

Date Published: 1st Oct 2014

Projects: C: Liver lobule level

Journal: Journal of Hepatology

Citation: Journal of Hepatology 61(4) : 951

Scales: Not specified

Abstract:

Not specified

Created: 7th Nov 2014 at 15:09   Last updated: 7th Nov 2014 at 15:09


 

The Virtual Liver Network: systems understanding from bench to bedside


Author: Adriano Henney

DOI: 10.4155/FMC.14.127

Date Published: 1st Oct 2014

Projects: No Projects

Journal: Future Medicinal Chemistry

Citation: Future Medicinal Chemistry 6(16) : 1735

Scales: Not specified

Abstract:

Not specified

Created: 28th Nov 2014 at 17:48


 

Evolutionary game theory: molecules as players


Authors: Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Günter Theißen, Anja Schroeter

PubMed ID: 25248454

Date Published: 25th Sep 2014

Projects: No Projects

Journal: Mol Biosyst

Citation: Mol Biosyst 10(12): 3066-74

Scales: Not specified

Abstract (Expand)

In this and an accompanying paper we review the use of game theoretical concepts in cell biology and molecular biology. This review focuses on the subcellular level by considering viruses, genes, and ...

Created: 3rd Dec 2014 at 20:29


 

Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach


Authors: T Ricken, D Werner, H G Holzhütter, M König, U Dahmen, O Dirsch

PubMed ID: 25236798

Date Published: 19th Sep 2014

Projects: A1: Cellular metabolism, C: Liver lobule level, E: Model integration

Journal: Biomech Model Mechanobiol

Citation: Biomech Model Mechanobiol 14(3): 515-36

Scales: Cell and Liver lobule

Abstract (Expand)

This study focuses on a two-scale, continuum multicomponent model for the description of blood perfusion and cell metabolism in the liver. The model accounts for a spatial and time depending ...

Created: 30th Jun 2015 at 07:09


 

Pregnane X receptor activation and silencing promote steatosis of human hepatic cells by distinct lipogenic mechanisms


Authors: Andreas Bitter, Petra Rümmele, Kathrin Klein, Benjamin A Kandel, Jessica K Rieger, Andreas K Nüssler, Ulrich M Zanger, Michael Trauner, Matthias Schwab, Oliver Burk

PubMed ID: 25182422

Date Published: 3rd Sep 2014

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G1: Clinical Translation to Invasively Characterized Patients, G3: Clinical Translation to Pharmaceutical Drug Development, Showcase Steatosis

Journal: Arch. Toxicol.

Citation: Arch. Toxicol. :

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

In addition to its well-characterized role in the regulation of drug metabolism and transport by xenobiotics, pregnane X receptor (PXR) critically impacts on lipid homeostasis. In mice, both ligand-dependent ...

Created: 5th Dec 2014 at 12:44


 

Treatment of NASH with human mesenchymal stem cells in the immunodeficient mouse


Authors: Sandra Winkler, Bruno Christ

PubMed ID: 25173373

Date Published: 1st Sep 2014

Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase Steatosis

Journal: Methods Mol. Biol.

Citation: Methods Mol. Biol. 1213: 51-6

Scales: Cell and Liver

Abstract (Expand)

Nonalcoholic steatohepatitis (NASH) as a severe form of nonalcoholic liver diseases (NAFLD) is one of the prominent liver diseases worldwide. Under favoring conditions it may progress into liver cirrhosis ...

Created: 15th Jan 2015 at 10:47


 

The many faces of Hedgehog signalling in the liver: Recent progress reveals striking cellular diversity and the importance of microenvironments


Authors: Madlen Matz-Soja, Rolf Gebhardt

PubMed ID: 25152210

Date Published: 26th Aug 2014

Projects: A: Cellular level

Journal: J. Hepatol.

Citation: J. Hepatol. :

Scales: Not specified

Abstract:

Not specified

Created: 1st Dec 2014 at 15:54


 

On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics


Authors: Jonathan C. Fuller, Michael Martinez, Rebecca C. Wade

DOI: 10.1371/journal.pone.0104778

Date Published: 20th Aug 2014

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: PLoS ONE

Citation: PLoS ONE 9(8) : e104778

Scales: Cell

Abstract (Expand)

Many signaling events require the binding of cytoplasmic proteins to cell membranes by recognition of specific charged lipids, such as phosphoinositol-phosphates. As a model for a protein-membrane ...

Created: 20th Aug 2014 at 19:55   Last updated: 20th Aug 2014 at 19:57


 

Foxf1 SiRNA Delivery to Hepatic Stellate Cells by DBTC Lipoplex Formulations Ameliorates Fibrosis in Livers of Bile Duct Ligated Mice


Authors: Kerstin Abshagen, Malte Brensel, Berit Genz, Kira Roth, Maria Thomas, Volker Fehring, Ute Schaeper, Brigitte Vollmar

PubMed ID: 25619889

Date Published: 11th Aug 2014

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Curr Gene Ther

Citation: Curr Gene Ther :

Scales: Cell

Abstract (Expand)

Activation of hepatic stellate cells (HSCs) is a key event in pathogenesis of liver fibrosis and represents an orchestral interplay of inhibiting and activating transcription factors like forkhead box ...

Created: 27th Jan 2015 at 10:19


 

Cause and cure of sloppiness in ordinary differential equation models


Authors: Christian Tönsing, Jens Timmer, Clemens Kreutz

PubMed ID: 25215847

Date Published: 11th Aug 2014

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: Phys Rev E Stat Nonlin Soft Matter Phys

Citation: Phys Rev E Stat Nonlin Soft Matter Phys 90(2): 023303

Scales: Cell

Abstract (Expand)

Data-based mathematical modeling of biochemical reaction networks, e.g., by nonlinear ordinary differential equation (ODE) models, has been successfully applied. In this context, parameter estimation ...

Created: 30th Jan 2015 at 15:58


 

Resistance of ferroportin to hepcidin binding causes exocrine pancreatic failure and fatal iron overload


Authors: Sandro Altamura, Regina Kessler, Hermann-Josef Gröne, Norbert Gretz, Matthias W Hentze, Bruno Galy, Martina U Muckenthaler

PubMed ID: 25100063

Date Published: 8th Aug 2014

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Cell Metab.

Citation: Cell Metab. 20(2): 359-67

Scales: Intercellular, Liver and Organism

Abstract (Expand)

The regulatory axis between the iron hormone hepcidin and its receptor, the iron exporter ferroportin (FPN), is central to iron homeostasis. Mutations preventing hepcidin-mediated degradation of FPN ...

Created: 21st Jan 2015 at 10:21


 

morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring


Authors: Ines Wagner, Michael Volkmer, Malvika Sharan, Jose M Villaveces, Felix Oswald, Vineeth Surendranath, Bianca H Habermann

PubMed ID: 25096057

Date Published: 6th Aug 2014

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., A3: Crosslinking signalling metabolism and hepatocyte polarisation, C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 15(1): 263

Scales: Not specified

Abstract (Expand)

Searching the orthologs of a given protein or DNA sequence is one of the most important and most commonly used Bioinformatics methods in Biology. Programs like BLAST or the orthology search engine ...

Created: 11th Aug 2014 at 16:33


 

RPPApipe: A pipeline for the analysis of reverse-phase protein array data


Authors: Johannes Eichner, Yvonne Heubach, Manuel Ruff, Hella Kohlhof, Stefan Strobl, Barbara Mayer, Michael Pawlak, Markus F. Templin, Andreas Zell

DOI: 10.1016/j.biosystems.2014.06.009

Date Published: 1st Aug 2014

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Biosystems

Citation: Biosystems 122 : 19

Scales: Cell and Intercellular

Abstract (Expand)

Background and scope: Today, web-based data analysis pipelines exist for a wide variety of microarray platforms, such as ordinary gene-centered arrays, exon arrays and SNP arrays. However, most of the ...

Created: 17th Nov 2015 at 12:14   Last updated: 17th Nov 2015 at 12:15


 

Clinical Translation in the Virtual Liver Network


Authors: L Kuepfer, R Kerb, A M Henney

DOI: 10.1038/psp.2014.25

Date Published: 30th Jul 2014

Projects: G: Clinical translation

Journal: CPT: pharmacomet. syst. pharmacol.

Citation: CPT: pharmacomet. syst. pharmacol. 3(7) : e127

Scales: Organism

Abstract:

Not specified

Created: 13th Aug 2014 at 19:07   Last updated: 13th Aug 2014 at 19:12


 

Liver zonation: Novel aspects of its regulation and its impact on homeostasis


Authors: Rolf Gebhardt, Madlen Matz-Soja

PubMed ID: 25024605

Date Published: 16th Jul 2014

Projects: C3: Zonation of metabolism and its regulation, Virtual Liver

Journal: World J. Gastroenterol.

Citation: World J. Gastroenterol. 20(26): 8491-504

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

Liver zonation, the spatial separation of the immense spectrum of different metabolic pathways along the liver sinusoids, is fundamental for proper functioning of this organ. Recent progress in elucidating ...

Created: 26th Jan 2015 at 09:50


 

Recent advances in live cell imaging of hepatoma cells


Authors: Sandeep Salipalli, Prafull Kumar Singh, Jürgen Borlak

PubMed ID: 25005127

Date Published: 8th Jul 2014

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: BMC Cell Biol.

Citation: BMC Cell Biol. 15(1): 26

Scales: Cell

Abstract (Expand)

Live cell imaging enables the study of dynamic processes of living cells in real time by use of suitable reporter proteins and the staining of specific cellular structures and/or organelles. With the ...

Created: 10th Jul 2014 at 12:23


 

Explanted diseased livers - a possible source of metabolic competent primary human hepatocytes


Authors: Moritz Kleine, Marc Riemer, Till Krech, Daphne DeTemple, Mark D Jäger, Frank Lehner, Michael P Manns, Jürgen Klempnauer, Jürgen Borlak, Hueseyin Bektas, Florian W R Vondran

PubMed ID: 24999631

Date Published: 7th Jul 2014

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: PLoS ONE

Citation: PLoS ONE 9(7): e101386

Scales: Cell

Abstract (Expand)

Being an integral part of basic, translational and clinical research, the demand for primary human hepatocytes (PHH) is continuously growing while the availability of tissue resection material for the ...

Created: 10th Jul 2014 at 12:09


 

Adenoviral overexpression of Lhx2 attenuates cell viability but does not preserve the stem cell like phenotype of hepatic stellate cells


Authors: Berit Genz, Maria Thomas, Brigitte M Pützer, Marcin Siatkowski, Georg Fuellen, Brigitte Vollmar, Kerstin Abshagen

PubMed ID: 24995995

Date Published: 6th Jul 2014

Projects: A: Cellular level, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. :

Scales: Cell

Abstract (Expand)

Hepatic stellate cells (HSC) are well known initiators of hepatic fibrosis. After liver cell damage, HSC transdifferentiate into proliferative myofibroblasts, representing the major source of extracellular ...

Created: 7th Jul 2014 at 20:27


 

Targeting Nuclear Receptors with Lentivirus-Delivered Small RNAs in Primary Human Hepatocytes


Authors: Maria Thomas, Jessica K Rieger, Benjamin A Kandel, Kathrin Klein, Ulrich M Zanger

PubMed ID: 25012546

Date Published: 1st Jul 2014

Projects: A: Cellular level, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells, C: Liver lobule level

Journal: Cell. Physiol. Biochem.

Citation: Cell. Physiol. Biochem. 33(6): 2003-2013

Scales: Not specified

Abstract (Expand)

Background: RNA interference (RNAi) has tremendous potential for investigating gene function and for developing new therapies. Primary human hepatocytes (PHH) are the "gold standard" for ...

Created: 14th Jul 2014 at 13:17


 

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models


Authors: A. Ryll, J. Bucher, A. Bonin, S. Bongard, E. Gonçalves, J. Saez-Rodriguez, J. Niklas, S. Klamt

DOI: 10.1016/j.biosystems.2014.07.002

Date Published: 1st Jul 2014

Projects: A1: Cellular metabolism, A2.5: Integration of insulin and Wnt signalling in hepatocytes, A2: Integration of Signalling Pathways in Hepatocellular Response, A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD, A: Cellular level, Showcase Steatosis, Virtual Liver

Journal: Biosystems

Citation: Biosystems

Scales: Cell

Abstract (Expand)

Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling ...

Created: 6th Aug 2014 at 07:36   Last updated: 6th Aug 2014 at 07:50


 

Modelling proteasome and proteasome regulator activities


Authors: Juliane Liepe, Herman-Georg Holzhütter, Peter M Kloetzel, Michael P H Stumpf, Michele Mishto

PubMed ID: 24970232

Date Published: 28th Jun 2014

Projects: No Projects

Journal: Biomolecules

Citation: Biomolecules 4(2): 585-99

Scales: Not specified

Abstract (Expand)

Proteasomes are key proteases involved in a variety of processes ranging from the clearance of damaged proteins to the presentation of antigens to CD8+ T-lymphocytes. Which cleavage sites are used ...

Created: 6th Jan 2015 at 09:32


 

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model


Authors: Minjun Chen, Chun-Wei Tung, Qiang Shi, Lei Guo, Leming Shi, Hong Fang, Jürgen Borlak, Weida Tong

PubMed ID: 24958025

Date Published: 11th Jun 2014

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Arch. Toxicol.

Citation: Arch. Toxicol. 88(7): 1439-49

Scales: Cell

Abstract (Expand)

Drug-induced liver injury (DILI) is a major cause of drug failures in both the preclinical and clinical phase. Consequently, improving prediction of DILI at an early stage of drug discovery will reduce ...

Created: 28th Jun 2014 at 16:37


 

Concomitant use of tamoxifen and endoxifen in postmenopausal early breast cancer: prediction of plasma levels by physiologically-based pharmacokinetic modeling


Authors: Kristin Dickschen, Thomas Eissing, Thomas Mürdter, Matthias Schwab, Stefan Willmann, Georg Hempel

PubMed ID: 24936398

Date Published: 5th Jun 2014

Projects: G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Springerplus

Citation: Springerplus 3: 285

Scales: Not specified

Abstract (Expand)

To overcome cytochrome P450 2D6 (CYP2D6) mediated tamoxifen resistance in postmenopausal early breast cancer, CYP2D6 phenotype-adjusted tamoxifen dosing in patients with impaired CYP2D6 metabolism ...

Created: 7th Apr 2015 at 14:48


 

Predicting idiosyncratic drug-induced liver injury - some recent advances


Authors: Minjun Chen, Jürgen Borlak, Weida Tong

PubMed ID: 24857265

Date Published: 27th May 2014

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Expert Rev Gastroenterol Hepatol

Citation: Expert Rev Gastroenterol Hepatol : 1-3

Scales: Liver

Abstract (Expand)

Drug-induced liver injury (DILI) is a major challenge for the pharmaceutical industry, regulatory authorities, and clinicians. It is usually categorized into 'intrinsic' and 'idiosyncratic', ...

Created: 28th Jun 2014 at 16:40


 

Isoniazid mediates the CYP2B6*6 genotype-dependent interaction between efavirenz and antituberculosis drug therapy through mechanism-based inactivation of CYP2A6


Authors: Michael H Court, Fawziah E Almutairi, David J Greenblatt, Suwagmani Hazarika, Hongyan Sheng, Kathrin Klein, Ulrich M Zanger, Joanne Bourgea, Christopher J Patten, Awewura Kwara

PubMed ID: 24820076

Date Published: 12th May 2014

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G: Clinical translation

Journal: Antimicrob. Agents Chemother.

Citation: Antimicrob. Agents Chemother. 58(7): 4145-52

Scales: Not specified

Abstract (Expand)

Efavirenz is commonly used to treat patients coinfected with human immunodeficiency virus and tuberculosis. Previous clinical studies have observed paradoxically elevated efavirenz plasma concentrations ...

Created: 8th Dec 2014 at 09:49


 

Human mesenchymal stem cells towards non-alcoholic steatohepatitis in an immunodeficient mouse model


Authors: Sandra Winkler, Erawan Borkham-Kamphorst, Peggy Stock, Sandra Brückner, Matthias Dollinger, Ralf Weiskirchen, Bruno Christ

PubMed ID: 24786317

Date Published: 3rd May 2014

Projects: C4: Disturbance of liver lobule organization in NAFLD, C6: Organization and function of the sinusoidal system and the liver lob..., G: Clinical translation, Showcase Steatosis

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. :

Scales: Cell and Liver

Abstract (Expand)

Non-alcoholic steatohepatitis (NASH) is a frequent clinical picture characterised by hepatic inflammation, lipid accumulation and fibrosis. When untreated, NASH bears a high risk of developing liver ...

Created: 19th May 2014 at 20:13


 

Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis


Authors: Seddik Hammad, Stefan Hoehme, Adrian Friebel, Iris von Recklinghausen, Amnah Othman, Brigitte Begher-Tibbe, Raymond Reif, Patricio Godoy, Tim Johann, Amruta Vartak, Klaus Golka, Petru O. Bucur, Eric Vibert, Rosemarie Marchan, Bruno Christ, Steven Dooley, Christoph Meyer, Iryna Ilkavets, Uta Dahmen, Olaf Dirsch, Jan Böttger, Rolf Gebhardt, Dirk Drasdo, Jan G. Hengstler

DOI: 10.1007/s00204-014-1243-5

Date Published: 1st May 2014

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob..., CTU Confocal microscopy, CTU Image Processing

Journal: Arch Toxicol

Citation: Arch Toxicol 88(5) : 1161

Scales: Liver lobule and Liver

Abstract:

Not specified

Created: 7th Nov 2014 at 15:11   Last updated: 7th Nov 2014 at 15:11


 

Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration


Authors: Freimut Schliess, Stefan Hoehme, Sebastian G. Henkel, Ahmed Ghallab, Dominik Driesch, Jan Böttger, Reinhard Guthke, Michael Pfaff, Jan G. Hengstler, Rolf Gebhardt, Dieter Häussinger, Dirk Drasdo, Sebastian Zellmer

DOI: 10.1002/hep.27136

Date Published: 1st May 2014

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A2.1: Multi-level regulation of signalling pathways important for primin..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., A3.4: Linking signalling to metabolic functions

Journal: Hepatology

Citation: Hepatology : n/a

Scales: Not specified

Abstract:

Not specified

Created: 7th Nov 2014 at 15:12   Last updated: 7th Nov 2014 at 15:12


 

Data extraction for the reaction kinetics database SABIO-RK


Authors: Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller

DOI: 10.1016/j.pisc.2014.02.004

Date Published: 1st May 2014

Projects: F3: Kinetic data handling

Journal: Perspectives in Science

Citation: Perspectives in Science 1(1-6) : 33

Scales: Not specified

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting ...

Created: 3rd Feb 2015 at 10:55   Last updated: 3rd Feb 2015 at 11:03


 

Human bone marrow mesenchymal stem cell-derived hepatocytes improve the mouse liver after acute acetaminophen intoxication by preventing progress of injury


Authors: Peggy Stock, Sandra Brückner, Sandra Winkler, Matthias M Dollinger, Bruno Christ

PubMed ID: 24758938

Date Published: 25th Apr 2014

Projects: A1: Cellular metabolism, C6: Organization and function of the sinusoidal system and the liver lob..., G: Clinical translation, Showcase HGF and Regeneration

Journal: Int J Mol Sci

Citation: Int J Mol Sci 15(4): 7004-28

Scales: Liver lobule and Liver

Abstract (Expand)

Mesenchymal stem cells from human bone marrow (hMSC) have the potential to differentiate into hepatocyte-like cells in vitro and continue to maintain important hepatocyte functions in vivo after ...

Created: 19th May 2014 at 20:04


 

The transcription factor CHOP, a central component of the transcriptional regulatory network induced upon CCl4 intoxication in mouse liver, is not a critical mediator of hepatotoxicity


Authors: Gisela Campos, Wolfgang Schmidt-Heck, Ahmed Ghallab, Katharina Rochlitz, Larissa Pütter, Danilo B Medinas, Claudio Hetz, Agata Widera, Cristina Cadenas, Brigitte Begher-Tibbe, Raymond Reif, Georgia Günther, Agapios Sachinidis, Jan G Hengstler, Patricio Godoy

PubMed ID: 24748426

Date Published: 20th Apr 2014

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., C6: Organization and function of the sinusoidal system and the liver lob..., Showcase HGF and Regeneration

Journal: Arch. Toxicol.

Citation: Arch. Toxicol. 88(6): 1267-80

Scales: Not specified

Abstract (Expand)

Since xenobiotics enter the organism via the liver, hepatocytes must cope with numerous perturbations, including modifications of proteins leading to endoplasmic reticulum stress (ER-stress). This ...

Created: 20th Jan 2015 at 13:25


 

How useful are clinical liver function tests in in-vitro human hepatotoxicity assays


Authors: Jürgen Borlak, Anil Chougule, Prafull Kumar Singh

PubMed ID: 24685772

Date Published: 2nd Apr 2014

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Toxicol In Vitro

Citation: Toxicol In Vitro :

Scales: Cell

Abstract (Expand)

In preclinical hepatotoxicity testing cell based assays are frequently employed. However, prediction of clinical drug induced liver injury (DILI) remains a major challenge. Here we examined the usefulness ...

Created: 4th Apr 2014 at 16:13


 

How Does a Single Cell Know When the Liver Has Reached Its Correct Size?


Authors: Nadine Hohmann, Wei Weiwei, Uta Dahmen, Olaf Dirsch, Andreas Deutsch, Anja Voss-Böhme

DOI: 10.1371/journal.pone.0093207

Date Published: 1st Apr 2014

Projects: D4: Regeneration and Liver Size

Journal: PLoS ONE

Citation: PLoS ONE 9(4) : e93207

Scales: Intercellular, Liver lobule and Liver

Abstract (Expand)

The liver is a multi-functional organ that regulates major physiological processes and that possesses a remarkable regeneration capacity. After loss of functional liver mass the liver grows back to its ...

Created: 24th Apr 2014 at 14:21   Last updated: 24th Apr 2014 at 14:26


 

Potential Roles of Bone Morphogenetic Protein (BMP)-9 in Human Liver Diseases


Authors: Blanca Herrera, Steven Dooley, Katja Breitkopf-Heinlein

PubMed ID: 24670474

Date Published: 29th Mar 2014

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A3.3: Hepatocyte polarity, B2.1: Hepatic stellate cells as source and target for hepatocellular gro..., B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., Showcase HGF and Regeneration, Showcase LPS and Inflammation

Journal: Int J Mol Sci

Citation: Int J Mol Sci 15(4): 5199-220

Scales: Not specified

Abstract (Expand)

Bone morphogenetic proteins (BMP-2 to BMP-15) belong to the Transforming Growth Factor (TGF)-β superfamily and, besides their well-documented roles during embryogenesis and bone formation, some of them ...

Created: 31st Mar 2014 at 11:18


 

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)


Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

DOI: 10.4056/sigs.5279417

Date Published: 15th Mar 2014

Projects: F1: The data management system

Journal: Stand. Genomic Sci.

Citation: Stand. Genomic Sci. 9(3) : 1285

Scales: Not specified

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report ...

Created: 3rd Feb 2015 at 11:07   Last updated: 3rd Feb 2015 at 11:12


 

Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver


Authors: Lars Ole Schwen, Markus Krauss, Christoph Niederalt, Felix Gremse, Fabian Kiessling, Andrea Schenk, Tobias Preusser, Lars Kuepfer

DOI: 10.1371/journal.pcbi.1003499

Date Published: 13th Mar 2014

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 10(3) : e1003499

Scales: Liver and Organism

Abstract (Expand)

The liver is the central organ for detoxification of xenobiotics in the body. In pharmacokinetic modeling, hepatic metabolization capacity is typically quantified as hepatic clearance computed as ...

Created: 14th Mar 2014 at 09:13   Last updated: 14th Mar 2014 at 09:28


 

Recent insights into the molecular pathophysiology of lipid droplet formation in hepatocytes


Authors: Nishika Sahini, Jürgen Borlak

PubMed ID: 24607340

Date Published: 13th Mar 2014

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Prog. Lipid Res.

Citation: Prog. Lipid Res. 54C: 86-112

Scales: Cell

Abstract (Expand)

Triacyglycerols are a major energy reserve of the body and are normally stored in adipose tissue as lipid droplets (LDs). The liver, however, stores energy as glycogen and digested triglycerides in the ...

Created: 31st Mar 2014 at 14:53


 

Estimating Dose Painting Effects in Radiotherapy: A Mathematical Model


Authors: Juan Carlos López Alfonso, Nick Jagiella, Luis Núñez, Miguel A. Herrero, Dirk Drasdo

DOI: 10.1371/journal.pone.0089380

Date Published: 26th Feb 2014

Projects: No Projects

Journal: PLoS ONE

Citation: PLoS ONE 9(2) : e89380

Scales: Not specified

Abstract:

Not specified

Created: 7th Nov 2014 at 15:14   Last updated: 7th Nov 2014 at 15:14


 

Hepatic Hedgehog signaling contributes to the regulation of IGF1 and IGFBP1 serum levels


Authors: Madlen Matz-Soja, Susanne Aleithe, Eugenia Marbach, Jan Böttger, Katrin Arnold, Wolfgang Schmidt-Heck, Jürgen Kratzsch, Rolf Gebhardt

PubMed ID: 24548465

Date Published: 18th Feb 2014

Projects: Virtual Liver

Journal: Cell Commun. Signal

Citation: Cell Commun. Signal 12(1): 11

Scales: Organism

Abstract (Expand)

Hedgehog signaling plays an important role in embryonic development, organogenesis and cancer. In the adult liver, Hedgehog signaling in non-parenchymal cells has been found to play a role in certain ...

Created: 11th Mar 2014 at 14:51


 

Toward predictive models for drug-induced liver injury in humans: are we there yet


Authors: Minjun Chen, Halil Bisgin, Lillian Tong, Huixiao Hong, Hong Fang, Jürgen Borlak, Weida Tong

PubMed ID: 24521015

Date Published: 14th Feb 2014

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Biomark Med

Citation: Biomark Med 8(2): 201-13

Scales: Liver

Abstract (Expand)

Drug-induced liver injury (DILI) is a frequent cause for the termination of drug development programs and a leading reason of drug withdrawal from the marketplace. Unfortunately, the current preclinical ...

Created: 28th Jun 2014 at 16:31


 

KEGGViewer, a BioJS component to visualize KEGG Pathways


Authors: Jose M Villaveces, Rafael C Jimenez, Bianca H Habermann

PubMed ID: 24715980

Date Published: 13th Feb 2014

Projects: No Projects

Journal: F1000Res

Citation: F1000Res 3: 43

Scales: Not specified

Abstract (Expand)

Signaling pathways provide essential information on complex regulatory processes within the cell. They are moreover widely used to interpret and integrate data from large-scale studies, such as expression ...

Created: 11th Aug 2014 at 16:29


 

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers


Authors: Jose M Villaveces, Rafael C Jimenez, Bianca H Habermann

PubMed ID: 25075287

Date Published: 13th Feb 2014

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., A3: Crosslinking signalling metabolism and hepatocyte polarisation, C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: F1000Res

Citation: F1000Res 3: 44

Scales: Not specified

Abstract (Expand)

Protein interaction networks have become an essential tool in large-scale data analysis, integration, and the visualization of high-throughput data in the context of complex cellular networks. Many ...

Created: 11th Aug 2014 at 16:31


 

Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology


Authors: J. Starruss, W. d. Back, L. Brusch, A. Deutsch

DOI: 10.1093/bioinformatics/btt772

Date Published: 17th Jan 2014

Projects: A3.3: Hepatocyte polarity, A3: Crosslinking signalling metabolism and hepatocyte polarisation, B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., B3: Intercellular communication through cell adhesion, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells, C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob..., E2: Integration on the liver lobule scale: Image processing and mathemat..., E3: Horizontal integration on organ scale, E: Model integration, Showcase LIAM (Liver Image Analysis Based Model), Virtual Liver

Journal: Bioinformatics

Citation: Bioinformatics

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of ...

Created: 20th Jan 2014 at 15:49   Last updated: 20th Jan 2014 at 16:16


 

The apoptotic pore on mitochondria: are we breaking through or still stuck


Authors: C Borner, D W Andrews

PubMed ID: 24413197

Date Published: 15th Jan 2014

Projects: No Projects

Journal: Cell Death Differ.

Citation: Cell Death Differ. 21(2): 187-91

Scales: Not specified

Abstract:

Not specified

Created: 22nd Jan 2014 at 15:13


 

Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to the proliferative Ras/RAF and the nutrient-dependent mTOR signaling pathways


Authors: Katarzyna Mleczko-Sanecka, Franziska Roche, Ana Rita da Silva, Debora Call, Flavia D'Alessio, Anan Ragab, Philip E Lapinski, Ramesh Ummanni, Ulrike Korf, Christopher Oakes, Georg Damm, Lorenza A D'Alessandro, Ursula Klingmüeller, Philip D King, Michael Boutros, Matthias W Hentze, Martina U Muckenthaler

PubMed ID: 24385536

Date Published: 5th Jan 2014

Projects: A3.4: Linking signalling to metabolic functions, B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Blood

Citation: Blood :

Scales: Cell and Intercellular

Abstract (Expand)

The hepatic hormone hepcidin is a key regulator of systemic iron metabolism. Its expression is largely regulated by two signaling pathways, the 'iron-regulated' bone morphogenetic protein ...

Created: 14th Jan 2014 at 12:06


 

A Novel Mitochondrial MAVS/Caspase-8 Platform Links RNA Virus-Induced Innate Antiviral Signaling to Bax/Bak-Independent Apoptosis


Authors: Souhayla El Maadidi, Laura Faletti, Birgit Berg, Christin Wenzl, Katrin Wieland, Zhijian J Chen, Ulrich Maurer, Christoph Borner

PubMed ID: 24391214

Date Published: 3rd Jan 2014

Projects: No Projects

Journal: J. Immunol.

Citation: J. Immunol. 192(3): 1171-83

Scales: Not specified

Abstract (Expand)

Semliki Forest virus (SFV) requires RNA replication and Bax/Bak for efficient apoptosis induction. However, cells lacking Bax/Bak continue to die in a caspase-dependent manner. In this study, we show ...

Created: 22nd Jan 2014 at 15:15


 

A multi-scale model of hepcidin promoter regulation reveals factors controlling systemic iron homeostasis


Authors: Guillem Casanovas, Anashua Banerji, Flavia d'Alessio, Martina U Muckenthaler, Stefan Legewie

PubMed ID: 24391488

Date Published: 2nd Jan 2014

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 10(1): e1003421

Scales: Cell

Abstract (Expand)

Systemic iron homeostasis involves a negative feedback circuit in which the expression level of the peptide hormone hepcidin depends on and controls the iron blood levels. Hepcidin expression is regulated ...

Created: 14th Jan 2014 at 11:56


 

SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques


Authors: Christian Bölling, Michael Weidlich, Hermann-Georg Holzhütter

DOI: 10.1186/2041-1480-5-S1-S1

Date Published: 2014

Projects: F2: The Liver Knowledge Base (LKB)

Journal: J Biomed Sem

Citation: J Biomed Sem 5(Suppl 1) : S1

Scales: Not specified

Abstract (Expand)

Background Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and ...

Created: 17th Jun 2014 at 13:09   Last updated: 17th Jun 2014 at 13:13


 

Enabling multiscale modeling in systems medicine


Authors: Olaf Wolkenhauer, Charles Auffray, Olivier Brass, Jean Clairambault, Andreas Deutsch, Dirk Drasdo, Francesco Gervasio, Luigi Preziosi, Philip Maini, Anna Marciniak-Czochra, Christina Kossow, Lars Kuepfer, Katja Rateitschak, Ignacio Ramis-Conde, Benjamin Ribba, Andreas Schuppert, Rod Smallwood, Georgios Stamatakos, Felix Winter, Helen Byrne

DOI: 10.1186/gm538

Date Published: 2014

Projects: No Projects

Journal: Genome Med

Citation: Genome Med 6(3) : 21

Scales: Not specified

Abstract:

Not specified

Created: 7th Nov 2014 at 15:10   Last updated: 7th Nov 2014 at 15:10


 

Mathematical Modeling of Regenerative Processes


Authors: Osvaldo Chara, Elly M. Tanaka, Lutz Brusch

DOI: 10.1016/B978-0-12-391498-9.00011-5

Date Published: 2014

Projects: A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., B3: Intercellular communication through cell adhesion, C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob..., D4: Regeneration and Liver Size, Showcase LIAM (Liver Image Analysis Based Model)

Book: Mechanisms of Regeneration

Citation: Current Topics in Developmental Biology 108 : 283

Scales: Not specified

Abstract:

Not specified

Created: 22nd Jan 2015 at 16:09   Last updated: 22nd Jan 2015 at 16:11


 

TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors


Authors: Johannes Eichner, Florian Topf, Andreas Dräger, Clemens Wrzodek, Dierk Wanke, Andreas Zell

DOI: 10.1371/journal.pone.0082238

Date Published: 12th Dec 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: PLoS ONE

Citation: PLoS ONE 8(12) : e82238

Scales: Cell and Intercellular

Abstract (Expand)

One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF) and cis-regulatory elements in gene promoters. The elucidation of these specific ...

Created: 17th Nov 2015 at 12:27   Last updated: 17th Nov 2015 at 12:28


 

Determinants of Cell-to-Cell Variability in Protein Kinase Signaling


Authors: Matthias Jeschke, Stephan Baumgärtner, Stefan Legewie

PubMed ID: 24339758

Date Published: 5th Dec 2013

Projects: A2.4: Linking signalling pathways regulating liver regeneration and orga..., B1.2: Reciprocal effect of cell-cell communication on information proces..., B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 9(12): e1003357

Scales: Not specified

Abstract (Expand)

Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein ...

Created: 20th Jan 2014 at 16:29


 

Dynamics of VEGF matrix-retention in vascular network patterning


Authors: A Köhn-Luque, W de Back, Y Yamaguchi, K Yoshimura, M A Herrero, T Miura

DOI: 10.1088/1478-3975/10/6/066007

Date Published: 1st Dec 2013

Projects: B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., B3: Intercellular communication through cell adhesion, C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/...

Journal: Phys. Biol.

Citation: Phys. Biol. 10(6) : 066007

Scales: Intercellular

Abstract (Expand)

Vascular endothelial growth factor (VEGF) is a central regulator of blood vessel morphogenesis, although its role in patterning of endothelial cells into vascular networks is not fully understood. It ...

Created: 24th Jan 2014 at 13:54   Last updated: 24th Jan 2014 at 13:57


 

No activation of human PXR by hyperforin-related phloroglucinols


Authors: Benjamin A Kandel, Sean Ekins, Kristina Leuner, Wolfgang E Thasler, Christian Harteneck, Ulrich M Zanger

PubMed ID: 24259679

Date Published: 22nd Nov 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: J. Pharmacol. Exp. Ther.

Citation: J. Pharmacol. Exp. Ther. :

Scales: Not specified

Abstract (Expand)

The acylated phloroglucinol, hyperforin, the main active ingredient of St John's wort, exerts anti-depressant properties via indirect inhibition of serotonin reuptake by selectively activating the ...

Created: 8th Jan 2014 at 13:53


 

Genetics, epigenetics and regulation of drug metabolizing cytochrome P450 enzymes


Authors: Ulrich M Zanger, Kathrin Klein, Maria Thomas, Jessica K Rieger, Roman Tremmel, Benjamin A Kandel, Marcus Klein, Tarek Magdy

PubMed ID: 24196843

Date Published: 8th Nov 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Clin. Pharmacol. Ther.

Citation: Clin. Pharmacol. Ther. :

Scales: Not specified

Abstract (Expand)

Of 57 functional human cytochromes P450 (CYP) about a dozen liver-expressed, highly variable forms are responsible for the biotransformation of most drugs. Owing to numerous genetic and non-genetic ...

Created: 8th Jan 2014 at 13:58


 

A fat option for the pig: Hepatocytic differentiated mesenchymal stem cells for translational research


Authors: Sandra Brückner, Hans-Michael Tautenhahn, Sandra Winkler, Peggy Stock, Matthias Dollinger, Bruno Christ

PubMed ID: 24200501

Date Published: 4th Nov 2013

Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase Steatosis

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. 321(2): 267-75

Scales: Cell and Liver

Abstract (Expand)

Study background: Extended liver resection is the only curative treatment option of liver cancer. Yet, the residual liver may not accomplish the high metabolic and regenerative capacity needed, which ...

Created: 10th Feb 2014 at 17:22


 

Challenges for an enzymatic reaction kinetics database


Authors: Ulrike Wittig, Maja Rey, Renate Kania, Meik Bittkowski, Lei Shi, Martin Golebiewski, Andreas Weidemann, Wolfgang Müller, Isabel Rojas

PubMed ID: 24165050

Date Published: 30th Oct 2013

Projects: F3: Kinetic data handling, F: Data management

Journal: FEBS J.

Citation: FEBS J. :

Scales: Not specified

Abstract (Expand)

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create ...

Created: 27th Nov 2013 at 13:21


 

Manganese superoxide dismutase is reduced in the liver of male but not female humans and rodents with non-alcoholic fatty liver disease


Authors: Sabrina Krautbauer, Kristina Eisinger, Madeleine Lupke, Josef Wanninger, Petra Ruemmele, Yvonne Hader, Thomas S Weiss, Christa Buechler

PubMed ID: 24161595

Date Published: 22nd Oct 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Exp. Mol. Pathol.

Citation: Exp. Mol. Pathol. 95(3): 330-5

Scales: Cell, Liver and Organism

Abstract (Expand)

Non-alcoholic fatty liver disease (NAFLD) is among the most common liver diseases. Oxidative stress is one of the pathogenic mechanisms contributing to the progression of simple fatty liver to non-alcoholic ...

Created: 30th Jan 2014 at 16:27


 

Zonation of nitrogen and glucose metabolism gene expression upon acute liver damage in mouse


Authors: Shahrouz Ghafoory, Katja Breitkopf-Heinlein, Qi Li, Catharina Scholl, Steven Dooley, Stefan Wölfl

PubMed ID: 24147127

Date Published: 17th Oct 2013

Projects: C5: Structural changes and functional consequences of the liver lobular/..., Showcase HGF and Regeneration

Journal: PLoS ONE

Citation: PLoS ONE 8(10): e78262

Scales: Not specified

Abstract (Expand)

Zonation of metabolic activities within specific structures and cell types is a phenomenon of liver organization and ensures complementarity of variant liver functions like protein production, glucose ...

Created: 5th Feb 2014 at 12:26


 

Phosphorylation of the Smo tail is controlled by membrane localisation and is dispensable for clustering


Authors: A. P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bokel

DOI: 10.1242/​jcs.128926

Date Published: 11th Oct 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Journal of Cell Science

Citation: Journal of Cell Science 126(20) : 4684

Scales: Cell

Abstract (Expand)

The Hedgehog (Hh) signalling cascade is highly conserved and involved in development and disease throughout evolution. Nevertheless, in comparison with other pathways, our mechanistic understanding of ...

Created: 24th Jan 2014 at 14:15   Last updated: 24th Jan 2014 at 14:21


 

Human parenchymal and non-parenchymal liver cell isolation, culture and characterization


Authors: Georg Damm, Elisa Pfeiffer, Britta Burkhardt, Jan Vermehren, Andreas K. Nüssler, Thomas S. Weiss

DOI: 10.1007/s12072-013-9475-7

Date Published: 1st Oct 2013

Projects: CTU SOP Hepatic stellate cells, human, CTU SOP Human Hepatocytes, CTU SOP Kupffer cells/macrophages, human, CTU SOP Liver sinusoidal endothelial cells, human

Journal: Hepatol Int

Citation: Hepatol Int 7(4) : 951

Scales: Cell

Abstract:

Not specified

Created: 30th Jan 2014 at 16:52   Last updated: 30th Jan 2014 at 16:54


 

Lessons learned from quantitative dynamical modeling in systems biology


Authors: Andreas Raue, Marcel Schilling, Julie Bachmann, Andrew Matteson, Max Schelke, Daniel Kaschek, Sabine Hug, Clemens Kreutz, Brian D Harms, Fabian J Theis, Ursula Klingmüller, Jens Timmer

PubMed ID: 24098642

Date Published: 30th Sep 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: PLoS ONE

Citation: PLoS ONE 8(9): e74335

Scales: Cell

Abstract (Expand)

Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines ...

Created: 14th Jan 2014 at 11:35


 

Serum acute phase reactants hallmark healthy individuals at risk for acetaminophen-induced liver injury


Authors: Jürgen Borlak, Bijon Chatterji, Kishor B Londhe, Paul B Watkins

PubMed ID: 24070255

Date Published: 27th Sep 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, CTU Proteomics

Journal: Genome Med

Citation: Genome Med 5(9): 86

Scales: Liver and Organism

Abstract (Expand)

Acetaminophen (APAP) is a commonly used analgesic. However, its use is associated with drug induced liver injury (DILI). It is a prominent cause of acute liver failure, with APAP hepatotoxicity far ...

Created: 22nd Oct 2013 at 11:09   Last updated: 24th Oct 2013 at 16:14


 

Isolation of human hepatocytes by a two-step collagenase perfusion procedure


Authors: Serene M L Lee, Celine Schelcher, Maresa Demmel, Maria Hauner, Wolfgang E Thasler

PubMed ID: 24056912

Date Published: 24th Sep 2013

Projects: A: Cellular level, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells, CTUs, Show cases, Virtual Liver

Journal: J Vis Exp

Citation: J Vis Exp (79):

Scales: Cell

Abstract (Expand)

The liver, an organ with an exceptional regeneration capacity, carries out a wide range of functions, such as detoxification, metabolism and homeostasis. As such, hepatocytes are an important model for ...

Created: 13th Jan 2014 at 15:48


 

ABCC11/MRP8 polymorphisms affect 5-fluorouracil-induced severe toxicity and hepatic expression


Authors: Tarek Magdy, Rudolf Arlanov, Stefan Winter, Thomas Lang, Kathrin Klein, Yu Toyoda, Toshihisa Ishikawa, Matthias Schwab, Ulrich M Zanger

PubMed ID: 24024896

Date Published: 13th Sep 2013

Projects: A3.4: Linking signalling to metabolic functions, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Pharmacogenomics

Citation: Pharmacogenomics 14(12): 1433-48

Scales: Not specified

Abstract (Expand)

Because 5-fluorodeoxyuridine monophosphate (5-FdUMP), an anabolic active metabolite of 5-fluorouracil (5-FU), is a substrate of MRP8 (encoded by ABCC11), we investigated whether ABCC11 polymorphisms ...

Created: 8th Jan 2014 at 14:01


 

Implications of enzyme deficiencies on mitochondrial energy metabolism and reactive oxygen species formation of neurons involved in rotenone-induced Parkinson's disease: a model-based analysis


Authors: Nikolaus Berndt, Herrmann-Georg Holzhütter, Sascha Bulik

PubMed ID: 23937586

Date Published: 12th Sep 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: FEBS J.

Citation: FEBS J. 280(20): 5080-93

Scales: Not specified

Abstract (Expand)

Steadily growing experimental evidence suggests that mitochondrial dysfunction plays a key role in the age-dependent impairment of nerve cells underlying several neurodegenerative diseases. In particular, ...

Created: 20th Jan 2014 at 10:41


 

What can we learn from Einstein and Arrhenius about the optimal flow of our blood


Authors: Stefan Schuster, Heiko Stark

PubMed ID: 24021886

Date Published: 8th Sep 2013

Projects: C3: Zonation of metabolism and its regulation

Journal: Biochim. Biophys. Acta

Citation: Biochim. Biophys. Acta 1840(1): 271-6

Scales: Organism

Abstract (Expand)

The oxygen flow in humans and other higher animals depends on the erythrocyte-to-blood volume ratio, the hematocrit. Since it is physiologically favourable when the flow of oxygen transport is maximum ...

Created: 4th Feb 2014 at 09:02


 

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs


Authors: Ioannis N Melas, Regina Samaga, Leonidas G Alexopoulos, Steffen Klamt

PubMed ID: 24039561

Date Published: 5th Sep 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 9(9): e1003204

Scales: Cell

Abstract (Expand)

Cross-referencing experimental data with our current knowledge of signaling network topologies is one central goal of mathematical modeling of cellular signal transduction networks. We present a new ...

Created: 13th Dec 2013 at 17:20


 

A theoretical study of lipid accumulation in the liver-implications for nonalcoholic fatty liver disease


Authors: J Schleicher, R Guthke, U Dahmen, O Dirsch, H G Holzhuetter, S Schuster

PubMed ID: 23999488

Date Published: 4th Sep 2013

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Biochim. Biophys. Acta

Citation: Biochim. Biophys. Acta 1841(1): 62-69

Scales: Cell

Abstract (Expand)

A hallmark of the nonalcoholic fatty liver disease is the accumulation of lipids. We developed a mathematical model of the hepatic lipid dynamics to simulate the fate of fatty acids in hepatocytes. Our ...

Created: 23rd Oct 2013 at 14:55   Last updated: 24th Oct 2013 at 16:14


 

Quantitative structure-activity relationship models for predicting drug-induced liver injury based on FDA-approved drug labeling annotation and using a large collection of drugs


Authors: Minjun Chen, Huixiao Hong, Hong Fang, Reagan Kelly, Guangxu Zhou, Jürgen Borlak, Weida Tong

PubMed ID: 23997115

Date Published: 31st Aug 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Toxicol. Sci.

Citation: Toxicol. Sci. 136(1): 242-9

Scales: Liver

Abstract (Expand)

Drug-induced liver injury (DILI) is one of the leading causes of the termination of drug development programs. Consequently, identifying the risk of DILI in humans for drug candidates during the early ...

Created: 19th Jan 2014 at 17:57


 

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME


Authors: Patricio Godoy, Nicola J Hewitt, Ute Albrecht, Melvin E Andersen, Nariman Ansari, Sudin Bhattacharya, Johannes Georg Bode, Jennifer Bolleyn, Christoph Borner, Jan Böttger, Albert Braeuning, Robert A Budinsky, Britta Burkhardt, Neil R Cameron, Giovanni Camussi, Chong-Su Cho, Yun-Jaie Choi, J Craig Rowlands, Uta Dahmen, Georg Damm, Olaf Dirsch, María Teresa Donato, Jian Dong, Steven Dooley, Dirk Drasdo, Rowena Eakins, Karine Sá Ferreira, Valentina Fonsato, Joanna Fraczek, Rolf Gebhardt, Andrew Gibson, Matthias Glanemann, Chris E P Goldring, María José Gómez-Lechón, Geny M M Groothuis, Lena Gustavsson, Christelle Guyot, David Hallifax, Seddik Hammad, Adam Hayward, Dieter Häussinger, Claus Hellerbrand, Philip Hewitt, Stefan Hoehme, Hermann-Georg Holzhütter, J Brian Houston, Jens Hrach, Kiyomi Ito, Hartmut Jaeschke, Verena Keitel, Jens M Kelm, B Kevin Park, Claus Kordes, Gerd A Kullak-Ublick, Edward L LeCluyse, Peng Lu, Jennifer Luebke-Wheeler, Anna Lutz, Daniel J Maltman, Madlen Matz-Soja, Patrick McMullen, Irmgard Merfort, Simon Messner, Christoph Meyer, Jessica Mwinyi, Dean J Naisbitt, Andreas K Nussler, Peter Olinga, Francesco Pampaloni, Jingbo Pi, Linda Pluta, Stefan A Przyborski, Anup Ramachandran, Vera Rogiers, Cliff Rowe, Celine Schelcher, Kathrin Schmich, Michael Schwarz, Bijay Singh, Ernst H K Stelzer, Bruno Stieger, Regina Stöber, Yuichi Sugiyama, Ciro Tetta, Wolfgang E Thasler, Tamara Vanhaecke, Mathieu Vinken, Thomas S Weiss, Agata Widera, Courtney G Woods, Jinghai James Xu, Kathy M Yarborough, Jan G Hengstler

PubMed ID: 23974980

Date Published: 23rd Aug 2013

Projects: CTU SOP Human Hepatocytes, CTU SOP Monolayer/sandwich culture hepatocytes, CTU SOP Mouse Hepatocytes, Virtual Liver

Journal: Arch. Toxicol.

Citation: Arch. Toxicol. 87(8): 1315-530

Scales: Not specified

Abstract (Expand)

This review encompasses the most important advances in liver functions and hepatotoxicity and analyzes which mechanisms can be studied in vitro. In a complex architecture of nested, zonated lobules, ...

Created: 9th Sep 2013 at 15:23   Last updated: 24th Oct 2013 at 16:14


 

Comparative analysis of TGF-beta/Smad signaling dependent cytostasis in human hepatocellular carcinoma cell lines


Authors: J. Dzieran, J. Fabian, T. Feng, C. Coulouarn, I. Ilkavets, A. Kyselova, K. Breuhahn, S. Dooley, N. M. Meindl-Beinker

PubMed ID: 23991075

Date Published: 22nd Aug 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: PLoS One

Citation: PLoS One. 2013 Aug 22;8(8):e72252. doi: 10.1371/journal.pone.0072252. eCollection 2013.

Scales: Not specified

Abstract (Expand)

Hepatocellular carcinoma (HCC) is a major public health problem due to increased incidence, late diagnosis and limited treatment options. TGF-beta is known to provide cytostatic signals during early ...

Created: 27th Jul 2015 at 07:19


 

Assessment of hepatic detoxification activity: proposal of an improved variant of the (13)c-methacetin breath test


Authors: Hermann-Georg Holzhütter, Johan Friso Lock, Pouria Taheri, Sascha Bulik, Andrean Goede, Martin Stockmann

PubMed ID: 23967104

Date Published: 15th Aug 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, E4: Vertical integration across biological scales

Journal: PLoS ONE

Citation: PLoS ONE 8(8): e70780

Scales: Not specified

Abstract (Expand)

Breath tests based on the administration of a (13)C-labeled drug and subsequent monitoring of (13)CO2 in the breath (quantified as DOB - delta over baseline) liberated from the drug during hepatic ...

Created: 9th Sep 2013 at 15:13   Last updated: 24th Oct 2013 at 16:14


 

Systems genetics of hepatocellular damage in vivo and in vitro: identification of a critical network on chromosome 11 in mouse


Authors: Roman Liebe, Rabea A Hall, Robert W Williams, Steven Dooley, Frank Lammert

PubMed ID: 23943854

Date Published: 13th Aug 2013

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., Showcase LPS and Inflammation

Journal: Physiol. Genomics

Citation: Physiol. Genomics 45(20): 931-9

Scales: Not specified

Abstract (Expand)

Quantitative trait locus (QTL) mapping is a powerful method to find modifier loci that influence disease risk and progression without prior knowledge of underlying genetic mechanisms. The aim of this ...

Created: 6th Dec 2013 at 09:19


 

Out of balance--systemic iron homeostasis in iron-related disorders


Authors: Andrea U Steinbicker, Martina U Muckenthaler

PubMed ID: 23917168

Date Published: 7th Aug 2013

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Nutrients

Citation: Nutrients 5(8): 3034-61

Scales: Cell, Intercellular and Organism

Abstract (Expand)

Iron is an essential element in our daily diet. Most iron is required for the de novo synthesis of red blood cells, where it plays a critical role in oxygen binding to hemoglobin. Thus, iron deficiency ...

Created: 20th Jan 2014 at 11:06


 

Chemerin is highly expressed in hepatocytes and is induced in non-alcoholic steatohepatitis liver


Authors: Sabrina Krautbauer, Josef Wanninger, Kristina Eisinger, Yvonne Hader, Michael Beck, Andrea Kopp, Andreas Schmid, Thomas S Weiss, Christoph Dorn, Christa Buechler

PubMed ID: 23906870

Date Published: 29th Jul 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A3.6: Transcription factor network and links to metabolism in NAFLD, CTU SOP Human Hepatocytes, Show cases

Journal: Exp. Mol. Pathol.

Citation: Exp. Mol. Pathol. 95(2): 199-205

Scales: Cell and Liver

Abstract (Expand)

Chemerin is a recently described adipokine whose adipose tissue and serum levels are increased in obesity. Chemerin is expressed in the liver, and here, expression of chemerin has been studied in liver ...

Created: 30th Jan 2014 at 17:11


 

Rapid degradation of solid-phase bound peptides by the 20S proteasome


Authors: Marc Hovestädt, Ulrike Kuckelkorn, Agathe Niewienda, Christin Keller, Andrean Goede, Bernhard Ay, Stefan Günther, Katharina Janek, Rudolf Volkmer, Hermann-Georg Holzhütter

PubMed ID: 23893543

Date Published: 28th Jul 2013

Projects: No Projects

Journal: J. Pept. Sci.

Citation: J. Pept. Sci. 19(9): 588-97

Scales: Not specified

Abstract (Expand)

Proteasomes are cellular proteases involved in the degradation of numerous cellular proteins. The 20S proteasome is a cylindrical 28-mer protein complex composed of two outer heptameric α-rings forming ...

Created: 9th Sep 2013 at 15:19   Last updated: 24th Oct 2013 at 16:14


 

DNA methylation of the SLC16A3 promoter regulates expression of the human lactate transporter MCT4 in renal cancer with consequences for clinical outcome


Authors: Pascale Fisel, Stephan Kruck, Stefan Winter, Jens Bedke, Jörg Hennenlotter, Anne T Nies, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Matthias Schwab, Elke Schaeffeler

PubMed ID: 23881922

Date Published: 23rd Jul 2013

Projects: B5: Cell-cell communication influences detoxifying functions in hepatocytes, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin. Cancer Res.

Citation: Clin. Cancer Res. 19(18): 5170-81

Scales: Not specified

Abstract (Expand)

The monocarboxylate transporter 4 (MCT4) is a metabolic target in tumor biology because it mediates lactate transport across membranes resulting in antiapoptotic effects. Cell experiments support the ...

Created: 20th Jan 2014 at 14:16


 

Nrf2 activates augmenter of liver regeneration (ALR) via antioxidant response element and links oxidative stress to liver regeneration


Authors: Rania Dayoub, Arndt Vogel, Jutta Schuett, Madeleine Lupke, Susannah M Spieker, Nadja Kettern, Eberhard Hildt, Michael Melter, Thomas S Weiss

PubMed ID: 23887691

Date Published: 23rd Jul 2013

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., CTU SOP Human Hepatocytes

Journal: Mol. Med.

Citation: Mol. Med. 19: 237-44

Scales: Cell and Liver

Abstract (Expand)

Liver regeneration can be impaired by permanent oxidative stress and activation of nuclear factor erythroid 2-related factor 2 (Nrf2), known to regulate the cellular antioxidant response, and has been ...

Created: 30th Jan 2014 at 17:06


 

Evaluation of 41 candidate gene variants for obesity in the EPIC-potsdam cohort by multi-locus stepwise regression


Authors: Sven Knüppel, Klaus Rohde, Karina Meidtner, Dagmar Drogan, Hermann-Georg Holzhütter, Heiner Boeing, Eva Fisher

PubMed ID: 23874820

Date Published: 12th Jul 2013

Projects: No Projects

Journal: PLoS ONE

Citation: PLoS ONE 8(7): e68941

Scales: Not specified

Abstract (Expand)

Obesity has become a leading preventable cause of morbidity and mortality in many parts of the world. It is thought to originate from multiple genetic and environmental determinants. The aim of the ...

Created: 20th Jan 2014 at 10:28


 

Apoptosis induced by the fungal pathogen gliotoxin requires a triple phosphorylation of Bim by JNK


Authors: A Geissler, F Haun, D O Frank, K Wieland, M M Simon, M Idzko, R J Davis, U Maurer, C Borner

PubMed ID: 23832115

Date Published: 5th Jul 2013

Projects: No Projects

Journal: Cell Death Differ.

Citation: Cell Death Differ. 20(10): 1317-29

Scales: Not specified

Abstract (Expand)

We previously reported that gliotoxin (GT), the major virulence factor of the mold Aspergillus fumigatus causing invasive aspergillosis (IA) in immunocompromised patients, induces apoptosis in a ...

Created: 22nd Jan 2014 at 15:18


 

GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML


Authors: S. Vlaic, B. Hoffmann, P. Kupfer, M. Weber, A. Drager

DOI: 10.1093/bioinformatics/btt370

Date Published: 26th Jun 2013

Projects: A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Bioinformatics

Citation: Bioinformatics 29(17) : 2216

Scales: Cell

Abstract (Expand)

Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in SBML. Providing a graphical user interface, the networks can be annotated via the SOAP-based ...

Created: 1st Jul 2013 at 23:57   Last updated: 24th Oct 2013 at 16:14


 

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks


Authors: Regina Samaga, Steffen Klamt

PubMed ID: 23803171

Date Published: 26th Jun 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg...

Journal: Cell Commun. Signal

Citation: Cell Commun. Signal 11(1): 43

Scales: Cell

Abstract (Expand)

A central goal of systems biology is the construction of predictive models of bio-molecular networks. Cellular networks of moderate size have been modeled successfully in a quantitative way based on ...

Created: 13th Dec 2013 at 17:23


 

Image-based analysis of lipid nanoparticle-mediated siRNA delivery, intracellular trafficking and endosomal escape


Authors: Jerome Gilleron, William Querbes, Anja Zeigerer, Anna Borodovsky, Giovanni Marsico, Undine Schubert, Kevin Manygoats, Sarah Seifert, Cordula Andree, Martin Stöter, Hila Epstein-Barash, Ligang Zhang, Victor Koteliansky, Kevin Fitzgerald, Eugenio Fava, Marc Bickle, Yannis Kalaidzidis, Akin Akinc, Martin Maier, Marino Zerial

PubMed ID: 23792630

Date Published: 23rd Jun 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Nat. Biotechnol.

Citation: Nat. Biotechnol. 31(7): 638-46

Scales: Cell, Intercellular and Liver

Abstract (Expand)

Delivery of short interfering RNAs (siRNAs) remains a key challenge in the development of RNA interference (RNAi) therapeutics. A better understanding of the mechanisms of siRNA cellular uptake, ...

Created: 15th Jul 2013 at 11:10   Last updated: 24th Oct 2013 at 16:14


 

Practical quantification of necrosis in histological whole-slide images


Authors: André Homeyer, Andrea Schenk, Janine Arlt, Uta Dahmen, Olaf Dirsch, Horst K Hahn

PubMed ID: 23796718

Date Published: 21st Jun 2013

Projects: CTU Image Processing, D4: Regeneration and Liver Size

Journal: Comput Med Imaging Graph

Citation: Comput Med Imaging Graph 37(4): 313-22

Scales: Liver lobule and Liver

Abstract (Expand)

Since the histological quantification of necrosis is a common task in medical research and practice, we evaluate different image analysis methods for quantifying necrosis in whole-slide images. In a ...

Created: 7th Nov 2013 at 08:56


 

TNFα-induced lysosomal membrane permeability is downstream of MOMP and triggered by caspase-mediated NDUFS1 cleavage and ROS formation


Authors: Jisen Huai, F-Nora Vögtle, Lars Jöckel, Yunbo Li, Thomas Kiefer, Jean-Ehrland Ricci, Christoph Borner

PubMed ID: 23788428

Date Published: 20th Jun 2013

Projects: No Projects

Journal: J. Cell. Sci.

Citation: J. Cell. Sci. 126(Pt 17): 4015-25

Scales: Not specified

Abstract (Expand)

When NF-κB activation or protein synthesis is inhibited, tumor necrosis factor alpha (TNFα) can induce apoptosis through Bax- and Bak-mediated mitochondrial outer membrane permeabilization (MOMP) leading ...

Created: 22nd Jan 2014 at 15:18


 

Isolation and hepatocyte differentiation of mesenchymal stem cells from porcine bone marrow--"surgical waste" as a novel MSC source


Authors: S Brückner, H-M Tautenhahn, S Winkler, P Stock, S Jonas, M Dollinger, B Christ

PubMed ID: 23769107

Date Published: 19th Jun 2013

Projects: C6: Organization and function of the sinusoidal system and the liver lob..., G: Clinical translation, Showcase Steatosis

Journal: Transplant. Proc.

Citation: Transplant. Proc. 45(5): 2056-8

Scales: Organism

Abstract (Expand)

Mesenchymal stem cells (MSC) isolated from bone marrow and differentiated into hepatocyte-like cells have increasingly gained attention for clinical cell therapy of liver diseases because of their high ...

Created: 19th Nov 2013 at 11:47


 

Expression variability of absorption, distribution, metabolism, excretion-related microRNAs in human liver: influence of nongenetic factors and association with gene expression


Authors: Jessica K Rieger, Kathrin Klein, Stefan Winter, Ulrich M Zanger

PubMed ID: 23733276

Date Published: 3rd Jun 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Drug Metab. Dispos.

Citation: Drug Metab. Dispos. 41(10): 1752-62

Scales: Not specified

Abstract (Expand)

Genes that are important for the detoxification of drugs and other xenobiotics show a high degree of interindividual variation attributable to regulation by diverse genetic, nongenetic, and epigenetic ...

Created: 8th Jan 2014 at 14:05


 

Alkyne lipids as substrates for click chemistry-based in vitro enzymatic assays


Authors: Anne Gaebler, Robin Milan, Leon Straub, Dominik Hoelper, Lars Kuerschner, Christoph Thiele

PubMed ID: 23709689

Date Published: 23rd May 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: J. Lipid Res.

Citation: J. Lipid Res. 54(8): 2282-90

Scales: Not specified

Abstract (Expand)

Click chemistry is evolving as a powerful tool in biological applications because it allows the sensitive and specific detection of compounds with alkyne or azido groups. Here we describe the use of ...

Created: 6th Jan 2014 at 11:19


 

Profile likelihood in systems biology


Authors: Clemens Kreutz, Andreas Raue, Daniel Kaschek, Jens Timmer

PubMed ID: 23581573

Date Published: 9th May 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: FEBS J.

Citation: FEBS J. 280(11): 2564-71

Scales: Not specified

Abstract (Expand)

Inferring knowledge about biological processes by a mathematical description is a major characteristic of Systems Biology. To understand and predict system's behavior the available experimental ...

Created: 14th Jan 2014 at 11:37


 

Metabolic Gradients as Key Regulators in Zonation of Tumor Energy Metabolism: A Tissue-scale Model Based Study


Authors: Matthias König, Hermann-Georg Holzhütter, Nikolaus Berndt

PubMed ID: 23589477

Date Published: 17th Apr 2013

Projects: C3: Zonation of metabolism and its regulation

Journal: Biotechnol J

Citation: Biotechnol J 8(9): 1058-69

Scales: Not specified

Abstract (Expand)

Characteristics of many tumor types are the reprogramming of metabolism and the occurrence of regional hypoxia. In this work we investigated the hypothesis that metabolic reprogramming in combination ...

Created: 6th May 2013 at 09:31   Last updated: 24th Oct 2013 at 16:14


 

Excemplify: a flexible template based solution, parsing and managing data in spreadsheets for experimentalists


Authors: L. Shi, L. Jong, U. Wittig, P. Lucarelli, M. Stepath, S. Mueller, L. A. D'Alessandro, U. Klingmuller, W. Muller

PubMed ID: 23549603

Date Published: 3rd Apr 2013

Projects: F1: The data management system

Journal: J Integr Bioinform

Citation: J Integr Bioinform. 2013 Apr 3;10(2):220. doi: 10.2390/biecoll-jib-2013-220.

Scales: Not specified

Abstract (Expand)

In systems biology, quantitative experimental data is the basis of building mathematical models. In most of the cases, they are stored in Excel files and hosted locally. To have a public database for ...

Created: 7th Aug 2015 at 12:16


 

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models


Authors: Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha, Julio Saez-Rodriguez

PubMed ID: 23525368

Date Published: 26th Mar 2013

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD, A: Cellular level, E: Model integration, Virtual Liver

Journal: Mol Biosyst

Citation: Mol Biosyst 9(7): 1576-83

Scales: Cell, Liver and Organism

Abstract (Expand)

Mathematical modelling is increasingly becoming an indispensable tool for the study of cellular processes, allowing their analysis in a systematic and comprehensive manner. In the vast majority of the ...

Created: 3rd Jun 2013 at 16:37   Last updated: 24th Oct 2013 at 16:14


 

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs


Authors: Philip Stegmaier, Alexander Kel, Edgar Wingender, Jürgen Borlak

DOI: 10.1371/journal.pcbi.1002958

Date Published: 21st Mar 2013

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 9(3) : e1002958

Scales: Cell

Abstract (Expand)

Algorithmic comparison of DNA sequence motifs is a problem in bioinformatics that has received increased attention during the last years. Its main applications concern characterization of potentially ...

Created: 28th Mar 2013 at 11:59   Last updated: 24th Oct 2013 at 16:14


 

Iron regulatory proteins control a mucosal block to intestinal iron absorption


Authors: Bruno Galy, Dunja Ferring-Appel, Christiane Becker, Norbert Gretz, Hermann-Josef Gröne, Klaus Schümann, Matthias W Hentze

PubMed ID: 23523353

Date Published: 21st Mar 2013

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Cell Rep

Citation: Cell Rep 3(3): 844-57

Scales: Not specified

Abstract (Expand)

Mammalian iron metabolism is regulated systemically by the hormone hepcidin and cellularly by iron regulatory proteins (IRPs) that orchestrate a posttranscriptional regulatory network. Through ...

Created: 14th Jan 2014 at 14:38


 

Biggest challenges in bioinformatics


Authors: Jonathan C Fuller, Pierre Khoueiry, Holger Dinkel, Kristoffer Forslund, Alexandros Stamatakis, Joseph Barry, Aidan Budd, Theodoros G Soldatos, Katja Linssen, Abdul Mateen Rajput

DOI: 10.1038/embor.2013.34

Date Published: 15th Mar 2013

Projects: F: Data management

Journal: EMBO Rep

Citation: EMBO Rep 14(4) : 302

Scales: Not specified

Abstract (Expand)

The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to ...

Created: 13th Jan 2014 at 15:08   Last updated: 13th Jan 2014 at 15:14


 

The High Energy Demand of Neuronal Cells Caused by Passive Leak Currents is Not a Waste of Energy


Authors: Nikolaus Berndt, Hermann-Georg Holzhütter

PubMed ID: 23479331

Date Published: 13th Mar 2013

Projects: No Projects

Journal: Cell Biochem. Biophys.

Citation: Cell Biochem Biophys. 67(2):527-35

Scales: Not specified

Abstract (Expand)

It is estimated that maintenance of the resting potential of neurons consumes between 15 % (in gray matter) and 44 % (in fully myelinated white matter) of the brain's total energy budget [1]. This ...

Created: 6th May 2013 at 09:24   Last updated: 24th Oct 2013 at 16:14


 

Novel CYP2B6 enzyme variants in a Rwandese population: functional characterization and assessment of in silico prediction tools


Authors: Robert Radloff, Alain Gras, Ulrich M Zanger, Cécile Masquelier, Karthik Arumugam, Jean-Claude Karasi, Vic Arendt, Carole Seguin-Devaux, Kathrin Klein

PubMed ID: 23418033

Date Published: 11th Mar 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Hum. Mutat.

Citation: Hum. Mutat. 34(5): 725-34

Scales: Not specified

Abstract (Expand)

Cytochrome P450 CYP2B6 is a highly polymorphic enzyme that metabolizes numerous drugs, pesticides, and environmental toxins. Sequence analysis of a Rwandese population identified eight functionally ...

Created: 13th Jan 2014 at 10:17


 

Pharmacogenetics of cytochrome P450 2B6 (CYP2B6): advances on polymorphisms, mechanisms, and clinical relevance


Authors: Ulrich M Zanger, Kathrin Klein

PubMed ID: 23467454

Date Published: 5th Mar 2013

Projects: A3.4: Linking signalling to metabolic functions

Journal: Front Genet

Citation: Front Genet 4: 24

Scales: Not specified

Abstract (Expand)

Cytochrome P450 2B6 (CYP2B6) belongs to the minor drug metabolizing P450s in human liver. Expression is highly variable both between individuals and within individuals, owing to non-genetic factors, ...

Created: 8th Jan 2014 at 14:10


 

A community-driven global reconstruction of human metabolism


Authors: Ines Thiele, Neil Swainston, Ronan M T Fleming, Andreas Hoppe, Swagatika Sahoo, Maike K Aurich, Hulda Haraldsdottir, Monica L Mo, Ottar Rolfsson, Miranda D Stobbe, Stefan G Thorleifsson, Rasmus Agren, Christian Bölling, Sergio Bordel, Arvind K Chavali, Paul Dobson, Warwick B Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon J Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le Novère, Naglis Malys, Alexander Mazein, Jason A Papin, Nathan D Price, Evgeni Selkov, Martin I Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes H G M van Beek, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans V Westerhoff, Douglas B Kell, Pedro Mendes, Bernhard Ø Palsson

PubMed ID: 23455439

Date Published: 3rd Mar 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A1.3: Identification of crucial metabolic processes during hepatocyte pr...

Journal: Nat. Biotechnol.

Citation: Nat. Biotechnol. 31(5): 419-25

Scales: Not specified

Abstract (Expand)

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', ...

Created: 19th Mar 2013 at 12:53   Last updated: 24th Oct 2013 at 16:15


 

Abnormal body iron distribution and erythropoiesis in a novel mouse model with inducible gain of iron regulatory protein (IRP)-1 function


Authors: D Casarrubea, L Viatte, T Hallas, A Vasanthakumar, R S Eisenstein, K Schümann, M W Hentze, B Galy

PubMed ID: 23455710

Date Published: 1st Mar 2013

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: J. Mol. Med.

Citation: J. Mol. Med. 91(7): 871-81

Scales: Not specified

Abstract (Expand)

Disorders of iron metabolism account for some of the most common human diseases. Cellular iron homeostasis is maintained by iron regulatory proteins (IRP)-1 and 2 through their binding to cis-regulatory ...

Created: 14th Jan 2014 at 14:40


 

Differently Saturated Fatty Acids Can Be Differentiated by (31)P NMR Subsequent to Derivatization with 2-Chloro-4,4,5,5-tetramethyldioxaphospholane: A Cautionary Note


Authors: Mandy Eibisch, Thomas Riemer, Beate Fuchs, Jürgen Schiller

PubMed ID: 23414224

Date Published: 26th Feb 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: J. Agric. Food Chem.

Citation: J. Agric. Food Chem. 61(11): 2696-700

Scales: Not specified

Abstract (Expand)

The analysis of free fatty acid (FFA) mixtures is a very important but, even nowadays, challenging task. This particularly applies as the so far most commonly used technique-gas chromatography/mass ...

Created: 6th Jan 2014 at 13:54


 

Pharmacogenomics of Cytochrome P450 3A4: Recent Progress Toward the "Missing Heritability" Problem


Authors: Kathrin Klein, Ulrich M Zanger

PubMed ID: 23444277

Date Published: 25th Feb 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Front Genet

Citation: Front Genet 4: 12

Scales: Not specified

Abstract (Expand)

CYP3A4 is the most important drug metabolizing enzyme in adult humans because of its prominent expression in liver and gut and because of its broad substrate specificity, which includes drugs from most ...

Created: 8th Jan 2014 at 14:16


 

Hedgehog signalling pathway in adult liver: a major new player in hepatocyte metabolism and zonation


Authors: Madlen Matz-Soja, Amalya Hovhannisyan, Rolf Gebhardt

PubMed ID: 23433827

Date Published: 21st Feb 2013

Projects: Virtual Liver

Journal: Med. Hypotheses

Citation: Med. Hypotheses 80(5): 589-94

Scales: Liver

Abstract (Expand)

Metabolic Zonation, i.e. the heterogeneous distribution of different metabolic pathways in different zones of the lobules, forms the basis of proper function of the liver in metabolic homeostasis and ...

Created: 4th Feb 2014 at 08:09


 

RNA-binding proteins in Mendelian disease


Authors: Alfredo Castello, Bernd Fischer, Matthias W Hentze, Thomas Preiss

PubMed ID: 23415593

Date Published: 15th Feb 2013

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Trends Genet.

Citation: Trends Genet. 29(5): 318-27

Scales: Not specified

Abstract (Expand)

RNA-binding proteins (RBPs) control all aspects of RNA fate, and defects in their function underlie a broad spectrum of human pathologies. We focus here on two recent studies that uncovered the in vivo ...

Created: 14th Jan 2014 at 14:42


 

System-wide identification of RNA-binding proteins by interactome capture


Authors: Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M Steinmetz, Jeroen Krijgsveld, Matthias W Hentze

PubMed ID: 23411631

Date Published: 14th Feb 2013

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Nat Protoc

Citation: Nat Protoc 8(3): 491-500

Scales: Not specified

Abstract (Expand)

Owing to their preeminent biological functions, the repertoire of expressed RNA-binding proteins (RBPs) and their activity states are highly informative about cellular systems. We have developed a novel ...

Created: 14th Jan 2014 at 14:41


 

A Unifying Ontology to Integrate Histological and Clinical Observations for Drug-Induced Liver Injury


Authors: Yuping Wang, Zhi Lin, Zhichao Liu, Stephen Harris, Reagan Kelly, Jie Zhang, Weigong Ge, Minjun Chen, Jürgen Borlak, Weida Tong

PubMed ID: 23395088

Date Published: 12th Feb 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Am. J. Pathol.

Citation: Am. J. Pathol. 182(4): 1180-7

Scales: Liver

Abstract (Expand)

Drug-induced liver injury (DILI) may present any morphologic characteristic of acute or chronic liver disease with no standardized terminology in place. Defining lexemes of DILI histopathology would ...

Created: 5th Mar 2013 at 16:36   Last updated: 24th Oct 2013 at 16:15


 

The Liver Toxicity Knowledge Base: A Systems Approach to a Complex End Point


Authors: M Chen, J Zhang, Y Wang, Z Liu, R Kelly, G Zhou, H Fang, J Borlak, W Tong

PubMed ID: 23486446

Date Published: 25th Jan 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Clin. Pharmacol. Ther.

Citation: Clin. Pharmacol. Ther. 93(5): 409-12

Scales: Cell

Abstract:

Not specified

Created: 15th Mar 2013 at 14:16   Last updated: 24th Oct 2013 at 16:15


 

A multi-scale modeling framework for individualized, spatiotemporal prediction of drug effects and toxicological risk


Authors: Juan G Diaz Ochoa, Joachim Bucher, Alexandre R R Péry, José M Zaldivar Comenges, Jens Niklas, Klaus Mauch

PubMed ID: 23346056

Date Published: 22nd Jan 2013

Projects: No Projects

Journal: Front Pharmacol

Citation: Front Pharmacol 3: 204

Scales: Not specified

Abstract (Expand)

In this study, we focus on a novel multi-scale modeling approach for spatiotemporal prediction of the distribution of substances and resulting hepatotoxicity by combining cellular models, a 2D liver ...

Created: 4th Feb 2013 at 11:46   Last updated: 24th Oct 2013 at 16:15


 

Molecular Interactions between NAFLD and Xenobiotic Metabolism


Authors: Adviti Naik, Aleš Belič, Ulrich M Zanger, Damjana Rozman

PubMed ID: 23346097

Date Published: 22nd Jan 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD, G1: Clinical Translation to Invasively Characterized Patients, Showcase Steatosis

Journal: Front Genet

Citation: Front Genet 4: 2

Scales: Not specified

Abstract (Expand)

Non-alcoholic fatty liver disease (NAFLD), the hepatic manifestation of the metabolic syndrome, is a complex multifactorial disease characterized by metabolic deregulations that include accumulation ...

Created: 8th Jan 2014 at 14:35


 

Caveolin-1 abrogates TGF-β mediated hepatocyte apoptosis


Authors: C Meyer, Y Liu, A Kaul, I Peipe, S Dooley

PubMed ID: 23328673

Date Published: 19th Jan 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity

Journal: Cell Death Dis

Citation: Cell Death Dis 4: e466

Scales: Cell

Abstract (Expand)

Transforming growth factor (TGF)-β has a dual role in liver, providing cytostatic effects during liver damage and regeneration, as well as carcinogenic functions in malignant transformation and ...

Created: 23rd Jan 2013 at 17:53   Last updated: 24th Oct 2013 at 16:15


 

Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation


Authors: Ulrich M Zanger, Matthias Schwab

PubMed ID: 23333322

Date Published: 16th Jan 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Pharmacol. Ther.

Citation: Pharmacol. Ther. 138(1): 103-41

Scales: Not specified

Abstract (Expand)

Cytochromes P450 (CYP) are a major source of variability in drug pharmacokinetics and response. Of 57 putatively functional human CYPs only about a dozen enzymes, belonging to the CYP1, 2, and 3 families, ...

Created: 8th Jan 2014 at 14:40


 

Genetics is a major determinant of expression of the human hepatic uptake transporter OATP1B1, but not of OATP1B3 and OATP2B1


Authors: Anne T Nies, Mikko Niemi, Oliver Burk, Stefan Winter, Ulrich M Zanger, Bruno Stieger, Matthias Schwab, Elke Schaeffeler

PubMed ID: 23311897

Date Published: 11th Jan 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Genome Med

Citation: Genome Med 5(1): 1

Scales: Not specified

Abstract (Expand)

ABSTRACT: BACKGROUND: Organic anion transporting polypeptide (OATP) 1B1, OATP1B3, and OATP2B1 (encoded by SLCO1B1, SLCO1B3, SLCO2B1) mediate the hepatic uptake of endogenous compounds like bile acids ...

Created: 16th Jan 2013 at 09:16   Last updated: 24th Oct 2013 at 16:15


 

Direct Transcriptional Regulation of Human Hepatic Cytochrome P450 3A4 (CYP3A4) by Peroxisome Proliferator-Activated Receptor Alpha (PPARα)


Authors: Maria Thomas, Oliver Burk, Britta Klumpp, Benjamin A Kandel, Georg Damm, Thomas S Weiss, Kathrin Klein, Matthias Schwab, Ulrich M Zanger

PubMed ID: 23295386

Date Published: 9th Jan 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, Showcase Steatosis

Journal: Mol. Pharmacol.

Citation: Mol. Pharmacol. 83(3): 709-18

Scales: Cell

Abstract (Expand)

The nuclear receptor peroxisome proliferator-activated receptor (PPAR)α is primarily known as a regulator of fatty acid metabolism, energy balance, and inflammation, but there is evidence suggesting a ...

Created: 9th Jan 2013 at 15:04   Last updated: 24th Oct 2013 at 16:15


 

Bone morphogenetic protein-9 (BMP-9) induces epithelial to mesenchymal transition (EMT) in hepatocellular carcinoma cells


Authors: Qi Li, Xing Gu, Honglei Weng, Shahrouz Ghafoory, Yan Liu, Teng Feng, Johanna Dzieran, Li Li, Iryna Ilkavets, Marianna Kruithof-de Julio, Stefan Munker, Alexander Marx, Albrecht Piiper, Eduardo Augusto Alonso, Norbert Gretz, Chunfang Gao, Stefan Wölfl, Steven Dooley, Katja Breitkopf-Heinlein

PubMed ID: 23281849

Date Published: 4th Jan 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A3.3: Hepatocyte polarity, B2.1: Hepatic stellate cells as source and target for hepatocellular gro..., B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd...

Journal: Cancer Sci.

Citation: Cancer Sci. 104(3): 398-408

Scales: Cell

Abstract (Expand)

80 - 90% of primary liver cancer cases originate from hepatocellular carcinoma (HCC), which has been regarded as the fifth most common cancer and the third most fatal reason responsible for cancer-related ...

Created: 18th Jan 2013 at 10:41   Last updated: 24th Oct 2013 at 16:15


 

Metformin and cancer: from the old medicine cabinet to pharmacological pitfalls and prospects


Authors: Arian Emami Riedmaier, Pascale Fisel, Anne T Nies, Elke Schaeffeler, Matthias Schwab

PubMed ID: 23277337

Date Published: 2nd Jan 2013

Projects: G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Trends Pharmacol. Sci.

Citation: Trends Pharmacol. Sci. 34(2): 126-35

Scales: Not specified

Abstract (Expand)

Metformin is a biguanide derivative used in the treatment of type II diabetes (T2D) and one of the world's most widely prescribed drugs. Owing to its safety profile, it has been recently promoted ...

Created: 8th Jan 2013 at 10:08   Last updated: 24th Oct 2013 at 16:15


 

Distinct dedifferentiation processes affect caveolin-1 expression in hepatocytes


Authors: Christoph Meyer, Johanna Dzieran, Yan Liu, Felizitas Schindler, Stefan Munker, Alexandra Müller, Cédric Coulouarn, Steven Dooley

DOI: 10.1186/1478-811X-11-6

Date Published: 2013

Projects: A3.3: Hepatocyte polarity

Journal: Cell Commun Signal

Citation: Cell Commun Signal 11(1) : 6

Scales: Cell

Abstract:

Not specified

Created: 23rd Jan 2013 at 17:57   Last updated: 24th Oct 2013 at 16:15


 

A Mechanistic, Model-Based Approach to Safety Assessment in Clinical Development


Authors: J Lippert, M Brosch, O von Kampen, M Meyer, H.-U Siegmund, C Schafmayer, T Becker, B Laffert, L Goerlitz, S Schreiber, PJ Neuvonen, M Niemi, J Hampe, L Kuepfer

DOI: 10.1038/psp.2012.22

Date Published: 2013

Projects: G3: Clinical Translation to Pharmaceutical Drug Development, G: Clinical translation

Journal: CPT: pharmacomet. syst. pharmacol.

Citation: CPT: pharmacomet. syst. pharmacol. 2(1) : e21

Scales: Not specified

Abstract:

Not specified

Created: 28th Jan 2013 at 09:55   Last updated: 24th Oct 2013 at 16:15


 

Precise generation of systems biology models from KEGG pathways


Authors: Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell

DOI: 10.1186/1752-0509-7-15

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 15

Scales: Cell and Intercellular

Abstract (Expand)

Background: The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG ...

Created: 23rd Feb 2013 at 23:19   Last updated: 24th Oct 2013 at 16:15


 

Modeling Wnt/β-Catenin Target Gene Expression in APC and Wnt Gradients Under Wild Type and Mutant Conditions


Authors: Uwe Benary, Bente Kofahl, Andreas Hecht, Jana Wolf

DOI: 10.3389/fphys.2013.00021

Date Published: 2013

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, B2.2: Importance of Wnt- and Hedgehog factors for hepatic stellate cells...

Journal: Front. Physiol.

Citation: Front. Physiol. 4

Scales: Cell

Abstract (Expand)

The Wnt/β-catenin pathway is involved in the regulation of a multitude of physiological processes by controlling the differential expression of target genes. In certain tissues such as the adult liver, ...

Created: 27th Feb 2013 at 10:06   Last updated: 24th Oct 2013 at 16:15


 

The systems biology simulation core algorithm


Authors: Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger

DOI: 10.1186/1752-0509-7-55

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 55

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

Abstract (Expand)

Background With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of ...

Created: 9th Jul 2013 at 04:12   Last updated: 24th Oct 2013 at 16:15


 

Metabolic Networks


Authors: Andreas Dräger, Hannes Planatscher

DOI: 10.1007/978-1-4419-9863-7_1277

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Book: Encyclopedia of Systems Biology

Citation: Encyclopedia of Systems Biology : 1249

Scales: Cell

Abstract (Expand)

Metabolic networks are interconnected pathways of biochemical reactions within living cells through which building blocks or compounds necessary for cellular functioning are assembled (anabolism) or ...

Created: 15th Aug 2013 at 23:34   Last updated: 23rd Jul 2015 at 13:38


 

Parameter Estimation, Metabolic Network Modeling


Authors: Andreas Dräger, Hannes Planatscher

DOI: 10.1007/978-1-4419-9863-7_1174

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Book: Encyclopedia of Systems Biology

Citation: Encyclopedia of Systems Biology : 1627

Scales: Cell

Abstract (Expand)

Metabolic networks can mathematically be modeled as a differential equation system. These models consist of a stoichiometric matrix, a modulation matrix, and a vector of reaction rates. The mathematical ...

Created: 15th Aug 2013 at 23:37   Last updated: 23rd Jul 2015 at 13:38


 

Using Bayesian-PBPK modeling for assessment of inter-individual variability and subgroup stratification


Authors: Markus Krauss, Rolf Burghaus, Jörg Lippert, Mikko Niemi, Pertti Neuvonen, Andreas Schuppert, Stefan Willmann, Lars Kuepfer, Linus Görlitz

DOI: 10.1186/2193-9616-1-6

Date Published: 2013

Projects: G: Clinical translation

Journal: In Silico Pharmacol

Citation: In Silico Pharmacol 1(1) : 6

Scales: Liver and Organism

Abstract (Expand)

Purpose Inter-individual variability in clinical endpoints and occurrence of potentially severe adverse effects represent an enormous challenge in drug development at all phases of (pre-)clinical ...

Created: 16th Sep 2013 at 13:50   Last updated: 24th Oct 2013 at 16:15


 

Path2Models: large-scale generation of computational models from biochemical pathway maps


Authors: Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère

DOI: 10.1186/1752-0509-7-116

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 116

Scales: Cell and Intercellular

Abstract (Expand)

Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de ...

Created: 4th Nov 2013 at 16:48   Last updated: 4th Nov 2013 at 16:54


 

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools


Authors: Claudine Chaouiya, Duncan Berenguier, Sarah M Keating, Aurelien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomá¿ Helikar

DOI: 10.1186/1752-0509-7-135

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 135

Scales: Cell and Intercellular

Abstract (Expand)

Background Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is ...

Created: 10th Dec 2013 at 18:07   Last updated: 10th Dec 2013 at 18:09


 

Systems Biology of Cell Death in Hepatocytes


Authors: Rebekka Schlatter, Kathrin Schmich, Christoph Borner, Michael Ederer, Irmgard Merfort

DOI: 10.1007/978-1-4614-4009-3_5

Date Published: 2013

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., Showcase LPS and Inflammation

Book: Systems Biology of Apoptosis

Citation: Systems Biology of Apoptosis : 101

Scales: Cell

Abstract (Expand)

The processes of liver regeneration and liver disease are regulated by a complex network of soluble and cell-associated apoptotic and inflammatory signals. To obtain insights into the mechanistic ...

Created: 7th Oct 2012 at 15:22   Last updated: 23rd Jul 2015 at 13:38


 

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0


Authors: Michael Weber, Sebastian G Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J van Zoelen, Dominik Driesch

DOI: 10.1186/1752-0509-7-1

Date Published: 2013

Projects: Virtual Liver

Journal: BMC Syst Biol

Citation: BMC Syst Biol 7(1) : 1

Scales: Not specified

Abstract (Expand)

BACKGROUND Inference of gene-regulatory networks (GRNs) is important for understanding behaviour and potential treatment of biological systems. Knowledge about GRNs gained from transcriptome analysis ...

Created: 2nd Jan 2013 at 10:24   Last updated: 24th Oct 2013 at 16:15


 

A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes


Authors: Federico Pinna, Sven Sahle, Katharina Beuke, Michaela Bissinger, Selcan Tuncay, Lorenz A D'Alessandro, Ralph Gauges, Andreas Raue, Jens Timmer, Ursula Klingmüller, Peter Schirmacher, Ursula Kummer, Kai Breuhahn

PubMed ID: 23293603

Date Published: 31st Dec 2012

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., B1.2: Reciprocal effect of cell-cell communication on information proces...

Journal: Front Physiol

Citation: Front Physiol 3: 466

Scales: Cell and Intercellular

Abstract (Expand)

The cytokine tumor necrosis factor-alpha (TNFα) is one of the key factors during the priming phase of liver regeneration as well as in hepatocarcinogenesis. TNFα activates the nuclear factor ...

Created: 16th Jan 2013 at 08:49   Last updated: 24th Oct 2013 at 16:15


 

High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury


Authors: Minjun Chen, Jürgen Borlak, Weida Tong

PubMed ID: 23258593

Date Published: 22nd Dec 2012

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Hepatology

Citation: Hepatology 58(1): 388-96

Scales: Liver

Abstract (Expand)

Drug induced liver injury (DILI) is a leading cause of drug failure in clinical trials and a major reason for drug withdrawals from the market. While there is evidence for doses of ≥ 100mg/day to be ...

Created: 28th Jan 2013 at 13:20   Last updated: 24th Oct 2013 at 16:15


 

Selective Protection of Human Liver Tissue in TNF-Targeting of Cancers of the Liver by Transient Depletion of Adenosine Triphosphate


Authors: Timo Weiland, Kathrin Klein, Martina Zimmermann, Tobias Speicher, Sascha Venturelli, Alexander Berger, Heike Bantel, Alfred Königsrainer, Martin Schenk, Thomas S Weiss, Albrecht Wendel, Matthias Schwab, Michael Bitzer, Ulrich M Lauer

PubMed ID: 23272249

Date Published: 18th Dec 2012

Projects: A3.4: Linking signalling to metabolic functions, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: PLoS ONE

Citation: PLoS ONE 7(12): e52496

Scales: Not specified

Abstract (Expand)

Tumor necrosis factor alpha (TNF) is able to kill cancer cells via receptor-mediated cell death requiring adenosine triphosphate (ATP). Clinical usage of TNF so far is largely limited by its profound ...

Created: 8th Jan 2013 at 10:43   Last updated: 24th Oct 2013 at 16:15


 

Hepatocyte-specific S100a8 and S100a9 transgene expression in mice causes Cxcl1 induction and systemic neutrophil enrichment


Authors: Lars Wiechert, Julia Németh, Tobias Pusterla, Christine Bauer, Aurora De Ponti, Sandra Manthey, Silke Marhenke, Arndt Vogel, Ursula Klingmüller, Jochen Hess, Peter Angel

PubMed ID: 23241281

Date Published: 15th Dec 2012

Projects: No Projects

Journal: Cell Commun. Signal

Citation: Cell Commun. Signal 10(1): 40

Scales: Not specified

Abstract:

ABSTRACT:

Created: 10th Jan 2013 at 14:31   Last updated: 24th Oct 2013 at 16:15


 

Cellular ERK Phospho-form Profiles with Conserved Preference for a Switch-like Pattern


Authors: Bettina Hahn, Lorenza Alice D Alessandro, Sofia Depner, Katharina Waldow, Martin Erich Boehm, Julie Bachmann, Marcel Schilling, Ursula Klingmüller, Wolf Dieter Lehmann

PubMed ID: 23210697

Date Published: 6th Dec 2012

Projects: No Projects

Journal: J. Proteome Res.

Citation: J. Proteome Res. 12(2): 637-46

Scales: Not specified

Abstract (Expand)

ERK is a member of the MAPK pathway with essential functions in cell proliferation, differentiation and survival. Complete ERK activation by the kinase MEK requires dual phosphorylation at T and Y ...

Created: 10th Jan 2013 at 14:19   Last updated: 24th Oct 2013 at 16:15


 

Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore�


Authors: Andreas Hoppe, Iryna Ilkavets, Steven Dooley, Hermann-Georg Holzhütter

DOI: 10.3390/metabo2040983

Date Published: 1st Dec 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd...

Journal: Metabolites

Citation: Metabolites 2(4) : 983

Scales: Cell

Abstract (Expand)

Abstract: TGFβ signaling plays a major role in the reorganization of liver tissue upon injury and is an important driver of chronic liver disease. This is achieved by a deep impact on a cohort of ...

Created: 28th Nov 2012 at 12:21   Last updated: 24th Oct 2013 at 16:15


 

The Extended TILAR Approach: A novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes


Authors: Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, Jörg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke, Rolf Gebhardt

PubMed ID: 23190768

Date Published: 29th Nov 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 147

Scales: Cell

Abstract (Expand)

ABSTRACT: BACKGROUND: Network inference is an important tool to reveal the underlying interactions of biological systems. In the liver, a complex system of transcription factors is active to distribute ...

Created: 30th Nov 2012 at 14:57   Last updated: 24th Oct 2013 at 16:15


 

Pharmacogenomics: a key component of personalized therapy


Authors: Matthias Schwab, Elke Schaeffeler

PubMed ID: 23194652

Date Published: 29th Nov 2012

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Genome Med

Citation: Genome Med 4(11): 93

Scales: Not specified

Abstract:

Not specified

Created: 5th Dec 2012 at 09:51   Last updated: 24th Oct 2013 at 16:15


 

Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration


Authors: René Meyer, Lorenza A D'Alessandro, Sandip Kar, Bernhard Kramer, Bin She, Daniel Kaschek, Bettina Hahn, David Wrangborg, Johan Karlsson, Mats Kvarnström, Mats Jirstrand, Wolf-Dieter Lehmann, Jens Timmer, Thomas Höfer, Ursula Klingmüller

PubMed ID: 23226133

Date Published: 28th Nov 2012

Projects: No Projects

Journal: Front Physiol

Citation: Front Physiol 3: 451

Scales: Not specified

Abstract (Expand)

In most solid cancers, cells harboring oncogenic mutations represent only a sub-fraction of the entire population. Within this sub-fraction the expression level of mutated proteins can vary significantly ...

Created: 10th Jan 2013 at 14:27   Last updated: 24th Oct 2013 at 16:15


 

Implication of hepatic stem cells in functional liver repopulation


Authors: Bruno Christ, Sandra Pelz

PubMed ID: 23184585

Date Published: 26th Nov 2012

Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase HGF and Regeneration

Journal: Cytometry A

Citation: Cytometry A 83(1): 90-102

Scales: Cell and Liver

Abstract (Expand)

The liver has an enormous potential to restore the parenchymal tissue loss due to injury. This is accomplished by the proliferation of either the hepatocytes or liver progenitor cells in cases where ...

Created: 19th Nov 2013 at 11:52


 

Oxygen consumption rates during three different neuronal activity states in the hippocampal CA3 network


Authors: Christine Huchzermeyer, Nikolaus Berndt, Hermann-Georg Holzhütter, Oliver Kann

PubMed ID: 23168532

Date Published: 21st Nov 2012

Projects: No Projects

Journal: J. Cereb. Blood Flow Metab.

Citation: J. Cereb. Blood Flow Metab. 33(2): 263-71

Scales: Not specified

Abstract (Expand)

The brain is an organ with high metabolic rate. However, little is known about energy utilization during different activity states of neuronal networks. We addressed this issue in area CA3 of hippocampal ...

Created: 6th May 2013 at 09:30   Last updated: 24th Oct 2013 at 16:15


 

Serum-free culture of primary human hepatocytes in a miniaturized hollow-fibre membrane bioreactor for pharmacological in vitro studies


Authors: Marc Lübberstedt, Ursula Müller-Vieira, Klaus M Biemel, Malin Darnell, Stefan A Hoffmann, Fanny Knöspel, Eva C Wönne, Daniel Knobeloch, Andreas K Nüssler, Jörg C Gerlach, Tommy B Andersson, Katrin Zeilinger

PubMed ID: 23165723

Date Published: 21st Nov 2012

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen...

Journal: J Tissue Eng Regen Med

Citation: J Tissue Eng Regen Med :

Scales: Intercellular

Abstract (Expand)

Primary human hepatocytes represent an important cell source for in vitro investigation of hepatic drug metabolism and disposition. In this study, a multi-compartment capillary membrane-based bioreactor ...

Created: 22nd Nov 2012 at 16:19   Last updated: 24th Oct 2013 at 16:15


 

A rapid screening assay to search for phosphorylated proteins in tissue extracts


Authors: Ignazio Garaguso, Juergen Borlak

PubMed ID: 23166814

Date Published: 15th Nov 2012

Projects: CTU Proteomics

Journal: PLoS ONE

Citation: PLoS ONE 7(11): e50025

Scales: Not specified

Abstract (Expand)

Reversible protein phosphorylation is an essential mechanism in the regulation of diverse biological processes, nonetheless is frequently altered in disease. As most phosphoproteome studies are based ...

Created: 14th Dec 2012 at 19:18   Last updated: 24th Oct 2013 at 16:15


 

Quantitative Evaluation and Prediction of Drug Effects and Toxicological Risk Using Mechanistic Multiscale Models


Authors: Jens Niklas, Juan G Diaz Ochoa, Joachim Bucher, Klaus Mauch

DOI: 10.1002/minf.201200043

Date Published: 14th Nov 2012

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Mol. Inf.

Citation: Mol. Inf. 32(1) : 14

Scales: Not specified

Abstract (Expand)

Integrating in vitro and in silico approaches has great potential for reducing experimental effort and delivering know-how and intellectual property in drug development. Here, we focus on a possible ...

Created: 16th Jan 2013 at 11:43   Last updated: 24th Oct 2013 at 16:15


 

Omics and Drug Response


Authors: Urs A Meyer, Ulrich M Zanger, Matthias Schwab

PubMed ID: 23140244

Date Published: 13th Nov 2012

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Annu. Rev. Pharmacol. Toxicol.

Citation: Annu. Rev. Pharmacol. Toxicol. 53: 475-502

Scales: Not specified

Abstract (Expand)

A new generation of technologies commonly named omics permits assessment of the entirety of the components of biological systems and produces an explosion of data and a major shift in our concepts of ...

Created: 5th Dec 2012 at 09:42   Last updated: 24th Oct 2013 at 16:15


 

Integrating Cellular Metabolism into a Multiscale Whole-Body Model


Authors: Markus Krauss, Stephan Schaller, Steffen Borchers, Rolf Findeisen, Jörg Lippert, Lars Kuepfer

DOI: 10.1371/journal.pcbi.1002750

Date Published: 25th Oct 2012

Projects: E4: Vertical integration across biological scales, E: Model integration

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 8(10) : e1002750

Scales: Cell, Liver and Organism

Abstract (Expand)

Cellular metabolism continuously processes an enormous range of external compounds into endogenous metabolites and is as such a key element in human physiology. The multifaceted physiological role of ...

Created: 29th Oct 2012 at 12:17   Last updated: 24th Oct 2013 at 16:15


 

Pattern-formation mechanisms in motility mutants of Myxococcus xanthus


Authors: J. Starruss, F. Peruani, V. Jakovljevic, L. Sogaard-Andersen, A. Deutsch, M. Bar

DOI: 10.1098/rsfs.2012.0034

Date Published: 25th Oct 2012

Projects: B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., B3: Intercellular communication through cell adhesion

Journal: Interface Focus

Citation: Interface Focus 2(6) : 774

Scales: Cell, Intercellular and Liver lobule

Abstract:

Not specified

Created: 12th Nov 2012 at 15:43   Last updated: 24th Oct 2013 at 16:15


 

SIRT7 oncogenic potential in human hepatocellular carcinoma and its regulation by the tumor suppressors mir-125a-5p and mir-125b


Authors: Jeong Kyu Kim, Ji Heon Noh, Kwang Hwa Jung, Jung Woo Eun, Hyun Jin Bae, Min Gyu Kim, Young Gyoon Chang, Qingyu Shen, Won Sang Park, Jung Young Lee, Jürgen Borlak, Suk Woo Nam

PubMed ID: 23079745

Date Published: 20th Oct 2012

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Hepatology

Citation: Hepatology 57(3): 1055-67

Scales: Cell

Abstract (Expand)

Sirtuins are NAD(+) -dependent deacetylases and function in cellular metabolism, stress resistance and ageing. For Sirtuin7 (SIRT7), a role in ribosomal gene transcription is proposed, but its function ...

Created: 28th Jan 2013 at 13:50   Last updated: 24th Oct 2013 at 16:15


 

Quantitative kinetic analysis of BMP2 uptake into cells and its modulation by BMP-antagonists


Authors: Hamed Alborzinia, Hannah Schmidt-Glenewinkel, Iryna Ilkavets, Katja Breitkopf-Heinlein, Xinlai Cheng, Peter Hortschansky, Steven Dooley, Stefan Wölfl

PubMed ID: 23077176

Date Published: 19th Oct 2012

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: J. Cell. Sci.

Citation: J. Cell. Sci. 126(Pt 1): 117-27

Scales: Not specified

Abstract (Expand)

Bone morphogenetic proteins (BMPs) are members of the TGFβ-family of signaling proteins and play an important role during development and in tissue formation. BMP signaling is a well studied process, ...

Created: 31st Oct 2012 at 09:20   Last updated: 24th Oct 2013 at 16:15


 

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail


Authors: Katrin Kolczyk, Regina Samaga, Holger Conzelmann, Sebastian Mirschel, Carsten Conradi

PubMed ID: 23020215

Date Published: 28th Sep 2012

Projects: E1: Integration on the cellular level

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 13: 251

Scales: Cell

Abstract (Expand)

Signaling systems typically involve large, structured molecules each consisting of a large number of subunits called molecule domains. In modeling such systems these domains can be considered as the ...

Created: 16th Jan 2014 at 11:29


 

Robustness of signal transduction pathways


Authors: Nils Blüthgen, Stefan Legewie

PubMed ID: 23007845

Date Published: 25th Sep 2012

Projects: A2.4: Linking signalling pathways regulating liver regeneration and orga..., B1.2: Reciprocal effect of cell-cell communication on information proces..., B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Cell. Mol. Life Sci.

Citation: Cell. Mol. Life Sci. 70(13): 2259-69

Scales: Cell and Intercellular

Abstract (Expand)

Signal transduction pathways transduce information about the outside of the cell to the nucleus, regulating gene expression and cell fate. To reliably inform the cell about its surroundings, information ...

Created: 20th Jan 2014 at 16:31


 

Tracing Fatty Acid Metabolism by Click Chemistry


Authors: Christoph Thiele, Cyrus Papan, Dominik Hoelper, Kalina Kusserow, Anne Gaebler, Mario Schoene, Kira Piotrowitz, Daniel Lohmann, Johanna Spandl, Ana Stevanovic, Andrej Shevchenko, Lars Kuerschner

PubMed ID: 22999348

Date Published: 25th Sep 2012

Projects: A1: Cellular metabolism

Journal: ACS Chem. Biol.

Citation: ACS Chem. Biol. 7(12): 2004-11

Scales: Cell

Abstract (Expand)

Fatty acids are abundant constituents of all biological systems, and their metabolism is important for normal function at all levels of an organism. Aberrations in fatty acid metabolism are associated ...

Created: 26th Oct 2012 at 16:36   Last updated: 24th Oct 2013 at 16:15


 

Multidrug and toxin extrusion proteins as transporters of antimicrobial drugs


Authors: Anne T Nies, Katja Damme, Elke Schaeffeler, Matthias Schwab

PubMed ID: 22970772

Date Published: 13th Sep 2012

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Expert Opin Drug Metab Toxicol

Citation: Expert Opin Drug Metab Toxicol 8(12): 1565-77

Scales: Not specified

Abstract (Expand)

INTRODUCTION: Antimicrobial drugs are essential in the treatment of infectious diseases. A better understanding of transport processes involved in drug disposition will improve the predictability of ...

Created: 10th Jan 2013 at 10:39   Last updated: 24th Oct 2013 at 16:15


 

Kinetic Modeling of Human Hepatic Glucose Metabolism in T2DM Predicts Higher Risk of Hypoglycemic Events in Rigorous Insulin Therapy


Authors: M. Koenig, H.-G. Holzhuetter

DOI: 10.1074/jbc.M112.382069

Date Published: 12th Sep 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A1: Cellular metabolism, A3.4: Linking signalling to metabolic functions

Journal: Journal of Biological Chemistry

Citation: Journal of Biological Chemistry 287(44) : 36978

Scales: Cell and Liver

Abstract (Expand)

A major problem in the insulin therapy of patients with diabetes type 2 (T2DM) is the increased occurrence of hypoglycemic events which, if left untreated, may cause confusion or fainting and in severe ...

Created: 4th Oct 2012 at 18:18   Last updated: 24th Oct 2013 at 16:15


 

Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model


Author: Anja Voss-Böhme

DOI: 10.1371/journal.pone.0042852

Date Published: 11th Sep 2012

Projects: A3.3: Hepatocyte polarity, B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., E2: Integration on the liver lobule scale: Image processing and mathemat...

Journal: PLoS ONE

Citation: PLoS ONE 7(9) : e42852

Scales: Cell

Abstract (Expand)

Cellular Potts models (CPMs) are used as a modeling framework to elucidate mechanisms of biological development. They allow a spatial resolution below the cellular scale and are applied particularly ...

Created: 21st Sep 2012 at 14:45   Last updated: 24th Oct 2013 at 16:15


 

Comprehensive estimation of input signals and dynamics in biochemical reaction networks


Authors: M Schelker, A Raue, J Timmer, C Kreutz

PubMed ID: 22962477

Date Published: 11th Sep 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: Bioinformatics

Citation: Bioinformatics 28(18): i529-i534

Scales: Cell

Abstract (Expand)

Cellular information processing can be described mathematically using differential equations. Often, external stimulation of cells by compounds such as drugs or hormones leading to activation has to ...

Created: 29th Oct 2012 at 10:19   Last updated: 24th Oct 2013 at 16:15


 

Smad6 and Smad7 are co-regulated with hepcidin in mouse models of iron overload


Authors: Maja Vujić Spasić, Richard Sparla, Katarzyna Mleczko-Sanecka, Mary C Migas, Katja Breitkopf-Heinlein, Steven Dooley, Sophie Vaulont, Robert E Fleming, Martina U Muckenthaler

PubMed ID: 22960056

Date Published: 11th Sep 2012

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag..., Show cases

Journal: Biochim. Biophys. Acta

Citation: Biochim. Biophys. Acta 1832(1): 76-84

Scales: Not specified

Abstract (Expand)

The inhibitory Smad7 acts as a critical suppressor of hepcidin, the major regulator of systemic iron homeostasis. In this study we define the mRNA expression of the two functionally related Smad proteins, ...

Created: 31st Oct 2012 at 09:07   Last updated: 24th Oct 2013 at 16:15


 

What mRNA Abundances Can Tell us about Metabolism


Author: Andreas Hoppe

DOI: 10.3390/metabo2030614

Date Published: 1st Sep 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Metabolites

Citation: Metabolites 2(4) : 614

Scales: Not specified

Abstract (Expand)

Inferring decreased or increased metabolic functions from transcript profiles is at first sight a bold and speculative attempt because of the functional layers in between: proteins, enzymatic activities, ...

Created: 23rd Oct 2012 at 12:30   Last updated: 24th Oct 2013 at 16:16


 

Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism


Authors: Susanna Bazzani, Andreas Hoppe, Hermann-Georg Holzhütter

PubMed ID: 22937810

Date Published: 31st Aug 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 118

Scales: Cell

Abstract (Expand)

ABSTRACT: BACKGROUND: The search for new drug targets for antibiotics against Plasmodium falciparum, a major cause of human deaths, is a pressing scientific issue, as multiple resistance strains spread ...

Created: 16th Nov 2012 at 14:21   Last updated: 24th Oct 2013 at 16:16


 

Sustained submicromolar H2O2 levels induce hepcidin via signal transducer and activator of transcription 3 (STAT3)


Authors: Gunda Millonig, Ingo Ganzleben, Teresa Peccerella, Guillem Casanovas, Lidia Brodziak-Jarosz, Katja Breitkopf-Heinlein, Tobias P Dick, Helmut-Karl Seitz, Martina U Muckenthaler, Sebastian Mueller

PubMed ID: 22932892

Date Published: 29th Aug 2012

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: J. Biol. Chem.

Citation: J. Biol. Chem. 287(44): 37472-82

Scales: Cell

Abstract (Expand)

The peptide hormone hepcidin regulates mammalian iron homeostasis by blocking ferroportin-mediated iron export from macrophages and the duodenum. During inflammation, hepcidin is strongly induced by ...

Created: 20th Jan 2014 at 11:13


 

CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism


Authors: Anja Karlstaedt, Daniela Fliegner, Georgios Kararigas, Hugo S Ruderisch, Vera Regitz-Zagrosek, Hermann G Holzhütter

PubMed ID: 22929619

Date Published: 29th Aug 2012

Projects: No Projects

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 114

Scales: Not specified

Abstract (Expand)

ABSTRACT: BACKGROUND: Availability of oxygen and nutrients in the coronary circulation is a crucial determinant of cardiac performance. Nutrient composition of coronary blood may significantly vary in ...

Created: 4th Jan 2013 at 12:48   Last updated: 24th Oct 2013 at 16:16


 

Nicotinic acid inhibits hepatic APOA gene expression: studies in humans and in transgenic mice


Authors: Indumathi Chennamsetty, Karam M Kostner, Thierry Claudel, Manjula Vinod, Sasa Frank, Thomas S Weiss, Michael Trauner, Gerhard M Kostner

PubMed ID: 22930813

Date Published: 28th Aug 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., CTU SOP Human Hepatocytes

Journal: J. Lipid Res.

Citation: J. Lipid Res. 53(11): 2405-12

Scales: Cell and Liver

Abstract (Expand)

Elevated plasma lipoprotein(a) (LPA) levels are recognized as an independent risk factor for cardiovascular diseases. Our knowledge on LPA metabolism is incomplete, which makes it difficult to develop ...

Created: 30th Jan 2014 at 17:14


 

Qualitative translation of relations from BioPAX to SBML qual


Authors: F. Buchel, C. Wrzodek, F. Mittag, A. Drager, J. Eichner, N. Rodriguez, N. L. Novere, A. Zell

DOI: 10.1093/bioinformatics/bts508

Date Published: 24th Aug 2012

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase Steatosis

Journal: Bioinformatics

Citation: Bioinformatics 28(20) : 2648

Scales: Cell and Intercellular

Abstract (Expand)

Motivation: The Biological Pathway Exchange Language (BioPAX) and the Systems Biology Markup Language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus ...

Created: 25th Aug 2012 at 21:46   Last updated: 24th Oct 2013 at 16:16


 

Multi-Target Regulation by Small RNAs Synchronizes Gene Expression Thresholds and May Enhance Ultrasensitive Behavior


Authors: Jörn Matthias Schmiedel, Ilka Maria Axmann, Stefan Legewie

PubMed ID: 22927924

Date Published: 21st Aug 2012

Projects: A2.4: Linking signalling pathways regulating liver regeneration and orga..., B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: PLoS ONE

Citation: PLoS ONE 7(8): e42296

Scales: Cell

Abstract (Expand)

Cells respond to external cues by precisely coordinating multiple molecular events. Co-regulation may be established by the so-called single-input module (SIM), where a common regulator controls multiple ...

Created: 3rd Sep 2012 at 11:02   Last updated: 24th Oct 2013 at 16:16


 

Genetic and functional identification of the likely causative variant for cholesterol gallstone disease at the ABCG5/8 lithogenic locus


Authors: Oliver von Kampen, Stephan Buch, Michael Nothnagel, Lorena Azocar, Hector Molina, Mario Brosch, Wiebke Erhart, Witigo von Schönfels, Jan Egberts, Marcus Seeger, Alexander Arlt, Tobias Balschun, Andre Franke, Markus M Lerch, Julia Mayerle, Wolfgang Kratzer, Bernhard O Boehm, Klaus Huse, Bodo Schniewind, Katharina Tiemann, Zhao-Yyan Jiang, Tian-Quan Han, Balraj Mittal, Anshika Srivastava, Mogens Fenger, Torben Jørgensen, Ramin Schirin-Sokhan, Anke Tönjes, Henning Wittenburg, Michael Stumvoll, Holger Kalthoff, Frank Lammert, Jürgen Tepel, Klaus Puschel, Thomas Becker, Stefan Schreiber, Matthias Platzer, Henry Völzke, Michael Krawczak, Juan Francisco Miquel, Clemens Schafmayer, Jochen Hampe

PubMed ID: 22898925

Date Published: 18th Aug 2012

Projects: G: Clinical translation

Journal: Hepatology

Citation: Hepatology 57(6): 2407-17

Scales: Organism

Abstract (Expand)

BACKGROUND & AIMS: The sterolin locus (ABCG5/ABCG8) has been solidly shown to confer susceptibility for cholesterol gallstone disease in humans. Both the responsible variant and the molecular ...

Created: 4th Oct 2012 at 19:37   Last updated: 24th Oct 2013 at 16:16


 

A variational approach to parameter estimation in ordinary differential equations


Authors: Daniel Kaschek, Jens Timmer

PubMed ID: 22892133

Date Published: 14th Aug 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 99

Scales: Cell

Abstract (Expand)

ABSTRACT: BACKGROUND: Ordinary differential equations are widely-used in the field of systems biology andchemical engineering to model chemical reaction networks. Numerous techniques havebeen developed ...

Created: 29th Oct 2012 at 10:50   Last updated: 24th Oct 2013 at 16:16


 

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting


Authors: Claudia Fritsch, Alexander Herrmann, Michael Nothnagel, Karol Szafranski, Klaus Huse, Frank Schumann, Stefan Schreiber, Matthias Platzer, Michael Krawczak, Jochen Hampe, Mario Brosch

PubMed ID: 22879431

Date Published: 9th Aug 2012

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, G: Clinical translation

Journal: Genome Res.

Citation: Genome Res. 22(11): 2208-18

Scales: Cell

Abstract (Expand)

So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells ...

Created: 4th Oct 2012 at 19:40   Last updated: 24th Oct 2013 at 16:16


 

Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS


Authors: Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen, Reinhold Schäfer

PubMed ID: 22864383

Date Published: 7th Aug 2012

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 8: 601

Scales: Cell

Abstract (Expand)

RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here, we used a ...

Created: 3rd Sep 2012 at 11:20   Last updated: 24th Oct 2013 at 16:16


 

A General Theoretical Framework to Infer Endosomal Network Dynamics from Quantitative Image Analysis


Authors: Lionel Foret, Jonathan E. Dawson, Roberto Villaseñor, Claudio Collinet, Andreas Deutsch, Lutz Brusch, Marino Zerial, Yannis Kalaidzidis, Frank Jülicher

DOI: 10.1016/j.cub.2012.06.021

Date Published: 1st Aug 2012

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc...

Journal: Current Biology

Citation: Current Biology 22(15) : 1381

Scales: Intercellular

Abstract (Expand)

Background: Endocytosis allows the import and distribution of cargo into a series of endosomes with distinct morphological and biochemical characteristics. Our current understanding of endocytic cargo ...

Created: 21st Sep 2012 at 14:35   Last updated: 24th Oct 2013 at 16:16


 

Central energy metabolism remains robust in acute steatotic hepatocytes challenged by a high free fatty acid load


Authors: Jens Niklas, Anne Bonin, Stefanie Mangin, Joachim Bucher, Stephanie Kopacz, Madlen Matz-Soja, Carlo Thiel, Rolf Gebhardt, Ute Hofmann, Klaus Mauch

PubMed ID: 22831974

Date Published: 27th Jul 2012

Projects: A1: Cellular metabolism, A: Cellular level

Journal: BMB Rep

Citation: BMB Rep 45(7): 396-401

Scales: Not specified

Abstract (Expand)

Overnutrition is one of the major causes of non-alcoholic fatty liver disease (NAFLD). NAFLD is characterized by an accumulation of lipids (triglycerides) in hepatocytes and is often accompanied by ...

Created: 14th Aug 2012 at 14:54   Last updated: 24th Oct 2013 at 16:16


 

Modulation of glutamine metabolism by the PI(3)K-PKB-FOXO network regulates autophagy


Authors: Kristan E van der Vos, Pernilla Eliasson, Tassula Proikas-Cezanne, Stephin J Vervoort, Ruben van Boxtel, Marrit Putker, Iris J van Zutphen, Mario Mauthe, Sebastian Zellmer, Cornelieke Pals, Liesbeth P Verhagen, Marian J A Groot Koerkamp, A Koen Braat, Tobias B Dansen, Frank C Holstege, Rolf Gebhardt, Boudewijn M Burgering, Paul J Coffer

PubMed ID: 22820375

Date Published: 22nd Jul 2012

Projects: A1: Cellular metabolism, A: Cellular level

Journal: Nat. Cell Biol.

Citation: Nat. Cell Biol. 14(8): 829-37

Scales: Cell

Abstract (Expand)

The PI(3)K-PKB-FOXO signalling network provides a major intracellular hub for the regulation of cell proliferation, survival and stress resistance. Here we report an unexpected role for FOXO transcription ...

Created: 14th Aug 2012 at 14:52   Last updated: 24th Oct 2013 at 16:16


 

Experimental design for parameter estimation of gene regulatory networks


Authors: Bernhard Steiert, Andreas Raue, Jens Timmer, Clemens Kreutz

PubMed ID: 22815723

Date Published: 16th Jul 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: PLoS ONE

Citation: PLoS ONE 7(7): e40052

Scales: Cell

Abstract (Expand)

Systems biology aims for building quantitative models to address unresolved issues in molecular biology. In order to describe the behavior of biological cells adequately, gene regulatory networks (GRNs) ...

Created: 8th Aug 2012 at 11:44   Last updated: 24th Oct 2013 at 16:16


 

Detecting and investigating substrate cycles in a genome-scale human metabolic network


Authors: Juliane Gebauer, Stefan Schuster, Luís F de Figueiredo, Christoph Kaleta

PubMed ID: 22776428

Date Published: 11th Jul 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: The FEBS journal

Citation: FEBS J. 279(17): 3192-202

Scales: Cell

Abstract (Expand)

Substrate cycles, also known as futile cycles, are cyclic metabolic routes that dissipate energy by hydrolysing cofactors such as ATP. They were first described in the 1970s occurring in muscles of ...

Created: 1st Aug 2012 at 11:45   Last updated: 24th Oct 2013 at 16:16


 

CySBML: a Cytoscape plugin for SBML


Authors: Matthias König, Andreas Dräger, Hermann-Georg Holzhütter

PubMed ID: 22772946

Date Published: 10th Jul 2012

Projects: A1: Cellular metabolism, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, F: Data management

Journal: Bioinformatics (Oxford, England)

Citation: Bioinformatics 28(18): 2402-3

Scales: Not specified

Abstract (Expand)

SUMMARY: CySBML is a plugin designed to work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts ...

Created: 12th Jul 2012 at 08:37   Last updated: 24th Oct 2013 at 16:16


 

Mesenchymal stem cell-derived hepatocytes for functional liver replacement


Authors: Bruno Christ, Peggy Stock

PubMed ID: 22737154

Date Published: 22nd Jun 2012

Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase HGF and Regeneration, Virtual Liver

Journal: Front Immunol

Citation: Front Immunol 3: 168

Scales: Cell and Liver

Abstract (Expand)

Mesenchymal stem cells represent an alternate cell source to substitute for primary hepatocytes in hepatocyte transplantation because of their multiple differentiation potential and nearly unlimited ...

Created: 19th Nov 2013 at 11:55


 

Quantifying the contribution of the liver to glucose homeostasis: a detailed kinetic model of human hepatic glucose metabolism


Authors: Matthias König, Sascha Bulik, Hermann-Georg Holzhütter

PubMed ID: 22761565

Date Published: 21st Jun 2012

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A1: Cellular metabolism, A2.5: Integration of insulin and Wnt signalling in hepatocytes, A2: Integration of Signalling Pathways in Hepatocellular Response, A3.4: Linking signalling to metabolic functions

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 8(6): e1002577

Scales: Cell and Liver

Abstract (Expand)

Despite the crucial role of the liver in glucose homeostasis, a detailed mathematical model of human hepatic glucose metabolism is lacking so far. Here we present a detailed kinetic model of glycolysis, ...

Created: 12th Jul 2012 at 08:46   Last updated: 24th Oct 2013 at 16:16


 

Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification


Authors: Andrej Vasilj, Marc Gentzel, Elke Ueberham, Rolf Gebhardt, Andrej Shevchenko

PubMed ID: 22671763

Date Published: 21st Jun 2012

Projects: A: Cellular level

Journal: J. Proteome Res.

Citation: J. Proteome Res. 11(7): 3680-9

Scales: Cell

Abstract (Expand)

Label-free methods streamline quantitative proteomics of tissues by alleviating the need for metabolic labeling of proteins with stable isotopes. Here we detail and implement solutions to common problems ...

Created: 20th Jul 2012 at 10:20   Last updated: 24th Oct 2013 at 16:16


 

Analysis of drug metabolism activities in a miniaturized liver cell bioreactor for use in pharmacological studies


Authors: Stefan A Hoffmann, Ursula Müller-Vieira, Klaus Biemel, Daniel Knobeloch, Sandra Heydel, Marc Lübberstedt, Andreas K Nüssler, Tommy B Andersson, Jörg C Gerlach, Katrin Zeilinger

PubMed ID: 22688505

Date Published: 13th Jun 2012

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen...

Journal: Biotechnology and bioengineering

Citation: Biotechnol. Bioeng. 109(12): 3172-81

Scales: Intercellular

Abstract (Expand)

Based on a hollow fiber perfusion technology with internal oxygenation, a miniaturized bioreactor with a volume of 0.5 mL for in vitro studies was recently developed. Here, the suitability of this novel ...

Created: 24th Aug 2012 at 11:07   Last updated: 24th Oct 2013 at 16:16


 

Kinetic Modeling of the Mitochondrial Energy Metabolism of Neuronal Cells: The Impact of Reduced α-Ketoglutarate Dehydrogenase Activities on ATP Production and Generation of Reactive Oxygen Species


Authors: Nikolaus Berndt, Sascha Bulik, Hermann-Georg Holzhütter

PubMed ID: 22719765

Date Published: 10th Jun 2012

Projects: A1: Cellular metabolism

Journal: Int J Cell Biol

Citation: Int J Cell Biol 2012: 757594

Scales: Not specified

Abstract (Expand)

Reduced activity of brain α-ketoglutarate dehydrogenase complex (KGDHC) occurs in a number of neurodegenerative diseases like Parkinson's disease and Alzheimer's disease. In order to quantify ...

Created: 18th Jul 2012 at 10:01   Last updated: 24th Oct 2013 at 16:16


 

Identification of RARRES1 as a core regulator in liver fibrosis


Authors: Andreas Teufel, Diana Becker, Susanne N Weber, Steven Dooley, Katja Breitkopf-Heinlein, Thorsten Maass, Katrin Hochrath, Markus Krupp, Jens U Marquardt, Martin Kolb, Bernhard Korn, Christof Niehrs, Tim Zimmermann, Patricio Godoy, Peter R Galle, Frank Lammert

PubMed ID: 22669512

Date Published: 6th Jun 2012

Projects: B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: Journal of molecular medicine (Berlin, Germany)

Citation: J. Mol. Med. 90(12): 1439-47

Scales: Not specified

Abstract (Expand)

Genetic factors contribute to progression and modulation of hepatic fibrosis. High throughput genomics/transcriptomics approaches aiming at identifying key regulators of fibrosis development are tainted ...

Created: 31st Jul 2012 at 11:24   Last updated: 24th Oct 2013 at 16:16


 

Concurrent epigenetic silencing of wnt/β-catenin pathway inhibitor genes in B cell chronic lymphocytic leukaemia


Authors: Evgeny A Moskalev, Katrin Luckert, Ivan A Vorobjev, Sergey E Mastitsky, Aleena A Gladkikh, Achim Stephan, Marita Schrenk, Kamil D Kaplanov, Olga B Kalashnikova, Oliver Pötz, Thomas O Joos, Jörg D Hoheisel

PubMed ID: 22672427

Date Published: 6th Jun 2012

Projects: No Projects

Journal: BMC Cancer

Citation: BMC Cancer 12: 213

Scales: Not specified

Abstract:

ABSTRACT:

Created: 27th Nov 2012 at 13:25   Last updated: 24th Oct 2013 at 16:16


 

The promise and challenge of personalized medicine: aging populations, complex diseases, and unmet medical need


Author: Adriano M Henney

PubMed ID: 22661132

Date Published: 5th Jun 2012

Projects: Project Management, Virtual Liver

Journal: Croat. Med. J.

Citation: Croat. Med. J. 53(3): 207-10

Scales: Not specified

Abstract (Expand)

The concept of personalized medicine is not new. It is being discussed with increasing interest in the medical, scientific, and general media because of the availability of advanced scientific and ...

Created: 12th Jun 2012 at 10:11   Last updated: 24th Oct 2013 at 16:16


 

MYC-regulated genes involved in liver cell dysplasia identified in a transgenic model of liver cancer


Authors: Danele Hunecke, Reinhard Spanel, Florian Länger, Suk Woo Nam, Juergen Borlak

PubMed ID: 22653869

Date Published: 2nd Jun 2012

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: J. Pathol.

Citation: J. Pathol. :

Scales: Cell

Abstract (Expand)

Foci of liver cell dysplasia (LCD) are distinct morphological entities and may evolve into hepatocellular carcinomas (HCCs). While most HCCs overexpress c-Myc, its role in LCD remains uncertain. ...

Created: 14th Dec 2012 at 19:25   Last updated: 24th Oct 2013 at 16:16


 

Time-dependent intensity changes of free fatty acids detected by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry in the presence of 1,8-bis-(dimethylamino)naphthalene--a cautionary note


Authors: Mandy Eibisch, Rosmarie Süss, Jürgen Schiller

PubMed ID: 22638975

Date Published: 29th May 2012

Projects: No Projects

Journal: Rapid Commun. Mass Spectrom.

Citation: Rapid Commun. Mass Spectrom. 26(13): 1573-6

Scales: Not specified

Abstract:

Not specified

Created: 4th Aug 2012 at 16:26   Last updated: 24th Oct 2013 at 16:16


 

Rab5 is necessary for the biogenesis of the endolysosomal system in vivo


Authors: Anja Zeigerer, Jerome Gilleron, Roman L Bogorad, Giovanni Marsico, Hidenori Nonaka, Sarah Seifert, Hila Epstein-Barash, Satya Kuchimanchi, Chang Geng Peng, Vera M Ruda, Perla Del Conte-Zerial, Jan G Hengstler, Yannis Kalaidzidis, Victor Koteliansky, Marino Zerial

PubMed ID: 22622570

Date Published: 25th May 2012

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., B3: Intercellular communication through cell adhesion

Journal: Nature

Citation: Nature 485(7399): 465-70

Scales: Cell

Abstract (Expand)

An outstanding question is how cells control the number and size of membrane organelles. The small GTPase Rab5 has been proposed to be a master regulator of endosome biogenesis. Here, to test this ...

Created: 6th Aug 2012 at 14:00   Last updated: 24th Oct 2013 at 16:16


 

Choline-releasing glycerophosphodiesterase EDI3 drives tumor cell migration and metastasis


Authors: J. D. Stewart, R. Marchan, M. S. Lesjak, J. Lambert, R. Hergenroeder, J. K. Ellis, C.-H. Lau, H. C. Keun, G. Schmitz, J. Schiller, M. Eibisch, C. Hedberg, H. Waldmann, E. Lausch, B. Tanner, J. Sehouli, J. Sagemueller, H. Staude, E. Steiner, J. G. Hengstler

DOI: 10.1073/pnas.1117654109

Date Published: 22nd May 2012

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Proceedings of the National Academy of Sciences

Citation: Proceedings of the National Academy of Sciences 109(21) : 8155

Scales: Not specified

Abstract:

Not specified

Created: 29th Oct 2012 at 12:28   Last updated: 24th Oct 2013 at 16:16


 

Comparison of various approaches to calculating the optimal hematocrit in vertebrates


Authors: Heiko Stark, Stefan Schuster

PubMed ID: 22604890

Date Published: 19th May 2012

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver

Journal: Journal of applied physiology (Bethesda, Md. : 1985)

Citation: J. Appl. Physiol. 113(3): 355-67

Scales: Liver

Abstract (Expand)

An interesting problem in hemorheology is to calculate that volume fraction of erythrocytes (hematocrit) that is optimal for transporting a maximum amount of oxygen. If the hematocrit is too low, too ...

Created: 1st Aug 2012 at 11:57   Last updated: 24th Oct 2013 at 16:16


 

Insulin/IGF signaling drives cell proliferation in part via Yorkie/YAP


Authors: Katrin Straßburger, Marcel Tiebe, Federico Pinna, Kai Breuhahn, Aurelio A Teleman

PubMed ID: 22609549

Date Published: 16th May 2012

Projects: A2.4: Linking signalling pathways regulating liver regeneration and orga...

Journal: Dev. Biol.

Citation: Dev. Biol. 367(2): 187-96

Scales: Cell

Abstract (Expand)

The insulin/IGF signaling (IIS) pathway is a potent inducer of cell proliferation in normal development and in cancer. The mechanism by which this occurs, however, is not completely understood. The ...

Created: 16th Jan 2013 at 09:03   Last updated: 24th Oct 2013 at 16:16


 

Sustained liver regeneration after portal vein embolization --a human molecular pilot study


Authors: Falk Rauchfuss, Sandro Lambeck, Ralf A Claus, Janina Ullmann, Thomas Schulz, Martina Weber, Katrin Katenkamp, Reinhard Guthke, Michael Bauer, Utz Settmacher

PubMed ID: 22561445

Date Published: 5th May 2012

Projects: C3: Zonation of metabolism and its regulation

Journal: Dig Liver Dis

Citation: Dig Liver Dis 44(8): 681-8

Scales: Not specified

Abstract (Expand)

Portal vein embolization is a treatment option to achieve a sufficient future remnant liver volume for patients with central liver tumours requiring an extended resection with an extensive parenchymal ...

Created: 30th Nov 2012 at 14:45   Last updated: 24th Oct 2013 at 16:16


 

Modeling the impact of granular embedding media, and pulling versus pushing cells on growing cell clones


Authors: Dirk Drasdo, Stefan Hoehme

DOI: 10.1088/1367-2630/14/5/055025

Date Published: 1st May 2012

Projects: No Projects

Journal: New J. Phys.

Citation: New J. Phys. 14(5) : 055025

Scales: Not specified

Abstract (Expand)

In this paper, we explore how potential biomechanical influences on cell cycle entrance and cell migration affect the growth dynamics of cell populations. We consider cell populations growing in free, ...

Created: 10th Sep 2012 at 17:48   Last updated: 24th Oct 2013 at 16:16


 

Decreased levels of active SMAD2 correlate with poor prognosis in gastric cancer


Authors: Yijun Wu, Qi Li, Xinhui Zhou, Jiren Yu, Yunchuan Mu, Stefan Munker, Chengfu Xu, Zhe Shen, Roman Müllenbach, Yan Liu, Li Li, Norbert Gretz, Derek Zieker, Jun Li, Kouichi Matsuzaki, Youming Li, Steven Dooley, Honglei Weng

PubMed ID: 22539990

Date Published: 23rd Apr 2012

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., Show cases

Journal: PLoS ONE

Citation: PLoS ONE 7(4): e35684

Scales: Not specified

Abstract (Expand)

TGF-β plays a dual role in the progression of human cancer. During the early stages of carcinogenesis, TGF-β functions as a tumor suppressor. During the late stages of tumor development, however, TGF-β ...

Created: 31st Oct 2012 at 09:13   Last updated: 24th Oct 2013 at 16:16


 

PPARA: A Novel Genetic Determinant of CYP3A4 In Vitro and In Vivo


Authors: Kathrin Klein, Maria Thomas, Stefan Winter, Andreas K Nussler, Mikko Niemi, Matthias Schwab, Ulrich M Zanger

PubMed ID: 22510778

Date Published: 18th Apr 2012

Projects: A3.4: Linking signalling to metabolic functions

Journal: Clinical pharmacology and therapeutics

Citation: Clin. Pharmacol. Ther. 91(6): 1044-52

Scales: Not specified

Abstract (Expand)

Interindividual variability in cytochrome P450 3A4 (CYP3A4) is believed to be largely heritable; however, predictive genetic factors have remained scarce. Using a candidate-gene approach in a human ...

Created: 14th May 2012 at 09:40   Last updated: 24th Oct 2013 at 16:16


 

TSSi--an R package for transcription start site identification from 5' mRNA tag data


Authors: C Kreutz, J S Gehring, D Lang, R Reski, J Timmer, S A Rensing

PubMed ID: 22513994

Date Published: 17th Apr 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: Bioinformatics

Citation: Bioinformatics 28(12): 1641-2

Scales: Cell

Abstract (Expand)

High-throughput sequencing has become an essential experimental approach for the investigation of transcriptional mechanisms. For some applications like ChIP-seq, several approaches for the prediction ...

Created: 8th Aug 2012 at 12:11   Last updated: 24th Oct 2013 at 16:16


 

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity


Authors: Matthias Stein, Manohar Pilli, Sabine Bernauer, Bianca H Habermann, Marino Zerial, Rebecca C Wade

PubMed ID: 22523562

Date Published: 16th Apr 2012

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: PLoS ONE

Citation: PLoS ONE 7(4): e34870

Scales: Cell

Abstract (Expand)

Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator ...

Created: 19th Jul 2012 at 09:45   Last updated: 24th Oct 2013 at 16:16


 

ChemSpot: a hybrid system for chemical named entity recognition


Authors: Tim Rocktäschel, Michael Weidlich, Ulf Leser

PubMed ID: 22500000

Date Published: 12th Apr 2012

Projects: F2: The Liver Knowledge Base (LKB), F: Data management

Journal: Bioinformatics

Citation: Bioinformatics 28(12): 1633-40

Scales: Not specified

Abstract (Expand)

The accurate identification of chemicals in text is important for many applications, including computer-assisted reconstruction of metabolic networks or retrieval of information about substances in ...

Created: 11th Jul 2012 at 08:21   Last updated: 24th Oct 2013 at 16:16


 

Using Mean Field Theory to Guide Biofunctional Materials Design


Authors: Uwe Freudenberg, Jens-Uwe Sommer, Kandice R. Levental, Petra B. Welzel, Andrea Zieris, Karolina Chwalek, Katja Schneider, Silvana Prokoph, Marina Prewitz, Ron Dockhorn, Carsten Werner

DOI: 10.1002/adfm.201101868

Date Published: 10th Apr 2012

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc..., B3: Intercellular communication through cell adhesion

Journal: Adv. Funct. Mater.

Citation: Adv. Funct. Mater. 22(7) : 1391

Scales: Not specified

Abstract (Expand)

Cell-instructive characteristics of extracellular matrices (ECM) resulting from a subtle balance of biomolecular and biophysical signals must be recapitulated in engineered biomaterials to facilitate ...

Created: 29th Nov 2012 at 16:44   Last updated: 24th Oct 2013 at 16:16


 

Interleukin-22 promotes proliferation of liver stem/progenitor cells in mice and patients with chronic hepatitis B virus infection


Authors: Dechun Feng, Xiaoni Kong, Honglei Weng, Ogyi Park, Hua Wang, Steven Dooley, M Eric Gershwin, Bin Gao

PubMed ID: 22484119

Date Published: 3rd Apr 2012

Projects: Showcase LPS and Inflammation

Journal: Gastroenterology

Citation: Gastroenterology 143(1): 188-98.e7

Scales: Not specified

Abstract (Expand)

Proliferation of liver stem/progenitor cells (LPCs), which can differentiate into hepatocytes or biliary epithelial cells, is often observed in chronically inflamed regions of liver in patients. We ...

Created: 31st Oct 2012 at 09:09   Last updated: 24th Oct 2013 at 16:16


 

Rodent animal models for surrogate analysis of cell therapy in acute liver failure


Authors: Bruno Christ, Sandra Brückner

PubMed ID: 22485094

Date Published: 2nd Apr 2012

Projects: C6: Organization and function of the sinusoidal system and the liver lob..., Showcase HGF and Regeneration, Virtual Liver

Journal: Front Physiol

Citation: Front Physiol 3: 78

Scales: Cell and Liver

Abstract (Expand)

Without therapeutic intervention acute liver failure (ALF) is the consequence of a progredient destruction of the liver parenchyma due to metabolic exhaustion of the hepatocytes. Perivenous hepatocytes ...

Created: 19th Nov 2013 at 11:57


 

Human pregnane X receptor genotype of the donor but not of the recipient is a risk factor for delayed graft function after renal transplantation


Authors: I A Hauser, S Kruck, S Gauer, A T Nies, S Winter, J Bedke, H Geiger, H Hoefeld, J Kleemann, A Asbe-Vollkopf, J Engel, O Burk, M Schwab, E Schaeffeler

PubMed ID: 22453193

Date Published: 28th Mar 2012

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: Clin. Pharmacol. Ther.

Citation: Clin. Pharmacol. Ther. 91(5): 905-16

Scales: Not specified

Abstract (Expand)

Delayed graft function (DGF) is an important complication in renal transplantation, contributing significantly to decrease in long-term allograft survival. In addition to donor- and recipient-related ...

Created: 18th Jul 2012 at 13:01   Last updated: 24th Oct 2013 at 16:16


 

Organic anion transporters and their implications in pharmacotherapy


Authors: Arian Emami Riedmaier, Anne T Nies, Elke Schaeffeler, Matthias Schwab

PubMed ID: 22457399

Date Published: 28th Mar 2012

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: Pharmacol. Rev.

Citation: Pharmacol. Rev. 64(3): 421-49

Scales: Not specified

Abstract (Expand)

Organic anion transporters play an essential role in the distribution and excretion of numerous endogenous metabolic products and exogenous organic anions, including a host of widely prescribed drugs. ...

Created: 18th Jul 2012 at 13:36   Last updated: 24th Oct 2013 at 16:16


 

An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes


Authors: Jérémy Huard, Stephanie Mueller, Ernst D Gilles, Ursula Klingmüller, Steffen Klamt

PubMed ID: 22443451

Date Published: 27th Mar 2012

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., E1: Integration on the cellular level

Journal: The FEBS journal

Citation: FEBS J. 279(18): 3290-313

Scales: Intercellular

Abstract (Expand)

During liver regeneration, quiescent hepatocytes re-enter the cell cycle to proliferate and compensate for lost tissue. Multiple signals including hepatocyte growth factor, epidermal growth factor, ...

Created: 18th Jul 2012 at 09:45   Last updated: 24th Oct 2013 at 16:16


 

Transcriptional regulators in hepatocarcinogenesis--key integrators of malignant transformation


Authors: Mona Malz, Federico Pinna, Peter Schirmacher, Kai Breuhahn

PubMed ID: 22446689

Date Published: 21st Mar 2012

Projects: A2.4: Linking signalling pathways regulating liver regeneration and orga...

Journal: J. Hepatol.

Citation: J. Hepatol. 57(1): 186-95

Scales: Not specified

Abstract (Expand)

Hepatocellular carcinoma (HCC) is one of the most frequent human malignancies with poor prognosis and increasing incidence in the Western world. Only for a minority of HCC patients, surgical treatment ...

Created: 16th Jan 2013 at 09:04   Last updated: 24th Oct 2013 at 16:16


 

Low perforin expression of early differentiated HCV-specific CD8+ T cells limits their hepatotoxic potential


Authors: Juandy Jo, Bertram Bengsch, Bianca Seigel, Sibylle J Rau, Julia Schmidt, Emmanuel Bisse, Peter Aichele, Ulrike Aichele, Lars Joeckel, Cathy Royer, Karine Sá Ferreira, Christoph Borner, Thomas F Baumert, Hubert E Blum, Volker Lohmann, Richard Fischer, Robert Thimme

PubMed ID: 22425625

Date Published: 14th Mar 2012

Projects: No Projects

Journal: J. Hepatol.

Citation: J. Hepatol. 57(1): 9-16

Scales: Not specified

Abstract (Expand)

Perforin plays a central role in the immunopathogenesis of different viral infections. However, its role in hepatitis C virus (HCV) infection has not been fully understood. Here, we analyzed two closely ...

Created: 22nd Jan 2014 at 15:20


 

SFRS10--a splicing factor gene reduced in human obesity


Authors: Mario Brosch, Witigo von Schönfels, Marcus Ahrens, Michael Nothnagel, Michael Krawczak, Matthias Laudes, Bence Sipos, Thomas Becker, Stefan Schreiber, Christoph Röcken, Clemens Schafmayer, Jochen Hampe

PubMed ID: 22405059

Date Published: 13th Mar 2012

Projects: G: Clinical translation

Journal: Cell Metab.

Citation: Cell Metab. 15(3): 265-6; author reply 267-9

Scales: Organism

Abstract:

Not specified

Created: 18th Jul 2012 at 07:07   Last updated: 24th Oct 2013 at 16:16


 

Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics


Authors: Irina Surovtsova, Natalia Simus, Katrin Hübner, Sven Sahle, Ursula Kummer

PubMed ID: 22390191

Date Published: 5th Mar 2012

Projects: HepatoSys, Virtual Liver

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 14

Scales: Cell

Abstract (Expand)

Given the complex mechanisms underlying biochemical processes systems biology researchers tend to build ever increasing computational models. However, dealing with complex systems entails a variety of ...

Created: 30th Aug 2012 at 13:03   Last updated: 24th Oct 2013 at 16:16


 

Multiparametric image analysis reveals role of Caveolin1 in endosomal progression rather than internalization of EGFR


Authors: Hannah Schmidt-Glenewinkel, Eileen Reinz, Svetlana Bulashevska, Joel Beaudouin, Stefan Legewie, Angel Alonso, Roland Eils

PubMed ID: 22575653

Date Published: 1st Mar 2012

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: FEBS Lett.

Citation: FEBS Lett. 586(8): 1179-89

Scales: Cell

Abstract (Expand)

Endosomes constitute a central layer in the regulation of growth factor signaling. We applied flow cytometry, confocal microscopy and automated image quantification to define the role of Caveolin1 ...

Created: 11th Sep 2012 at 11:34   Last updated: 24th Oct 2013 at 16:16


 

Functional characterization of protein variants of the human multidrug transporter ABCC2 by a novel targeted expression system in fibrosarcoma cells


Authors: Rudolf Arlanov, Andrew Porter, Dennis Strand, Rachel Brough, Darja Karpova, Reinhold Kerb, Leszek Wojnowski, Matthias Schwab, Thomas Lang

PubMed ID: 22290738

Date Published: 28th Feb 2012

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: Hum. Mutat.

Citation: Hum. Mutat. 33(4): 750-62

Scales: Not specified

Abstract (Expand)

The multidrug resistance-associated protein 2 (MRP2/ABCC2) is involved in the efflux of endogenous and xenobiotic substrates, including several anticancer and antiviral drugs. The functional consequences ...

Created: 18th Jul 2012 at 13:34   Last updated: 24th Oct 2013 at 16:16


 

In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems


Authors: Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin Kb Sy, Verena Becker, Ursula Klingmüller, Jens Timmer

PubMed ID: 22369292

Date Published: 27th Feb 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 13

Scales: Cell

Abstract:

ABSTRACT:

Created: 10th Aug 2012 at 09:33   Last updated: 24th Oct 2013 at 16:16


 

Pharmacogenomics of Codeine, Morphine, and Morphine-6-Glucuronide: Model-Based Analysis of the Influence of CYP2D6 Activity, UGT2B7 Activity, Renal Impairment, and CYP3A4 Inhibition


Authors: Thomas Eissing, Jörg Lippert, Stefan Willmann

PubMed ID: 22352453

Date Published: 23rd Feb 2012

Projects: E4: Vertical integration across biological scales, G: Clinical translation

Journal: Mol Diagn Ther

Citation: Mol Diagn Ther 16(1): 43-53

Scales: Organism

Abstract (Expand)

Background and Objective: The analgesic effect of codeine depends on the formation of the opioid metabolites morphine and morphine-6-glucuronide. Different factors have been shown or suspected to affect ...

Created: 1st Mar 2012 at 16:49   Last updated: 24th Oct 2013 at 16:16


 

A hypothetical model of cargo-selective rab recruitment during organelle maturation


Authors: Bernd Binder, Hermann-Georg Holzhütter

PubMed ID: 22328341

Date Published: 14th Feb 2012

Projects: A3.3: Hepatocyte polarity, A3.5: The impact of cell polarity on metabolism detoxification and endoc...

Journal: Cell Biochem. Biophys.

Citation: Cell Biochem. Biophys. 63(1): 59-71

Scales: Cell

Abstract (Expand)

Rabs constitute a group of small GTPases that confer directionality to intracellular vesicle transport by promoting on the membrane of transport vesicles in the formation of specific protein complexes ...

Created: 18th Jul 2012 at 13:01   Last updated: 24th Oct 2013 at 16:16


 

The macrophage response towards LPS and its control through the p38(MAPK)-STAT3 axis


Authors: Johannes G Bode, Christian Ehlting, Dieter Häussinger

PubMed ID: 22330073

Date Published: 4th Feb 2012

Projects: B1.1: Differential communication of wound healing and hepatoxic macropha..., B1.2: Reciprocal effect of cell-cell communication on information proces...

Journal: Cell. Signal.

Citation: Cell. Signal. 24(6): 1185-94

Scales: Cell

Abstract (Expand)

In macrophages detection of gram-negative bacteria particularly involves binding of the outer-wall component lipopolysaccharide (LPS) to its cognate receptor complex, comprising Toll like receptor 4 ...

Created: 31st Aug 2012 at 11:41   Last updated: 24th Oct 2013 at 16:17


 

Using expression data for quantification of active processes in physiologically based pharmacokinetic modeling


Authors: Michaela Meyer, Sebastian Schneckener, Bernd Ludewig, Lars Kuepfer, Joerg Lippert

PubMed ID: 22293118

Date Published: 31st Jan 2012

Projects: G: Clinical translation

Journal: Drug Metab. Dispos.

Citation: Drug Metab. Dispos. 40(5): 892-901

Scales: Organism

Abstract (Expand)

Active processes involved in drug metabolization and distribution mediated by enzymes, transporters, or binding partners mostly occur simultaneously in various organs. However, a quantitative description ...

Created: 27th Apr 2012 at 10:34   Last updated: 24th Oct 2013 at 16:17


 

Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis


Authors: Sven Knüppel, Jorge Esparza-Gordillo, Ingo Marenholz, Hermann-Georg Holzhütter, Anja Bauerfeind, Andreas Ruether, Stephan Weidinger, Young-Ae Lee, Klaus Rohde

PubMed ID: 22284537

Date Published: 27th Jan 2012

Projects: No Projects

Journal: BMC Med. Genet.

Citation: BMC Med. Genet. 13: 8

Scales: Not specified

Abstract (Expand)

Genome-wide association studies (GWAS) provide an increasing number of single nucleotide polymorphisms (SNPs) associated with diseases. Our aim is to exploit those closely spaced SNPs in candidate ...

Created: 4th Jan 2013 at 13:03   Last updated: 24th Oct 2013 at 16:17


 

Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes


Authors: Karine Sá Ferreira, Clemens Kreutz, Sabine Macnelly, Karin Neubert, Angelika Haber, Matthew Bogyo, Jens Timmer, Christoph Borner

PubMed ID: 22246639

Date Published: 17th Jan 2012

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...

Journal: Apoptosis : an international journal on programmed cell death

Citation: Apoptosis 17(5): 503-15

Scales: Not specified

Abstract (Expand)

The TNF-R1 like receptor Fas is highly expressed on the plasma membrane of hepatocytes and plays an essential role in liver homeostasis. We recently showed that in collagen-cultured primary mouse ...

Created: 20th Mar 2012 at 21:32   Last updated: 24th Oct 2013 at 16:17


 

The virtual liver: a multidisciplinary, multilevel challenge for systems biology


Authors: Hermann-Georg Holzhütter, Dirk Drasdo, Tobias Preusser, Jörg Lippert, Adriano M Henney

PubMed ID: 22246674

Date Published: 13th Jan 2012

Projects: Virtual Liver

Journal: Wiley Interdiscip Rev Syst Biol Med

Citation: Wiley Interdiscip Rev Syst Biol Med 4(3): 221-35

Scales: Not specified

Abstract (Expand)

The liver is the central metabolic organ in human physiology, with functions that are fundamentally important to the detoxification of xenobiotics (drugs), the maintenance of homeostasis of numerous ...

Created: 19th Apr 2012 at 16:03   Last updated: 24th Oct 2013 at 16:17


 

A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins


Authors: Katrin Luckert, Taranjit S Gujral, Marina Chan, Mark Sevecka, Thomas O Joos, Peter K Sorger, Gavin Macbeath, Oliver Pötz

PubMed ID: 22234610

Date Published: 12th Jan 2012

Projects: CTU Protein Arrays

Journal: Sci Signal

Citation: Sci Signal 5(206): pl1

Scales: Not specified

Abstract (Expand)

A system-wide analysis of cell signaling requires detecting and quantifying many different proteins and their posttranslational modification states in the same cellular sample. Here, we present Protocols ...

Created: 27th Nov 2012 at 13:16   Last updated: 24th Oct 2013 at 16:17


 

Dynamics and feedback loops in the transforming growth factor β signaling pathway


Authors: Katja Wegner, Anastasia Bachmann, Jan-Ulrich Schad, Philippe Lucarelli, Sven Sahle, Peter Nickel, Christoph Meyer, Ursula Klingmüller, Steven Dooley, Ursula Kummer

PubMed ID: 22284904

Date Published: 5th Jan 2012

Projects: HepatoSys, Virtual Liver

Journal: Biophys. Chem.

Citation: Biophys. Chem. 162: 22-34

Scales: Cell

Abstract (Expand)

Transforming growth factor β (TGF-β) ligands activate a signaling cascade with multiple cell context dependent outcomes. Disruption or disturbance leads to variant clinical disorders. To develop ...

Created: 30th Aug 2012 at 13:08   Last updated: 24th Oct 2013 at 16:17


 

Analysis and Algorithmic Generation of Hepatic Vascular Systems


Authors: Lars Ole Schwen, Tobias Preusser

DOI: 10.1155/2012/357687

Date Published: 2012

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: International Journal of Hepatology

Citation: International Journal of Hepatology 2012(3) : 1

Scales: Liver

Abstract (Expand)

A proper geometric model of the vascular systems in the liver is crucial for modeling blood flow, the connection between the organ and the rest of the organism. In vivo imaging does not provide sufficient ...

Created: 27th Sep 2012 at 16:42   Last updated: 24th Oct 2013 at 16:17


 

Likelihood based observability analysis and confidence intervals for predictions of dynamic models


Authors: Clemens Kreutz, Andreas Raue, Jens Timmer

DOI: 10.1186/1752-0509-6-120

Date Published: 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6(1) : 120

Scales: Cell

Abstract:

Not specified

Created: 29th Oct 2012 at 10:26   Last updated: 24th Oct 2013 at 16:17


 

DNA methylation is associated with downregulation of the organic cation transporter OCT1 (SLC22A1) in human hepatocellular carcinoma


Authors: Elke Schaeffeler, Claus Hellerbrand, Anne T Nies, Stefan Winter, Stephan Kruck, Ute Hofmann, Heiko van der Kuip, Ulrich M Zanger, Hermann Koepsell, Matthias Schwab

PubMed ID: 22196450

Date Published: 23rd Dec 2011

Projects: C3: Zonation of metabolism and its regulation, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Genome Med

Citation: Genome Med 3(12): 82

Scales: Cell

Abstract (Expand)

Organic cation transporters (OCTs) determine not only physiological processes but are also involved in the cellular uptake of anticancer agents. Based on microarray analyses in hepatocellular carcinoma ...

Created: 27th Jun 2012 at 15:59   Last updated: 24th Oct 2013 at 16:17


 

A Lattice-gas Cellular Automaton Model for in Vitro Sprouting Angiogenesis


Authors: C. Mente, I. Prade, L. Brusch, G. Breier, A. Deutsch

DOI: 10.5506/APhysPolBSupp.5.99

Date Published: 20th Dec 2011

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., D4: Regeneration and Liver Size

Journal: Acta Phys. Pol. B

Citation: Acta Phys. Pol. B Proc. Suppl. 5(1) : 99

Scales: Not specified

Abstract (Expand)

The mechanisms of sprout formation and branching during sprouting angiogenesis are only partially understood and mostly attributed to nonlocal signals mediated by the heterogeneous distribution of ...

Created: 23rd Oct 2012 at 15:55   Last updated: 24th Oct 2013 at 16:17


 

Multiscale mechanistic modeling in pharmaceutical research and development


Authors: Lars Kuepfer, Jörg Lippert, Thomas Eissing

PubMed ID: 22161351

Date Published: 14th Dec 2011

Projects: E4: Vertical integration across biological scales, G: Clinical translation

Journal: Adv. Exp. Med. Biol.

Citation: Adv. Exp. Med. Biol. 736: 543-61

Scales: Organism

Abstract (Expand)

Discontinuation of drug development projects due to lack of efficacy or adverse events is one of the main cost drivers in pharmaceutical research and development (R&D). Investments have to be ...

Created: 1st Mar 2012 at 16:42   Last updated: 24th Oct 2013 at 16:17


 

SABIO-RK--database for biochemical reaction kinetics


Authors: Ulrike Wittig, Renate Kania, Martin Golebiewski, Maja Rey, Lei Shi, Lenneke Jong, Enkhjargal Algaa, Andreas Weidemann, Heidrun Sauer-Danzwith, Saqib Mir, Olga Krebs, Meik Bittkowski, Elina Wetsch, Isabel Rojas, Wolfgang Müller

PubMed ID: 22102587

Date Published: 22nd Nov 2011

Projects: F3: Kinetic data handling

Journal: Nucleic acids research

Citation: Nucleic Acids Res. 40(Database issue): D790-6

Scales: Not specified

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually ...

Created: 29th Nov 2011 at 00:56   Last updated: 24th Oct 2013 at 16:17


 

Adiponectin upregulates hepatocyte CMKLR1 which is reduced in human fatty liver


Authors: Josef Wanninger, Sabrina Bauer, Kristina Eisinger, Thomas S Weiss, Roland Walter, Claus Hellerbrand, Andreas Schäffler, Akiko Higuchi, Kenneth Walsh, Christa Buechler

PubMed ID: 22118966

Date Published: 18th Nov 2011

Projects: CTU SOP Human Hepatocytes, Show cases

Journal: Mol. Cell. Endocrinol.

Citation: Mol. Cell. Endocrinol. 349(2): 248-54

Scales: Cell and Liver

Abstract (Expand)

Chemokine-like receptor 1 (CMKLR1) ligands chemerin and resolvin E1 are suggested to have a role in non-alcoholic fatty liver disease (NAFLD). Here, expression of CMKLR1 in liver cells and NAFLD was ...

Created: 30th Jan 2014 at 17:18


 

Hepatic acute phase proteins--regulation by IL-6- and IL-1-type cytokines involving STAT3 and its crosstalk with NF-κB-dependent signaling


Authors: Johannes G Bode, Ute Albrecht, Dieter Häussinger, Peter C Heinrich, Fred Schaper

PubMed ID: 22093287

Date Published: 16th Nov 2011

Projects: B1.1: Differential communication of wound healing and hepatoxic macropha..., B1.2: Reciprocal effect of cell-cell communication on information proces..., D2: Dynamics of metabolism, inflammation and ammonia detoxication during..., D3: Inflammation and Regeneration: the whole organ

Journal: Eur. J. Cell Biol.

Citation: Eur. J. Cell Biol. 91(6-7): 496-505

Scales: Cell and Liver

Abstract (Expand)

The function of the liver as an important constituent of the immune system involved in innate as well as adaptive immunity is warranted by different highly specialized cell populations. As the major ...

Created: 31st Aug 2012 at 11:44   Last updated: 24th Oct 2013 at 16:17


 

A methionine-choline-deficient diet elicits NASH in the immunodeficient mouse featuring a model for hepatic cell transplantation


Authors: Sandra Pelz, Peggy Stock, Sandra Brückner, Bruno Christ

PubMed ID: 22108588

Date Published: 13th Nov 2011

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. 318(3): 276-87

Scales: Cell, Liver lobule and Liver

Abstract (Expand)

Non-alcoholic staetohepatitis (NASH) is associated with fat deposition in the liver favoring inflammatory processes and development of fibrosis, cirrhosis and finally hepatocellular cancer. In Western ...

Created: 16th Aug 2012 at 08:13   Last updated: 24th Oct 2013 at 16:17


 

Oxidative changes of lipids monitored by MALDI MS


Authors: Beate Fuchs, Kristin Bresler, Jürgen Schiller

DOI: 10.1016/j.chemphyslip.2011.09.006

Date Published: 1st Nov 2011

Projects: No Projects

Journal: Chemistry and Physics of Lipids

Citation: Chemistry and Physics of Lipids 164(8) : 782

Scales: Not specified

Abstract (Expand)

Oxidation processes of lipids are of paramount interest from many viewpoints. For instance, oxidation processes are highly important under in vivo conditions because molecules with regulatory functions ...

Created: 4th Aug 2012 at 16:23   Last updated: 24th Oct 2013 at 16:17


 

Controlled vocabularies and semantics in systems biology


Authors: Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère

PubMed ID: 22027554

Date Published: 27th Oct 2011

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, F1: The data management system, F3: Kinetic data handling, Showcase Steatosis

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 7: 543

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

Abstract (Expand)

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in ...

Created: 27th Oct 2011 at 15:09   Last updated: 24th Oct 2013 at 16:17


 

Integration of Boolean models exemplified on hepatocyte signal transduction


Authors: Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar

PubMed ID: 22016404

Date Published: 20th Oct 2011

Projects: No Projects

Journal: Brief. Bioinformatics

Citation: Brief. Bioinformatics 13(3): 365-76

Scales: Not specified

Abstract (Expand)

The number of mathematical models for biological pathways is rapidly growing. In particular, Boolean modelling proved to be suited to describe large cellular signalling networks. Systems biology is at ...

Created: 22nd Jan 2014 at 15:26


 

Integration of Boolean models exemplified on hepatocyte signal transduction


Authors: Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar

PubMed ID: 22016404

Date Published: 20th Oct 2011

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response, B1.1: Differential communication of wound healing and hepatoxic macropha...

Journal: Brief. Bioinformatics

Citation: Brief. Bioinformatics 13(3): 365-76

Scales: Cell

Abstract (Expand)

The number of mathematical models for biological pathways is rapidly growing. In particular, Boolean modelling proved to be suited to describe large cellular signalling networks. Systems biology is at ...

Created: 8th Aug 2012 at 12:07   Last updated: 24th Oct 2013 at 16:17


 

TGF-β in progression of liver disease


Authors: Steven Dooley, Peter ten Dijke

PubMed ID: 22006249

Date Published: 19th Oct 2011

Projects: B2.3: Effect of hepatic stellate cells on hepatocyte polarity and transd..., Show cases

Journal: Cell Tissue Res.

Citation: Cell Tissue Res. 347(1): 245-56

Scales: Not specified

Abstract (Expand)

Transforming growth factor-β (TGF-β) is a central regulator in chronic liver disease contributing to all stages of disease progression from initial liver injury through inflammation and fibrosis to ...

Created: 31st Oct 2012 at 08:42   Last updated: 24th Oct 2013 at 16:17


 

Genomics of ADME gene expression: mapping expression quantitative trait loci relevant for absorption, distribution, metabolism and excretion of drugs in human liver


Authors: A Schröder, K Klein, S Winter, M Schwab, M Bonin, A Zell, U M Zanger

PubMed ID: 22006096

Date Published: 18th Oct 2011

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, C3: Zonation of metabolism and its regulation, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Not specified

Citation: Pharmacogenomics J. 13(1): 12-20

Scales: Not specified

Abstract (Expand)

Expression quantitative trait loci (eQTL) analysis is a powerful approach toward identifying genetic loci associated with quantitative changes in gene expression. We applied genome-wide association ...

Created: 3rd Nov 2011 at 10:45   Last updated: 24th Oct 2013 at 16:17


 

SABIO-RK: Access to Biochemical Reaction Kinetics Data


Authors: Martin Golebiewski, Martin Golebiewski

DOI: 10.1038/npre.2011.6506.1

Date Published: 7th Oct 2011

Projects: F3: Kinetic data handling

Journal: Nature Precedings

Citation: Nature Precedings

Scales: Not specified

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a curated database for biochemical reaction kinetics data drawn from different sources: from literature or direct submission by experimenters. The system offers ...

Created: 10th Oct 2011 at 15:42   Last updated: 24th Oct 2013 at 16:17


 

Normalization And Matching Of Chemical Compound Names


Authors: Martin Golebiewski, Martin Golebiewski, Meik Bittkowski, Henriette Slogsnat, Jasmin Saric, Isabel Rojas, Wolfgang Müller

DOI: 10.1038/npre.2011.6505.1

Date Published: 7th Oct 2011

Projects: F1: The data management system

Journal: Nature Precedings

Citation: Nature Precedings

Scales: Not specified

Abstract:

Not specified

Created: 13th Jul 2012 at 14:34   Last updated: 24th Oct 2013 at 16:17


 

Caspase-8 activity has an essential role in CD95/Fas-mediated MAPK activation


Authors: A M M Kober, S Legewie, C Pforr, N Fricker, R Eils, P H Krammer, I N Lavrik

PubMed ID: 21975294

Date Published: 7th Oct 2011

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...

Journal: Cell Death Dis

Citation: Cell Death Dis 2: e212

Scales: Cell

Abstract (Expand)

Stimulation of CD95/Fas/APO-1 results in the induction of both apoptotic and non-apoptotic signaling pathways. The processes regulating these two opposing pathways have not been thoroughly elucidated ...

Created: 3rd Sep 2012 at 11:25   Last updated: 24th Oct 2013 at 16:17


 

Large-scale network models of IL-1 and IL-6 signalling and their hepatocellular specification


Authors: Anke Ryll, Regina Samaga, Fred Schaper, Leonidas G Alexopoulos, Steffen Klamt

PubMed ID: 21968890

Date Published: 5th Oct 2011

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD, Interleukin-6 signalling

Journal: Not specified

Citation: Mol Biosyst 7(12): 3253-70

Scales: Cell

Abstract (Expand)

The pro-inflammatory cytokines interleukin 1 (IL-1) and 6 (IL-6) are crucially involved in the regulation of a multitude of physiological processes, in particular coordinating the immune response upon ...

Created: 8th Nov 2011 at 09:14   Last updated: 24th Oct 2013 at 16:17


 

Phosphatidylcholine dimers can be easily misinterpreted as cardiolipins in complex lipid mixtures: a matrix-assisted laser desorption/ionization time-of-flight mass spectrometric study of lipids from hepatocytes


Authors: Mandy Eibisch, Sebastian Zellmer, Rolf Gebhardt, Rosmarie Süss, Beate Fuchs, Jürgen Schiller

PubMed ID: 23657956

Date Published: 30th Sep 2011

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Rapid Commun. Mass Spectrom.

Citation: Rapid Commun. Mass Spectrom. 25(18): 2619-26

Scales: Cell and Liver

Abstract (Expand)

The liver is an important organ that is particularly involved in the lipid metabolism of the organism. Thus, high interest is nowadays focused on the lipid composition of the liver and particularly the ...

Created: 8th Jan 2014 at 13:25


 

Mammalian MATE (SLC47A) transport proteins: impact on efflux of endogenous substrates and xenobiotics


Authors: Katja Damme, Anne T Nies, Elke Schaeffeler, Matthias Schwab

PubMed ID: 21923552

Date Published: 17th Sep 2011

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G4: Whole-Body Detoxification in Mouse Models

Journal: Drug Metab. Rev.

Citation: Drug Metab. Rev. 43(4): 499-523

Scales: Not specified

Abstract (Expand)

Multidrug and toxin extrusion proteins (MATEs; SLC47A) are mammalian transporters being predominately expressed in the brush-border membrane of proximal tubule epithelial cells in the kidney and the ...

Created: 18th Jul 2012 at 13:10   Last updated: 24th Oct 2013 at 16:17


 

Glucocorticoids increase interleukin-6-dependent gene induction by interfering with the expression of the suppressor of cytokine signaling 3 feedback inhibitor


Authors: Anna Dittrich, Christina Khouri, Sara Dutton Sackett, Christian Ehlting, Oliver Böhmer, Ute Albrecht, Johannes G Bode, Christian Trautwein, Fred Schaper

PubMed ID: 21898505

Date Published: 8th Sep 2011

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Hepatology

Citation: Hepatology 55(1): 256-66

Scales: Cell

Abstract (Expand)

Glucocorticoids are known to be potent regulators of inflammation and have been used pharmacologically against inflammatory, immune, and lymphoproliferative diseases for more than 50 years. Due to their ...

Created: 31st Aug 2012 at 11:45   Last updated: 24th Oct 2013 at 16:17


 

Prominent regulatory but weak antigen-presenting cell function of hepatic stellate cells


Authors: Frank A. Schildberg, Christian Kurts, Percy A. Knolle

DOI: 10.1002/hep.24565

Date Published: 2nd Sep 2011

Projects: B4: Regulation of pro-inflammatory stimuli through communication of live...

Journal: Hepatology

Citation: Hepatology 54(3) : 1108

Scales: Not specified

Abstract:

Not specified

Created: 18th Jul 2012 at 17:23   Last updated: 24th Oct 2013 at 16:17


 

Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease


Authors: Yijing Zhang, Kathrin Klein, Aarathi Sugathan, Najlla Nassery, Alan Dombkowski, Ulrich M Zanger, David J Waxman

PubMed ID: 21858147

Date Published: 12th Aug 2011

Projects: A3.4: Linking signalling to metabolic functions

Journal: PLoS ONE

Citation: PLoS ONE 6(8): e23506

Scales: Not specified

Abstract (Expand)

Sex-differences in human liver gene expression were characterized on a genome-wide scale using a large liver sample collection, allowing for detection of small expression differences with high statistical ...

Created: 14th May 2012 at 09:54   Last updated: 24th Oct 2013 at 16:17


 

Metannogen: annotation of biological reaction networks


Authors: Christoph Gille, Katrin Hübner, Andreas Hoppe, Hermann-Georg Holzhütter

PubMed ID: 21824972

Date Published: 8th Aug 2011

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., F2: The Liver Knowledge Base (LKB)

Journal: Bioinformatics

Citation: Bioinformatics 27(19): 2763-4

Scales: Not specified

Abstract (Expand)

Semantic annotations of the biochemical entities constituting a biological reaction network are indispensable to create biologically meaningful networks. They further heighten efficient exchange, reuse ...

Created: 4th Jan 2013 at 10:45   Last updated: 24th Oct 2013 at 16:18


 

Paraoxonase (PON1 and PON3) Polymorphisms: Impact on Liver Expression and Atorvastatin-Lactone Hydrolysis


Authors: Stephan Riedmaier, Kathrin Klein, Stefan Winter, Ute Hofmann, Matthias Schwab, Ulrich M Zanger

PubMed ID: 21852972

Date Published: 27th Jul 2011

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Front Pharmacol

Citation: Front Pharmacol 2: 41

Scales: Cell

Abstract (Expand)

Atorvastatin δ-lactone, a major, pharmacologically inactive metabolite, has been associated with toxicity. In a previous study we showed that polymorphisms of UGT1A3 influence atorvastatin δ-lactone ...

Created: 27th Jun 2012 at 16:05   Last updated: 24th Oct 2013 at 16:18


 

Applications and trends in systems biology in biochemistry


Authors: Katrin Hübner, Sven Sahle, Ursula Kummer

PubMed ID: 21707921

Date Published: 26th Jul 2011

Projects: HepatoSys, Virtual Liver

Journal: FEBS J.

Citation: FEBS J. 278(16): 2767-857

Scales: Cell

Abstract (Expand)

Systems biology has received an ever increasing interest during the last decade. A large amount of third-party funding is spent on this topic, which involves quantitative experimentation integrated ...

Created: 30th Aug 2012 at 13:14   Last updated: 24th Oct 2013 at 16:18


 

In silico evidence for gluconeogenesis from fatty acids in humans


Authors: Christoph Kaleta, Luís F de Figueiredo, Sarah Werner, Reinhard Guthke, Michael Ristow, Stefan Schuster

PubMed ID: 21814506

Date Published: 21st Jul 2011

Projects: HepatoSys

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 7(7): e1002116

Scales: Not specified

Abstract (Expand)

The question whether fatty acids can be converted into glucose in humans has a long standing tradition in biochemistry, and the expected answer is "No". Using recent advances in Systems Biology ...

Created: 18th Jul 2012 at 08:43   Last updated: 24th Oct 2013 at 16:18


 

Inferring statin-induced gene regulatory relationships in primary human hepatocytes


Authors: Adrian Schröder, Johannes Wollnik, Clemens Wrzodek, Andreas Dräger, Michael Bonin, Oliver Burk, Maria Thomas, Wolfgang E Thasler, Ulrich M Zanger, Andreas Zell

PubMed ID: 21757465

Date Published: 16th Jul 2011

Projects: B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Bioinformatics

Citation: Bioinformatics 27(18): 2473-7

Scales: Not specified

Abstract (Expand)

MOTIVATION: Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, statins elicit pleitropic ...

Created: 28th Jul 2011 at 18:15   Last updated: 24th Oct 2013 at 16:18


 

Proton pump inhibitors inhibit metformin uptake by organic cation transporters (OCTs)


Authors: Anne T Nies, Ute Hofmann, Claudia Resch, Elke Schaeffeler, Maria Rius, Matthias Schwab

PubMed ID: 21779389

Date Published: 14th Jul 2011

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: PLoS ONE

Citation: PLoS ONE 6(7): e22163

Scales: Not specified

Abstract (Expand)

Metformin, an oral insulin-sensitizing drug, is actively transported into cells by organic cation transporters (OCT) 1, 2, and 3 (encoded by SLC22A1, SLC22A2, or SLC22A3), which are tissue specifically ...

Created: 18th Jul 2012 at 13:31   Last updated: 24th Oct 2013 at 16:18


 

Large-scale phosphosite quantification in tissues by a spike-in SILAC method


Authors: Mara Monetti, Nagarjuna Nagaraj, Kirti Sharma, Matthias Mann

PubMed ID: 21743459

Date Published: 10th Jul 2011

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., C5: Structural changes and functional consequences of the liver lobular/..., HepatoSys

Journal: Nat. Methods

Citation: Nat. Methods 8(8): 655-8

Scales: Not specified

Abstract (Expand)

Despite progress in mass spectrometry (MS)-based phosphoproteomics, large-scale in vivo analyses remain challenging. Here we report a 'spike-in' stable-isotope labeling with amino acids in ...

Created: 30th Jul 2012 at 13:35   Last updated: 24th Oct 2013 at 16:18


 

MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases


Authors: Jessica K Rieger, Denis A Bodan, Ulrich M Zanger

PubMed ID: 22303335

Date Published: 8th Jul 2011

Projects: A3.4: Linking signalling to metabolic functions

Journal: Front Genet

Citation: Front Genet 2: 39

Scales: Not specified

Abstract (Expand)

MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3'-untranslated region of target gene transcripts. ...

Created: 14th May 2012 at 09:52   Last updated: 24th Oct 2013 at 16:18


 

Murine hepatic stellate cells veto CD8 T cell activation by a CD54-dependent mechanism


Authors: Frank A. Schildberg, Alexandra Wojtalla, Sören V. Siegmund, Elmar Endl, Linda Diehl, Zeinab Abdullah, Christian Kurts, Percy A. Knolle

DOI: 10.1002/hep.24352

Date Published: 1st Jul 2011

Projects: B4: Regulation of pro-inflammatory stimuli through communication of live...

Journal: Hepatology

Citation: Hepatology 54(1) : 262

Scales: Not specified

Abstract (Expand)

The liver has a role in T cell tolerance induction, which is mainly achieved through the functions of tolerogenic hepatic antigen-presenting cells (APCs) and regulatory T cells. Hepatic stellate cells ...

Created: 18th Jul 2012 at 17:12   Last updated: 24th Oct 2013 at 16:18


 

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats


Authors: Clemens Wrzodek, Andreas Dräger, Andreas Zell

PubMed ID: 21700675

Date Published: 25th Jun 2011

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, Showcase Steatosis

Journal: Bioinformatics

Citation: Bioinformatics 27(16): 2314-5

Scales: Cell and Intercellular

Abstract (Expand)

SUMMARY: The KEGG PATHWAY database provides a widely used service for metabolic and non-metabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and ...

Created: 30th Jun 2011 at 08:35   Last updated: 24th Oct 2013 at 16:18


 

JSBML: a flexible Java library for working with SBML


Authors: Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, Michael Hucka

PubMed ID: 21697129

Date Published: 24th Jun 2011

Projects: A3.4: Linking signalling to metabolic functions

Journal: Bioinformatics

Citation: Bioinformatics 27(15): 2167-8

Scales: Not specified

Abstract (Expand)

SUMMARY: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model ...

Created: 24th Jun 2011 at 10:36   Last updated: 24th Oct 2013 at 16:18


 

Enzymatic features of the glucose metabolism in tumor cells


Authors: Anique Herling, Matthias König, Sascha Bulik, Hermann-Georg Holzhütter

PubMed ID: 21564549

Date Published: 10th Jun 2011

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: FEBS J.

Citation: FEBS J. 278(14): 2436-59

Scales: Not specified

Abstract (Expand)

Many tumor types exhibit an impaired Pasteur effect, i.e. despite the presence of oxygen, glucose is consumed at an extraordinarily high rate compared with the tissue from which they originate - the ...

Created: 4th Jan 2013 at 11:02   Last updated: 24th Oct 2013 at 16:18


 

Combined serum and tissue proteomic study applied to a c-Myc transgenic mouse model of hepatocellular carcinoma identified novel disease regulated proteins suitable for diagnosis and therapeutic intervention strategies


Authors: Maria Stella Ritorto, Jürgen Borlak

PubMed ID: 21644509

Date Published: 6th Jun 2011

Projects: CTU Proteomics

Journal: J. Proteome Res.

Citation: J. Proteome Res. 10(7): 3012-30

Scales: Liver

Abstract (Expand)

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death in the U.S. Notably, most HCCs display c-Myc hyperactivity but this transcription factor participates in the regulation of as ...

Created: 19th Jan 2014 at 17:53


 

Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes


Authors: Andreas Hoppe, Christine Richter, Hermann-Georg Holzhütter

PubMed ID: 21664944

Date Published: 2nd Jun 2011

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: BioSystems

Citation: BioSystems 105(2): 122-9

Scales: Cell

Abstract:

Not specified

Created: 23rd Oct 2012 at 12:32   Last updated: 24th Oct 2013 at 16:18


 

A simple TLC-MALDI method to monitor oxidation products of phosphatidylcholines and -ethanolamines


Authors: A. Bischoff, M. Eibisch, B. Fuchs, R. Süss, M. Schürenberg, D. Suckau, J. Schiller

DOI: 10.1556/AChrom.23.2011.2.13

Date Published: 1st Jun 2011

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Acta Chromatographica

Citation: Acta Chromatographica 23(2) : 365

Scales: Not specified

Abstract (Expand)

The analysis of lipid/phospholipid oxidation products is of primary importance. Although there are established HPLC and LC/MS techniques, it is shown here for the first time that the combination of ...

Created: 23rd Jun 2011 at 17:24   Last updated: 24th Oct 2013 at 16:18


 

Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization


Authors: Adrian Schroder, Clemens Wrzodek, Johannes Wollnik, Andreas Drager, Dierk Wanke, Kenneth W Berendzen, Andreas Zell

DOI: 10.1109/CEC.2011.5949899

Date Published: 1st Jun 2011

Projects: A3.4: Linking signalling to metabolic functions

Conference: 2011 IEEE Congress of Evolutionary Computation (CEC)

Citation: Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization : 2285

Scales: Intercellular

Abstract (Expand)

Higher organisms are able to respond to continuously changing external conditions by transducing cellular signals into specific regulatory programs, which control gene expression states of thousands ...

Created: 9th Jan 2012 at 13:53   Last updated: 24th Oct 2013 at 16:18


 

Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development


Authors: Malte Paulsen, Stefan Legewie, Roland Eils, Emil Karaulanov, Christof Niehrs

PubMed ID: 21633009

Date Published: 1st Jun 2011

Projects: A2.4: Linking signalling pathways regulating liver regeneration and orga..., B1.2: Reciprocal effect of cell-cell communication on information proces..., B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Proc. Natl. Acad. Sci. U.S.A.

Citation: Proc. Natl. Acad. Sci. U.S.A. 108(25): 10202-7

Scales: Cell

Abstract (Expand)

What makes embryogenesis a robust and canalized process is an important question in developmental biology. A bone morphogenetic protein (BMP) morphogen gradient plays a key role in embryonic development, ...

Created: 11th Sep 2012 at 11:36   Last updated: 24th Oct 2013 at 16:18


 

Distinct functions of the mitogen-activated protein kinase-activated protein (MAPKAP) kinases MK2 and MK3: MK2 mediates lipopolysaccharide-induced signal transducers and activators of transcription 3 (STAT3) activation by preventing negative regulatory effects of MK3


Authors: Christian Ehlting, Natalia Ronkina, Oliver Böhmer, Ute Albrecht, Konrad A Bode, Karl S Lang, Alexey Kotlyarov, Danuta Radzioch, Matthias Gaestel, Dieter Häussinger, Johannes G Bode

PubMed ID: 21586572

Date Published: 17th May 2011

Projects: B1.1: Differential communication of wound healing and hepatoxic macropha..., B1.2: Reciprocal effect of cell-cell communication on information proces...

Journal: J. Biol. Chem.

Citation: J. Biol. Chem. 286(27): 24113-24

Scales: Cell

Abstract (Expand)

In LPS-treated macrophages, activation of STAT3 is considered to be crucial for terminating the production of inflammatory cytokines. By analyzing the role of MAPK-activated protein kinase (MK) 2 and ...

Created: 31st Aug 2012 at 11:46   Last updated: 24th Oct 2013 at 16:18


 

A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes


Authors: Joachim Bucher, Stephan Riedmaier, Anke Schnabel, Katrin Marcus, Gabriele Vacun, Thomas S Weiss, Wolfgang E Thasler, Andreas K Nüssler, Ulrich M Zanger, Matthias Reuss

PubMed ID: 21548957

Date Published: 6th May 2011

Projects: A3.4: Linking signalling to metabolic functions

Journal: BMC Syst Biol

Citation: BMC Syst Biol 5: 66

Scales: Not specified

Abstract (Expand)

The individual character of pharmacokinetics is of great importance in the risk assessment of new drug leads in pharmacological research. Amongst others, it is severely influenced by the properties and ...

Created: 31st Jan 2012 at 11:59   Last updated: 24th Oct 2013 at 16:18


 

Lipid analysis by thin-layer chromatography—A review of the current state


Authors: Beate Fuchs, Rosmarie Süß, Kristin Teuber, Mandy Eibisch, Jürgen Schiller

DOI: 10.1016/j.chroma.2010.11.066

Date Published: 1st May 2011

Projects: No Projects

Journal: Journal of Chromatography A

Citation: Journal of Chromatography A 1218(19) : 2754

Scales: Not specified

Abstract (Expand)

High-performance thin-layer chromatography (HPTLC) is a widely used, fast and relatively inexpensive method of separating complex mixtures. It is particularly useful for smaller, apolar compounds and ...

Created: 4th Aug 2012 at 16:19   Last updated: 24th Oct 2013 at 16:18


 

Cell therapeutic options in liver diseases: cell types, medical devices and regulatory issues


Authors: Andreas K Nussler, Katrin Zeilinger, Lilianna Schyschka, Sabrina Ehnert, Jörg C Gerlach, Xueying Yan, Serene M L Lee, Maren Ilowski, Wolfgang E Thasler, Thomas S Weiss

PubMed ID: 21461918

Date Published: 3rd Apr 2011

Projects: CTU SOP Human Hepatocytes, HepatoSys

Journal: J Mater Sci Mater Med

Citation: J Mater Sci Mater Med 22(5): 1087-99

Scales: Cell

Abstract (Expand)

Although significant progress has been made in the field of orthotopic liver transplantation, cell-based therapies seem to be a promising alternative to whole-organ transplantation. The reasons are ...

Created: 30th Jan 2014 at 17:20


 

Addressing parameter identifiability by model-based experimentation


Authors: A Raue, C Kreutz, T Maiwald, U Klingmuller, J Timmer

PubMed ID: 21405200

Date Published: 17th Mar 2011

Projects: A2.1: Multi-level regulation of signalling pathways important for primin..., A2.3: Cross-talk and distinct properties of growth factor signalling reg..., A2.5: Integration of insulin and Wnt signalling in hepatocytes, B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: IET Syst Biol

Citation: IET Syst Biol 5(2): 120-30

Scales: Cell and Intercellular

Abstract (Expand)

Mathematical description of biological processes such as gene regulatory networks or signalling pathways by dynamic models utilising ordinary differential equations faces challenges if the model ...

Created: 18th Jul 2012 at 09:24   Last updated: 24th Oct 2013 at 16:18


 

Snapshots of protein dynamics and post-translational modifications in one experiment--beta-catenin and its functions


Authors: Katrin Luckert, Frank Götschel, Peter K Sorger, Andreas Hecht, Thomas O Joos, Oliver Pötz

PubMed ID: 21378377

Date Published: 4th Mar 2011

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, B2.2: Importance of Wnt- and Hedgehog factors for hepatic stellate cells...

Journal: Mol. Cell Proteomics

Citation: Mol. Cell Proteomics 10(5): M110.007377

Scales: Cell

Abstract (Expand)

β-catenin plays multiple roles in the canonical Wnt signaling pathway and in cell-cell adhesion complexes. In addition, β-catenin is a proto-oncogene and activating β-catenin mutations are relevant in ...

Created: 13th Sep 2012 at 13:58   Last updated: 24th Oct 2013 at 16:19


 

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice


Authors: Mirco Castoldi, Maja Vujic Spasic, Sandro Altamura, Joacim Elmén, Morten Lindow, Judit Kiss, Jens Stolte, Richard Sparla, Lorenza A D'Alessandro, Ursula Klingmüller, Robert E Fleming, Thomas Longerich, Hermann J Gröne, Vladimir Benes, Sakari Kauppinen, Matthias W Hentze, Martina U Muckenthaler

PubMed ID: 21364282

Date Published: 3rd Mar 2011

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: J. Clin. Invest.

Citation: J. Clin. Invest. 121(4): 1386-96

Scales: Cell, Liver and Organism

Abstract (Expand)

Systemic iron homeostasis is mainly controlled by the liver through synthesis of the peptide hormone hepcidin (encoded by Hamp), the key regulator of duodenal iron absorption and macrophage iron release. ...

Created: 11th Jul 2012 at 10:47   Last updated: 24th Oct 2013 at 16:19


 

[Pharmacogenomics: hype or hope?]


Authors: M Schwab, E Schaeffeler, U M Zanger, H Brauch, H K Kroemer

PubMed ID: 21365522

Date Published: 1st Mar 2011

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: Dtsch. Med. Wochenschr.

Citation: Dtsch. Med. Wochenschr. 136(10): 461-7

Scales: Cell

Abstract (Expand)

Pharmacogenomics follows the concept of individualized medicine via targeted and tailored therapy for each patient. This is aided by current progress in human genome research that provided the basis ...

Created: 27th Jun 2012 at 16:14   Last updated: 24th Oct 2013 at 16:19


 

Mouse granzyme K has pro-inflammatory potential


Authors: L T Joeckel, R Wallich, P Martin, D Sanchez-Martinez, F C Weber, S F Martin, C Borner, J Pardo, C Froelich, M M Simon

PubMed ID: 21311565

Date Published: 11th Feb 2011

Projects: No Projects

Journal: Cell Death Differ.

Citation: Cell Death Differ. 18(7): 1112-9

Scales: Not specified

Abstract (Expand)

Granzymes (gzms) are key components of T-killer (Tc) cells believed to mediate pro-apoptotic activities. Recent evidence suggests that gzms also possess non-cytotoxic activities that contribute to host ...

Created: 22nd Jan 2014 at 15:28


 

ABCB1 single-nucleotide polymorphisms determine tacrolimus response in patients with ulcerative colitis


Authors: K R Herrlinger, H Koc, S Winter, A Teml, E F Stange, K Fellermann, P Fritz, M Schwab, E Schaeffeler

PubMed ID: 21289623

Date Published: 2nd Feb 2011

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting

Journal: Clin. Pharmacol. Ther.

Citation: Clin. Pharmacol. Ther. 89(3): 422-8

Scales: Not specified

Abstract (Expand)

Tacrolimus (Tac) is effective in the treatment of steroid-refractory ulcerative colitis (UC); however, nonresponse and unpredictable side effects are major limitations. Because Tac response in patients ...

Created: 18th Jul 2012 at 12:30   Last updated: 24th Oct 2013 at 16:19


 

The influence of the chloride currents on action potential firing and volume regulation of excitable cells studied by a kinetic model


Authors: Nikolaus Berndt, Sabrina Hoffmann, Jan Benda, Hermann-Georg Holzhütter

PubMed ID: 21295041

Date Published: 2nd Feb 2011

Projects: No Projects

Journal: J. Theor. Biol.

Citation: J. Theor. Biol. 276(1): 42-9

Scales: Not specified

Abstract (Expand)

In excitable cells, the generation of an action potential (AP) is associated with transient changes of the intra- and extracellular concentrations of small ions such as Na(+), K(+) and Cl(-). If these ...

Created: 4th Jan 2013 at 11:22   Last updated: 24th Oct 2013 at 16:19


 

Does hepatic steatosis affect drug metabolizing enzymes in the liver


Authors: Christa Buechler, Thomas S Weiss

PubMed ID: 21222589

Date Published: 13th Jan 2011

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: Curr. Drug Metab.

Citation: Curr. Drug Metab. 12(1): 24-34

Scales: Liver

Abstract (Expand)

Bioavailability and effects of xenobiotics are dependent on absorption, metabolism and elimination of the respective compounds. Hepatocytes are critically important in drug modification and excretion. ...

Created: 30th Jan 2014 at 17:23


 

Identifiability and observability analysis for experimental design in nonlinear dynamical models


Authors: A Raue, V Becker, U Klingmüller, J Timmer

PubMed ID: 21198117

Date Published: 5th Jan 2011

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: Chaos

Citation: Chaos 20(4): 045105

Scales: Cell

Abstract (Expand)

Dynamical models of cellular processes promise to yield new insights into the underlying systems and their biological interpretation. The processes are usually nonlinear, high dimensional, and time-resolved ...

Created: 10th Aug 2012 at 09:43   Last updated: 24th Oct 2013 at 16:19


 

A comparison of sampling strategies for histological image analysis


Authors: André Homeyer, Uta Dahmen, Hai Huang, Andrea Schenk, Olaf Dirsch, HorstK Hahn

DOI: 10.4103/2153-3539.92034

Date Published: 2011

Projects: D4: Regeneration and Liver Size

Journal: J Pathol Inform

Citation: J Pathol Inform 2(2) : 11

Scales: Liver

Abstract (Expand)

Histological image analysis methods often employ machine-learning classifiers in order to adapt to the huge variability of histological images. To train these classifiers, the user must select samples ...

Created: 9th Mar 2012 at 15:42   Last updated: 24th Oct 2013 at 16:19


 

Germans cook up liver project


Author: Alison Abbott

PubMed ID: 21164453

Date Published: 18th Dec 2010

Projects: Virtual Liver

Journal: Nature

Citation: Nature 468(7326): 879

Scales: Not specified

Abstract:

Not specified

Created: 3rd Mar 2011 at 14:11   Last updated: 24th Oct 2013 at 16:19


 

Sphingomyelin is more sensitively detectable as a negative ion than phosphatidylcholine: a matrix-assisted laser desorption/ionization time-of-flight mass spectrometric study using 9-aminoacridine (9-AA) as matrix


Authors: Mandy Eibisch, Jürgen Schiller

PubMed ID: 21452388

Date Published: 15th Dec 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Rapid Commun. Mass Spectrom.

Citation: Rapid Commun. Mass Spectrom. 25(8): 1100-6

Scales: Not specified

Abstract (Expand)

Phospholipids (PLs) are increasingly analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and imaging MS. Different classes of PLs are preferentially ...

Created: 23rd Jun 2011 at 17:22   Last updated: 24th Oct 2013 at 16:19


 

Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets


Authors: Valentina Raia, Marcel Schilling, Martin Böhm, Bettina Hahn, Andreas Kowarsch, Andreas Raue, Carsten Sticht, Sebastian Bohl, Maria Saile, Peter Möller, Norbert Gretz, Jens Timmer, Fabian Theis, Wolf-Dieter Lehmann, Peter Lichter, Ursula Klingmüller

PubMed ID: 21127196

Date Published: 2nd Dec 2010

Projects: HepatoSys

Journal: Cancer Res.

Citation: Cancer Res. 71(3): 693-704

Scales: Not specified

Abstract (Expand)

Primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) share a frequent constitutive activation of JAK (Janus kinase)/STAT signaling pathway. Because of complex, nonlinear ...

Created: 10th Aug 2012 at 09:41   Last updated: 24th Oct 2013 at 16:19


 

HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition


Authors: Charles Richard Bradshaw, Vineeth Surendranath, Robert Henschel, Matthias Stefan Mueller, Bianca Hermine Habermann

PubMed ID: 21423752

Date Published: 16th Nov 2010

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: PLoS ONE

Citation: PLoS ONE 6(3): e17568

Scales: Not specified

Abstract (Expand)

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as ...

Created: 24th Jun 2011 at 16:19   Last updated: 24th Oct 2013 at 16:19


 

FASIMU: flexible software for flux-balance computation series in large metabolic networks


Authors: Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann-Georg Holzhütter

PubMed ID: 21255455

Date Published: 22nd Oct 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A3.4: Linking signalling to metabolic functions

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 12: 28

Scales: Not specified

Abstract (Expand)

ABSTRACT: BACKGROUND: Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and ...

Created: 7th Feb 2011 at 12:27   Last updated: 24th Oct 2013 at 16:19


 

Lipid analysis by thin-layer chromatography--a review of the current state


Authors: Beate Fuchs, Rosmarie Süss, Kristin Teuber, Mandy Eibisch, Jürgen Schiller

PubMed ID: 21167493

Date Published: 14th Oct 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: J Chromatogr A

Citation: J Chromatogr A 1218(19): 2754-74

Scales: Not specified

Abstract (Expand)

High-performance thin-layer chromatography (HPTLC) is a widely used, fast and relatively inexpensive method of separating complex mixtures. It is particularly useful for smaller, apolar compounds and ...

Created: 23rd Jun 2011 at 17:18   Last updated: 24th Oct 2013 at 16:19


 

Automated extraction of DNA and RNA from a single formalin-fixed paraffin-embedded tissue section for analysis of both single-nucleotide polymorphisms and mRNA expression


Authors: Guido Hennig, Mathias Gehrmann, Udo Stropp, Hiltrud Brauch, Peter Fritz, Michel Eichelbaum, Matthias Schwab, Werner Schroth

PubMed ID: 20947696

Date Published: 14th Oct 2010

Projects: No Projects

Journal: Clin. Chem.

Citation: Clin. Chem. 56(12): 1845-53

Scales: Not specified

Abstract (Expand)

There is an increasing need for the identification of both DNA and RNA biomarkers from pathodiagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples for the exploration of individualized therapy ...

Created: 18th Jul 2012 at 12:20   Last updated: 24th Oct 2013 at 16:19


 

Response of sinusoidal mouse liver cells to choline-deficient ethionine-supplemented diet


Authors: Elke Ueberham, Jan Böttger, Uwe Ueberham, Jens Grosche, Rolf Gebhardt

PubMed ID: 20942944

Date Published: 13th Oct 2010

Projects: A: Cellular level, B: Communication of Hepatocytes and Non-Parenchymal Liver Cells, C: Liver lobule level

Journal: Comp Hepatol

Citation: Comp Hepatol 9: 8

Scales: Cell, Intercellular, Liver lobule and Liver

Abstract (Expand)

Proliferation of oval cells, the bipotent precursor cells of the liver, requires impeded proliferation and loss of hepatocytes as well as a specific micro-environment, provided by adjacent sinusoidal ...

Created: 20th Jul 2012 at 10:16   Last updated: 24th Oct 2013 at 16:19


 

Modeling the TNFα-Induced Apoptosis Pathway in Hepatocytes


Authors: Rebekka Schlatter, Kathrin Schmich, Anna Lutz, Judith Trefzger, Oliver Sawodny, Michael Ederer, Irmgard Merfort

PubMed ID: 21533085

Date Published: 7th Oct 2010

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...

Journal: PLoS ONE

Citation: PLoS ONE 6(4): e18646

Scales: Cell

Abstract (Expand)

The proinflammatory cytokine TNFα fails to provoke cell death in isolated hepatocytes but has been implicated in hepatocyte apoptosis during liver diseases associated with chronic inflammation. Recently, ...

Created: 12th May 2011 at 15:13   Last updated: 24th Oct 2013 at 16:19


 

Phenotype and growth behavior of residual β-catenin-positive hepatocytes in livers of β-catenin-deficient mice


Authors: Albert Braeuning, Yasmin Singh, Benjamin Rignall, Albrecht Buchmann, Seddik Hammad, Amnah Othman, Iris von Recklinghausen, Patricio Godoy, Stefan Hoehme, Dirk Drasdo, Jan G Hengstler, Michael Schwarz

PubMed ID: 20886225

Date Published: 1st Oct 2010

Projects: No Projects

Journal: Histochem. Cell Biol.

Citation: Histochem. Cell Biol. 134(5): 469-81

Scales: Not specified

Abstract (Expand)

Signaling through the Wnt/β-catenin pathway is a crucial determinant of hepatic zonal gene expression, liver development, regeneration, and tumorigenesis. Transgenic mice with hepatocyte-specific ...

Created: 10th Sep 2012 at 17:18   Last updated: 24th Oct 2013 at 16:19


 

Tumor necrosis factor α sensitizes primary murine hepatocytes to Fas/CD95-induced apoptosis in a Bim- and Bid-dependent manner


Authors: Kathrin Schmich, Rebekka Schlatter, Nadia Corazza, Karine Sá Ferreira, Michael Ederer, Thomas Brunner, Christoph Borner, Irmgard Merfort

PubMed ID: 20872776

Date Published: 24th Sep 2010

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...

Journal: Hepatology

Citation: Hepatology 53(1): 282-92

Scales: Cell and Intercellular

Abstract (Expand)

Fas/CD95 is a critical mediator of cell death in many chronic and acute liver diseases and induces apoptosis in primary hepatocytes in vitro. In contrast, the proinflammatory cytokine tumor necrosis ...

Created: 16th Jul 2012 at 16:53   Last updated: 24th Oct 2013 at 16:19


 

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis


Authors: Carola Huthmacher, Andreas Hoppe, Sascha Bulik, Hermann-Georg Holzhütter

PubMed ID: 20807400

Date Published: 31st Aug 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: BMC Syst Biol

Citation: BMC Syst Biol 4: 120

Scales: Cell

Abstract (Expand)

Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances ...

Created: 4th Jan 2013 at 10:50   Last updated: 24th Oct 2013 at 16:19


 

Systems analysis of iron metabolism: the network of iron pools and fluxes


Authors: Tiago J S Lopes, Tatyana Luganskaja, Maja Vujić Spasić, Matthias W Hentze, Martina U Muckenthaler, Klaus Schümann, Jens G Reich

PubMed ID: 20704761

Date Published: 13th Aug 2010

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: BMC Syst Biol

Citation: BMC Syst Biol 4: 112

Scales: Organism

Abstract (Expand)

Every cell of the mammalian organism needs iron as trace element in numerous oxido-reductive processes as well as for transport and storage of oxygen. The very versatility of ionic iron makes it a toxic ...

Created: 19th Jul 2012 at 11:25   Last updated: 24th Oct 2013 at 16:19


 

A cell-based simulation software for multi-cellular systems


Authors: Stefan Hoehme, Dirk Drasdo

PubMed ID: 20709692

Date Published: 13th Aug 2010

Projects: No Projects

Journal: Bioinformatics

Citation: Bioinformatics 26(20): 2641-2

Scales: Not specified

Abstract (Expand)

CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates ...

Created: 10th Sep 2012 at 17:45   Last updated: 24th Oct 2013 at 16:19


 

Enzyme kinetics informatics: from instrument to browser


Authors: Neil Swainston, Martin Golebiewski, Hanan L Messiha, Naglis Malys, Renate Kania, Sylvestre Kengne, Olga Krebs, Saqib Mir, Heidrun Sauer-Danzwith, Kieran Smallbone, Andreas Weidemann, Ulrike Wittig, Douglas B Kell, Pedro Mendes, Wolfgang Müller, Norman W Paton, Isabel Rojas

PubMed ID: 20738395

Date Published: 3rd Aug 2010

Projects: F3: Kinetic data handling

Journal: FEBS J.

Citation: FEBS J. 277(18): 3769-79

Scales: Not specified

Abstract (Expand)

A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw ...

Created: 11th Jan 2011 at 11:11   Last updated: 24th Oct 2013 at 16:20


 

Iron regulatory proteins secure mitochondrial iron sufficiency and function


Authors: Bruno Galy, Dunja Ferring-Appel, Sven W Sauer, Sylvia Kaden, Saïd Lyoumi, Herve Puy, Stefan Kölker, Hermann-Josef Gröne, Matthias W Hentze

PubMed ID: 20674864

Date Published: 3rd Aug 2010

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag..., HepatoSys

Journal: Cell Metab.

Citation: Cell Metab. 12(2): 194-201

Scales: Cell

Abstract (Expand)

Mitochondria supply cells with ATP, heme, and iron sulfur clusters (ISC), and mitochondrial energy metabolism involves both heme- and ISC-dependent enzymes. Here, we show that mitochondrial iron supply ...

Created: 29th Oct 2012 at 11:00   Last updated: 24th Oct 2013 at 16:20


 

Synchrotron infrared spectroscopic ellipsometry for characterization of biofunctional surfaces


Authors: Guoguang Sun, Dana Maria Rosu, Xin Zhang, Marc Hovestädt, Simona Pop, Ulrich Schade, Dennis Aulich, Michael Gensch, Bernhard Ay, Hermann-Georg Holzhütter, Dietrich R. T. Zahn, Norbert Esser, Rudolf Volkmer, Jörg Rappich, Karsten Hinrichs

DOI: 10.1002/pssb.200983945

Date Published: 1st Aug 2010

Projects: No Projects

Journal: phys. stat. sol. (b)

Citation: phys. stat. sol. (b) 247(8) : 1925

Scales: Not specified

Abstract (Expand)

The structural and thickness homogeneity of different biofunctional surfaces after coating an Au substrate was studied by infrared spectroscopic ellipsometry (IRSE). Monolayer coverage was achieved by ...

Created: 4th Jan 2013 at 12:51   Last updated: 24th Oct 2013 at 16:20


 

Two to tango: regulation of Mammalian iron metabolism


Authors: Matthias W Hentze, Martina U Muckenthaler, Bruno Galy, Clara Camaschella

PubMed ID: 20603012

Date Published: 7th Jul 2010

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag..., HepatoSys

Journal: Cell

Citation: Cell 142(1): 24-38

Scales: Cell

Abstract (Expand)

Disruptions in iron homeostasis from both iron deficiency and overload account for some of the most common human diseases. Iron metabolism is balanced by two regulatory systems, one that functions ...

Created: 29th Oct 2012 at 11:04   Last updated: 24th Oct 2013 at 16:20


 

Fluxviz - cytoscape plug-in for visualization of flux distributions in networks


Authors: Matthias König, Hermann-Georg Holzhütter

PubMed ID: 22081592

Date Published: 1st Jul 2010

Projects: No Projects

Journal: Genome Inform

Citation: Genome Inform 24(1): 96-103

Scales: Not specified

Abstract (Expand)

Motivation: Methods like FBA and kinetic modeling are widely used to calculate fluxes in metabolic networks. For the analysis and understanding of simulation results and experimentally measured fluxes ...

Created: 4th Jan 2013 at 11:14   Last updated: 24th Oct 2013 at 16:20


 

Biochemical network-based drug-target prediction


Authors: Edda Klipp, Rebecca C Wade, Ursula Kummer

PubMed ID: 20554441

Date Published: 14th Jun 2010

Projects: HepatoSys

Journal: Curr. Opin. Biotechnol.

Citation: Curr. Opin. Biotechnol. 21(4): 511-6

Scales: Not specified

Abstract (Expand)

The use of networks to aid the drug discovery process is a rather new but booming endeavor. A vast variety of different types of networks are being constructed and analyzed for various different tasks ...

Created: 30th Aug 2012 at 13:17   Last updated: 24th Oct 2013 at 16:20


 

IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities


Authors: Kristian Rother, Sabrina Hoffmann, Sascha Bulik, Andreas Hoppe, Johann Gasteiger, Herrmann-Georg Holzhütter

PubMed ID: 20513391

Date Published: 2nd Jun 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Biophys. J.

Citation: Biophys. J. 98(11): 2478-86

Scales: Not specified

Abstract (Expand)

Mathematical analysis and modeling of biochemical reaction networks requires knowledge of the permitted directionality of reactions and membrane transport processes. This information can be gathered ...

Created: 4th Jan 2013 at 10:51   Last updated: 24th Oct 2013 at 16:20


 

Atypical protein kinase C zeta exhibits a proapoptotic function in ovarian cancer


Authors: Irina Nazarenko, Marcel Jenny, Jana Keil, Cornelia Gieseler, Karen Weisshaupt, Jalid Sehouli, Stefan Legewie, Lena Herbst, Wilko Weichert, Silvia Darb-Esfahani, Manfred Dietel, Reinhold Schäfer, Florian Ueberall, Christine Sers

PubMed ID: 20501645

Date Published: 25th May 2010

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg..., B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: Mol. Cancer Res.

Citation: Mol. Cancer Res. 8(6): 919-34

Scales: Cell

Abstract (Expand)

Intracellular signaling governed by serine/threonine kinases comprises the molecular interface between cell surface receptors and the nuclear transcriptional machinery. The protein kinase C (PKC) family ...

Created: 11th Sep 2012 at 11:39   Last updated: 24th Oct 2013 at 16:20


 

Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration


Authors: Stefan Hoehme, Marc Brulport, Alexander Bauer, Essam Bedawy, Wiebke Schormann, Matthias Hermes, Verena Puppe, Rolf Gebhardt, Sebastian Zellmer, Michael Schwarz, Ernesto Bockamp, Tobias Timmel, Jan G Hengstler, Dirk Drasdo

PubMed ID: 20484673

Date Published: 19th May 2010

Projects: B: Communication of Hepatocytes and Non-Parenchymal Liver Cells

Journal: Proc. Natl. Acad. Sci. U.S.A.

Citation: Proc. Natl. Acad. Sci. U.S.A. 107(23): 10371-6

Scales: Liver lobule

Abstract (Expand)

Only little is known about how cells coordinately behave to establish functional tissue structure and restore microarchitecture during regeneration. Research in this field is hampered by a lack of ...

Created: 14th Aug 2012 at 08:44   Last updated: 24th Oct 2013 at 16:20


 

An update of MALDI-TOF mass spectrometry in lipid research


Authors: Beate Fuchs, Rosmarie Süss, Jürgen Schiller

PubMed ID: 20643161

Date Published: 25th Apr 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Prog. Lipid Res.

Citation: Prog. Lipid Res. 49(4): 450-75

Scales: Not specified

Abstract (Expand)

Although matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS)--often but not exclusively coupled with a time-of-flight (TOF) mass analyzer--is primarily established in the ...

Created: 23rd Jun 2011 at 17:13   Last updated: 24th Oct 2013 at 16:20


 

Genome-wide comparison between IL-17 and combined TNF-alpha/IL-17 induced genes in primary murine hepatocytes


Authors: Titus Sparna, Julia Rétey, Kathrin Schmich, Ute Albrecht, Katrin Naumann, Norbert Gretz, Hans-Peter Fischer, Johannes G Bode, Irmgard Merfort

PubMed ID: 20374638

Date Published: 7th Apr 2010

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., HepatoSys

Journal: BMC Genomics

Citation: BMC Genomics 11: 226

Scales: Cell

Abstract (Expand)

Cytokines such as TNF-alpha and IL-1 beta are known for their contribution to inflammatory processes in liver. In contrast, the cytokine IL-17 has not yet been assigned a role in liver diseases. IL-17 ...

Created: 30th Aug 2012 at 12:22   Last updated: 24th Oct 2013 at 16:20


 

The generation of hepatocytes from mesenchymal stem cells and engraftment into murine liver


Authors: Peggy Stock, Sandra Brückner, Sabine Ebensing, Madlen Hempel, Matthias M Dollinger, Bruno Christ

PubMed ID: 20224562

Date Published: 11th Mar 2010

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Nat Protoc

Citation: Nat Protoc 5(4): 617-27

Scales: Liver

Abstract (Expand)

Donor organ shortage is still the major obstacle for the clinical application of hepatocyte transplantation in the treatment of liver diseases. However, generation of hepatocyte-like cells from mesenchymal ...

Created: 14th Jan 2014 at 10:13


 

Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes


Authors: Sebastian Zellmer, Wolfgang Schmidt-Heck, Patricio Godoy, Honglei Weng, Christoph Meyer, Thomas Lehmann, Titus Sparna, Wiebke Schormann, Seddik Hammad, Clemens Kreutz, Jens Timmer, Fritz von Weizsäcker, Petra A Thürmann, Irmgard Merfort, Reinhard Guthke, Steven Dooley, Jan G Hengstler, Rolf Gebhardt

PubMed ID: 20979052

Date Published: 5th Mar 2010

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Hepatology

Citation: Hepatology 52(6): 2127-36

Scales: Not specified

Abstract (Expand)

The cellular basis of liver regeneration has been intensely investigated for many years. However, the mechanisms initiating hepatocyte "plasticity" and priming for proliferation are not yet ...

Created: 13th Dec 2010 at 11:21   Last updated: 24th Oct 2013 at 16:20


 

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays


Authors: Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W Hentze, Thomas Dandekar, Martina U Muckenthaler

PubMed ID: 20193060

Date Published: 1st Mar 2010

Projects: HepatoSys

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 11: 112

Scales: Not specified

Abstract (Expand)

Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting ...

Created: 30th Oct 2012 at 08:53   Last updated: 24th Oct 2013 at 16:20


 

Systems survey of endocytosis by multiparametric image analysis


Authors: Claudio Collinet, Martin Stöter, Charles R Bradshaw, Nikolay Samusik, Jochen C Rink, Denise Kenski, Bianca Habermann, Frank Buchholz, Robert Henschel, Matthias S Mueller, Wolfgang E Nagel, Eugenio Fava, Yannis Kalaidzidis, Marino Zerial

PubMed ID: 20190736

Date Published: 28th Feb 2010

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Nature

Citation: Nature 464(7286): 243-9

Scales: Not specified

Abstract (Expand)

Endocytosis is a complex process fulfilling many cellular and developmental functions. Understanding how it is regulated and integrated with other cellular processes requires a comprehensive analysis ...

Created: 23rd Nov 2012 at 14:04   Last updated: 24th Oct 2013 at 16:20


 

Interpretation of non-invasive breath tests using (13)C-labeled substrates--a preliminary report with (13)C-methacetin


Authors: J F Lock, P Taheri, S Bauer, H-G Holzhütter, M Malinowski, P Neuhaus, M Stockmann

PubMed ID: 20149989

Date Published: 13th Feb 2010

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Eur. J. Med. Res.

Citation: Eur. J. Med. Res. 14: 547-50

Scales: Not specified

Abstract (Expand)

Non-invasive breath tests can serve as valuable diagnostic tools in medicine as they can determine particular enzymatic and metabolic functions in vivo. However, methodological pitfalls have limited ...

Created: 8th Jan 2013 at 11:53   Last updated: 24th Oct 2013 at 16:20


 

Computing combinatorial intervention strategies and failure modes in signaling networks


Authors: Regina Samaga, Axel Von Kamp, Steffen Klamt

PubMed ID: 20078396

Date Published: 19th Jan 2010

Projects: No Projects

Journal: J. Comput. Biol.

Citation: J. Comput. Biol. 17(1): 39-53

Scales: Not specified

Abstract (Expand)

The identification of combinatorial intervention strategies and the elucidation of failure modes that may cause aberrant behavior of cellular signaling networks are highly relevant topics in cell ...

Created: 14th Aug 2012 at 10:31   Last updated: 24th Oct 2013 at 16:20


 

Pathway-Targeted Pharmacogenomics of CYP1A2 in Human Liver


Authors: Kathrin Klein, Stefan Winter, Miia Turpeinen, Matthias Schwab, Ulrich M. Zanger

DOI: 10.3389/fphar.2010.00129

Date Published: 2010

Projects: B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Front. Pharmacol.

Citation: Front. Pharmacol. 1

Scales: Not specified

Abstract (Expand)

The human drug metabolizing cytochrome P450 (CYP) 1A2, is one of the major P450 isoforms contributing by about 5–20% to the hepatic P450 pool and catalyzing oxidative biotransformation of up to 10% of ...

Created: 27th Jan 2011 at 14:52   Last updated: 24th Oct 2013 at 16:20


 

ModuleMaster: A new tool to decipher transcriptional regulatory networks


Authors: Clemens Wrzodek, Adrian Schröder, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, Marcel Kronfeld, Klaus Harter, Andreas Zell

DOI: 10.1016/j.biosystems.2009.09.005

Date Published: 2010

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Biosystems

Citation: Biosystems 99(1) : 79

Scales: Not specified

Abstract (Expand)

In this article we present ModuleMaster, a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only ...

Created: 27th Jan 2011 at 14:58   Last updated: 24th Oct 2013 at 16:20


 

Automating Mathematical Modeling of Biochemical Reaction Networks


Authors: Andreas Dräger, Adrian Schröder, Andreas Zell

DOI: 10.1007/978-1-4419-5797-9_7

Date Published: 2010

Projects: A3.4: Linking signalling to metabolic functions

Book: Systems Biology for Signaling Networks

Citation: Systems Biology for Signaling Networks : 159

Scales: Not specified

Abstract (Expand)

In this chapter we introduce a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each single step and how to ...

Created: 11th Jul 2011 at 09:40   Last updated: 24th Oct 2013 at 16:20


 

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology


Authors: Christoph Gille, Christian Bölling, Andreas Hoppe, Sascha Bulik, Sabrina Hoffmann, Katrin Hübner, Anja Karlstädt, Ramanan Ganeshan, Matthias König, Kristian Rother, Michael Weidlich, Jörn Behre, Herrmann-Georg Holzhütter

PubMed ID: 20823849

Date Published: 30th Dec 2009

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A1.3: Identification of crucial metabolic processes during hepatocyte pr..., F2: The Liver Knowledge Base (LKB)

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 6: 411

Scales: Liver

Abstract (Expand)

We present HepatoNet1, the first reconstruction of a comprehensive metabolic network of the human hepatocyte that is shown to accomplish a large canon of known metabolic liver functions. The network ...

Created: 9th Dec 2010 at 13:39   Last updated: 24th Oct 2013 at 16:20


 

SMAD7 controls iron metabolism as a potent inhibitor of hepcidin expression


Authors: Katarzyna Mleczko-Sanecka, Guillem Casanovas, Anan Ragab, Katja Breitkopf, Alexandra Müller, Michael Boutros, Steven Dooley, Matthias W Hentze, Martina U Muckenthaler

PubMed ID: 20040761

Date Published: 29th Dec 2009

Projects: B1.3: Linking modulation of iron metabolism with the impact of macrophag...

Journal: Blood

Citation: Blood 115(13): 2657-65

Scales: Not specified

Abstract (Expand)

Hepcidin is the master regulatory hormone of systemic iron metabolism. Hepcidin deficiency causes common iron overload syndromes whereas its overexpression is responsible for microcytic anemias. Hepcidin ...

Created: 30th Oct 2012 at 08:51   Last updated: 24th Oct 2013 at 16:21


 

Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields


Authors: Matthias Stein, Razif R Gabdoulline, Rebecca C Wade

PubMed ID: 20024078

Date Published: 16th Dec 2009

Projects: F3: Kinetic data handling, HepatoSys

Journal: Mol Biosyst

Citation: Mol Biosyst 6(1): 152-64

Scales: Not specified

Abstract (Expand)

The electrostatic potential of an enzyme is a key determinant of its substrate interactions and catalytic turnover. Here we invoke comparative analysis of protein electrostatic potentials, along with ...

Created: 31st Oct 2012 at 14:08   Last updated: 24th Oct 2013 at 16:21


 

Nicotinamide phosphoribosyltransferase (NAMPT/PBEF/visfatin) is constitutively released from human hepatocytes


Authors: A Garten, S Petzold, A Barnikol-Oettler, A Körner, W E Thasler, J Kratzsch, W Kiess, R Gebhardt

PubMed ID: 19912992

Date Published: 11th Nov 2009

Projects: Showcase Steatosis

Journal: Biochem. Biophys. Res. Commun.

Citation: Biochem. Biophys. Res. Commun. 391(1): 376-81

Scales: Cell

Abstract (Expand)

Circulating NAMPT (PBEF/visfatin) has pleiotropic functions and is secreted from adipocytes. Since it is doubtful whether serum levels can be explained by secretion from adipocytes alone, we asked ...

Created: 20th Jul 2012 at 10:11   Last updated: 24th Oct 2013 at 16:21


 

4-Aminoethylamino-emodin--a novel potent inhibitor of GSK-3beta--acts as an insulin-sensitizer avoiding downstream effects of activated beta-catenin


Authors: Rolf Gebhardt, Katja S Lerche, Frank Götschel, Robert Günther, Jens Kolander, Lars Teich, Sebastian Zellmer, Hans-Jörg Hofmann, Kurt Eger, Andreas Hecht, Frank Gaunitz

PubMed ID: 19228266

Date Published: 3rd Oct 2009

Projects: HepatoSys

Journal: J. Cell. Mol. Med.

Citation: J. Cell. Mol. Med. 14(6A): 1276-93

Scales: Intercellular

Abstract (Expand)

Glycogen synthase kinase-3beta (GSK-3beta) is a key target and effector of downstream insulin signalling. Using comparative protein kinase assays and molecular docking studies we characterize the ...

Created: 19th Jul 2012 at 14:14   Last updated: 24th Oct 2013 at 16:21


 

Expression of organic cation transporters OCT1 (SLC22A1) and OCT3 (SLC22A3) is affected by genetic factors and cholestasis in human liver


Authors: Anne T. Nies, Hermann Koepsell, Stefan Winter, Oliver Burk, Kathrin Klein, Reinhold Kerb, Ulrich M. Zanger, Dietrich Keppler, Matthias Schwab, Elke Schaeffeler

DOI: 10.1002/hep.23103

Date Published: 1st Oct 2009

Projects: A3.4: Linking signalling to metabolic functions

Journal: Hepatology

Citation: Hepatology 50(4) : 1227

Scales: Intercellular

Abstract:

Not specified

Created: 3rd Aug 2012 at 08:37   Last updated: 24th Oct 2013 at 16:21


 

Finding one's way in proteomics: a protein species nomenclature


Authors: Hartmut Schlüter, Rolf Apweiler, Hermann-Georg Holzhütter, Peter R Jungblut

PubMed ID: 19740416

Date Published: 9th Sep 2009

Projects: No Projects

Journal: Chem Cent J

Citation: Chem Cent J 3: 11

Scales: Not specified

Abstract (Expand)

Our knowledge of proteins has greatly improved in recent years, driven by new technologies in the fields of molecular biology and proteome research. It has become clear that from a single gene not only ...

Created: 4th Jan 2013 at 12:56   Last updated: 24th Oct 2013 at 16:21


 

Organ patterning in the adult stage: the role of Wnt/beta-catenin signaling in liver zonation and beyond


Authors: Rolf Gebhardt, Amalya Hovhannisyan

PubMed ID: 19705440

Date Published: 26th Aug 2009

Projects: C: Liver lobule level, Showcase Steatosis

Journal: Dev. Dyn.

Citation: Dev. Dyn. 239(1): 45-55

Scales: Liver lobule and Liver

Abstract (Expand)

Wnt/beta-catenin signaling has been found to play key roles in metabolic zonation of adult liver, regeneration, and hepatocellular carcinogenesis. In this review, recent progress in this field is ...

Created: 20th Jul 2012 at 09:49   Last updated: 24th Oct 2013 at 16:21


 

Analysis of an apoptotic core model focused on experimental design using artificial data


Authors: R Schlatter, H Conzelmann, E D Gilles, O Sawodny, T Sauter

PubMed ID: 19640164

Date Published: 31st Jul 2009

Projects: No Projects

Journal: IET Syst Biol

Citation: IET Syst Biol 3(4): 255-65

Scales: Not specified

Abstract (Expand)

The activation of caspases is a central mechanism in apoptosis. To gain further insights into complex processes like this, mathematical modelling using ordinary differential equations (ODEs) can be a ...

Created: 3rd Dec 2010 at 10:00   Last updated: 24th Oct 2013 at 16:21


 

Accessible methods for the dynamic time-scale decomposition of biochemical systems


Authors: Irina Surovtsova, Natalia Simus, Thomas Lorenz, Artjom König, Sven Sahle, Ursula Kummer

PubMed ID: 19633098

Date Published: 24th Jul 2009

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 25(21): 2816-23

Scales: Not specified

Abstract (Expand)

The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the ...

Created: 30th Aug 2012 at 13:24   Last updated: 24th Oct 2013 at 16:21


 

A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles


Authors: Bernd Binder, Andrean Goede, Nikolaus Berndt, Hermann-Georg Holzhütter

PubMed ID: 20041124

Date Published: 21st Jul 2009

Projects: A3.3: Hepatocyte polarity

Journal: PLoS ONE

Citation: PLoS ONE 4(12): e8295

Scales: Not specified

Abstract (Expand)

Formation, degradation and renewal of cellular organelles is a dynamic process based on permanent budding, fusion and inter-organelle traffic of vesicles. These processes include many regulatory proteins ...

Created: 4th Feb 2011 at 12:47   Last updated: 24th Oct 2013 at 16:21


 

Estimation of gene induction enables a relevance-based ranking of gene sets


Authors: Kilian Bartholomé, Clemens Kreutz, Jens Timmer

PubMed ID: 19580524

Date Published: 8th Jul 2009

Projects: HepatoSys

Journal: J. Comput. Biol.

Citation: J. Comput. Biol. 16(7): 959-67

Scales: Cell

Abstract (Expand)

In order to handle and interpret the vast amounts of data produced by microarray experiments, the analysis of sets of genes with a common biological functionality has been shown to be advantageous ...

Created: 10th Aug 2012 at 11:44   Last updated: 24th Oct 2013 at 16:21


 

ON/OFF and beyond--a boolean model of apoptosis


Authors: Rebekka Schlatter, Kathrin Schmich, Ima Avalos Vizcarra, Peter Scheurich, Thomas Sauter, Christoph Borner, Michael Ederer, Irmgard Merfort, Oliver Sawodny

PubMed ID: 20011108

Date Published: 2nd Jul 2009

Projects: No Projects

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 5(12): e1000595

Scales: Not specified

Abstract (Expand)

Apoptosis is regulated by several signaling pathways which are extensively linked by crosstalks. Boolean or logical modeling has become a promising approach to capture the qualitative behavior of such ...

Created: 3rd Dec 2010 at 09:59   Last updated: 24th Oct 2013 at 16:21


 

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood


Authors: A Raue, C Kreutz, T Maiwald, J Bachmann, M Schilling, U Klingmüller, J Timmer

PubMed ID: 19505944

Date Published: 8th Jun 2009

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: Bioinformatics

Citation: Bioinformatics 25(15): 1923-9

Scales: Not specified

Abstract (Expand)

MOTIVATION: Mathematical description of biological reaction networks by differential equations leads to large models whose parameters are calibrated in order to optimally explain experimental data. ...

Created: 10th Dec 2010 at 12:16   Last updated: 24th Oct 2013 at 16:21


 

Heterogeneous expression of suppressor of cytokine signalling 2 (SOCS-2) in liver tissue


Authors: Sebastian Zellmer, Stephan Sickinger, Wolfgang Schmidt-Heck, Reinhard Guthke, Rolf Gebhardt

PubMed ID: 19470084

Date Published: 14th May 2009

Projects: No Projects

Journal: J. Anat.

Citation: J. Anat. 215(2): 176-83

Scales: Not specified

Abstract (Expand)

Suppressor of cytokine signalling 2 (SOCS-2), a dual effector of growth hormone signalling, was found to be heterogeneously expressed in murine liver parenchyma. Data from Affymetrix gene arrays, ...

Created: 28th Sep 2010 at 09:25   Last updated: 24th Oct 2013 at 16:21


 

Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection


Authors: Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar

PubMed ID: 19772631

Date Published: 12th May 2009

Projects: No Projects

Journal: BMC Syst Biol

Citation: BMC Syst Biol 3: 97

Scales: Not specified

Abstract (Expand)

BACKGROUND: The decision pro- or contra apoptosis is complex, involves a number of different inputs, and is central for the homeostasis of an individual cell as well as for the maintenance and regeneration ...

Created: 3rd Dec 2010 at 10:01   Last updated: 24th Oct 2013 at 16:21


 

Uncovering metabolic objectives pursued by changes of enzyme levels


Authors: Sabrina Hoffmann, Hermann-Georg Holzhütter

PubMed ID: 19348632

Date Published: 8th Apr 2009

Projects: No Projects

Journal: Ann. N. Y. Acad. Sci.

Citation: Ann. N. Y. Acad. Sci. 1158: 57-70

Scales: Not specified

Abstract (Expand)

Expression profiling and proteomic techniques reveal significant variations in the levels of thousands of mRNAs and proteins in response to environmental changes such as substrate depletion, oxidative ...

Created: 4th Jan 2013 at 12:53   Last updated: 24th Oct 2013 at 16:21


 

Systems-level interactions between insulin-EGF networks amplify mitogenic signaling


Authors: Nikolay Borisov, Edita Aksamitiene, Anatoly Kiyatkin, Stefan Legewie, Jan Berkhout, Thomas Maiwald, Nikolai P Kaimachnikov, Jens Timmer, Jan B Hoek, Boris N Kholodenko

PubMed ID: 19357636

Date Published: 7th Apr 2009

Projects: HepatoSys

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 5: 256

Scales: Not specified

Abstract (Expand)

Crosstalk mechanisms have not been studied as thoroughly as individual signaling pathways. We exploit experimental and computational approaches to reveal how a concordant interplay between the insulin ...

Created: 11th Sep 2012 at 11:41   Last updated: 24th Oct 2013 at 16:21


 

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports


Authors: Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell

PubMed ID: 19307240

Date Published: 23rd Mar 2009

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 25(11): 1455-6

Scales: Not specified

Abstract (Expand)

SUMMARY: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is ...

Created: 11th Jan 2011 at 11:11   Last updated: 24th Oct 2013 at 16:21


 

Erythropoietin-receptor gene regulation in neuronal cells


Authors: Iwona Wallach, Juan Zhang, Anika Hartmann, Frank K H van Landeghem, Anna Ivanova, Martin Klar, Christof Dame

PubMed ID: 19218878

Date Published: 17th Feb 2009

Projects: No Projects

Journal: Pediatr. Res.

Citation: Pediatr. Res. 65(6): 619-24

Scales: Not specified

Abstract (Expand)

Because erythropoietin (Epo) is intensively studied as neuroprotective agent, Epo receptor (EpoR) regulation in neurons is of particular interest. Herein, we investigated molecular mechanisms of EpoR ...

Created: 4th Jan 2013 at 11:24   Last updated: 24th Oct 2013 at 16:21


 

Systems biology: experimental design


Authors: Clemens Kreutz, Jens Timmer

PubMed ID: 19215298

Date Published: 14th Feb 2009

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: FEBS J.

Citation: FEBS J. 276(4): 923-42

Scales: Not specified

Abstract (Expand)

Experimental design has a long tradition in statistics, engineering and life sciences, dating back to the beginning of the last century when optimal designs for industrial and agricultural trials were ...

Created: 10th Dec 2010 at 12:14   Last updated: 24th Oct 2013 at 16:21


 

Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome


Authors: Dawadschargal Bech-Otschir, Annett Helfrich, Cordula Enenkel, Gesa Consiglieri, Michael Seeger, Hermann-Georg Holzhütter, Burkhardt Dahlmann, Peter-Michael Kloetzel

PubMed ID: 19169257

Date Published: 25th Jan 2009

Projects: No Projects

Journal: Nat. Struct. Mol. Biol.

Citation: Nat. Struct. Mol. Biol. 16(2): 219-25

Scales: Not specified

Abstract (Expand)

The 26S proteasome degrades polyubiquitylated (polyUb) proteins by an ATP-dependent mechanism. Here we show that binding of model polyUb substrates to the 19S regulator of mammalian and yeast 26S ...

Created: 4th Jan 2013 at 12:53   Last updated: 24th Oct 2013 at 16:21


 

Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws--a promising method for speeding up the kinetic modelling of complex metabolic networks


Authors: Sascha Bulik, Sergio Grimbs, Carola Huthmacher, Joachim Selbig, Hermann G Holzhütter

PubMed ID: 19137631

Date Published: 13th Jan 2009

Projects: No Projects

Journal: FEBS J.

Citation: FEBS J. 276(2): 410-24

Scales: Not specified

Abstract (Expand)

Kinetic modelling of complex metabolic networks - a central goal of computational systems biology - is currently hampered by the lack of reliable rate equations for the majority of the underlying ...

Created: 4th Jan 2013 at 11:06   Last updated: 24th Oct 2013 at 16:22


 

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts


Authors: Nils Blüthgen, Stefan Legewie, Szymon M Kielbasa, Anja Schramme, Oleg Tchernitsa, Jana Keil, Andrea Solf, Martin Vingron, Reinhold Schäfer, Hanspeter Herzel, Christine Sers

PubMed ID: 19154344

Date Published: 12th Jan 2009

Projects: HepatoSys

Journal: FEBS J.

Citation: FEBS J. 276(4): 1024-35

Scales: Not specified

Abstract (Expand)

Mitogen-activated protein kinase (MAPK) signaling determines crucial cell fate decisions in most cell types, and mediates cellular transformation in many types of cancer. The activity of MAPK is ...

Created: 11th Sep 2012 at 11:44   Last updated: 24th Oct 2013 at 16:22


 

BowTieBuilder: modeling signal transduction pathways


Authors: Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, Andreas Zell

DOI: 10.1186/1752-0509-3-67

Date Published: 2009

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: BMC Syst Biol

Citation: BMC Syst Biol 3(1) : 67

Scales: Not specified

Abstract (Expand)

Background Sensory proteins react to changing environmental conditions by transducing signals into the cell. These signals are integrated into core proteins that activate downstream target proteins ...

Created: 27th Jan 2011 at 14:51   Last updated: 24th Oct 2013 at 16:22


 

Kinetic mechanisms for overexpression insensitivity and oncogene cooperation


Authors: Stefan Legewie, Christine Sers, Hanspeter Herzel

PubMed ID: 19059249

Date Published: 4th Dec 2008

Projects: HepatoSys

Journal: FEBS Lett.

Citation: FEBS Lett. 583(1): 93-6

Scales: Not specified

Abstract (Expand)

Minor (5-10 fold) activation of mitogenic signalling cascades typically induces cell division upon extracellular stimulation and is sufficient to support tumourigenesis when permanently triggered by ...

Created: 11th Sep 2012 at 12:56   Last updated: 24th Oct 2013 at 16:22


 

Switch from type II to I Fas/CD95 death signaling on in vitro culturing of primary hepatocytes


Authors: Dorothée Walter, Kathrin Schmich, Sandra Vogel, Robert Pick, Thomas Kaufmann, Florian Christoph Hochmuth, Angelika Haber, Karin Neubert, Sabine McNelly, Fritz von Weizsäcker, Irmgard Merfort, Ulrich Maurer, Andreas Strasser, Christoph Borner

PubMed ID: 19003879

Date Published: 13th Nov 2008

Projects: HepatoSys

Journal: Hepatology

Citation: Hepatology 48(6): 1942-53

Scales: Cell

Abstract (Expand)

Fas/CD95-induced apoptosis of hepatocytes in vivo proceeds through the so-called type II pathway, requiring the proapoptotic BH3-only Bcl-2 family member Bid for mitochondrial death signaling. Consequently, ...

Created: 30th Aug 2012 at 12:31   Last updated: 24th Oct 2013 at 16:22


 

FGF acts as a co-transmitter through adenosine A(2A) receptor to regulate synaptic plasticity


Authors: Marc Flajolet, Zhongfeng Wang, Marie Futter, Weixing Shen, Nina Nuangchamnong, Jacob Bendor, Iwona Wallach, Angus C Nairn, D James Surmeier, Paul Greengard

PubMed ID: 18953346

Date Published: 26th Oct 2008

Projects: No Projects

Journal: Nat. Neurosci.

Citation: Nat. Neurosci. 11(12): 1402-9

Scales: Not specified

Abstract (Expand)

Abnormalities of striatal function have been implicated in several major neurological and psychiatric disorders, including Parkinson's disease, schizophrenia and depression. Adenosine, via activation ...

Created: 4th Jan 2013 at 11:25   Last updated: 24th Oct 2013 at 16:22


 

Systems analysis of MAPK signal transduction


Authors: Nils Blüthgen, Stefan Legewie

PubMed ID: 18793126

Date Published: 17th Sep 2008

Projects: HepatoSys

Journal: Essays Biochem.

Citation: Essays Biochem. 45: 95-107

Scales: Not specified

Abstract (Expand)

For more than a decade, the MAPK (mitogen-activated protein kinase) cascade has been studied using mathematical modelling and quantitative experimentation [1]. The MAPK cascade relays the presence of ...

Created: 11th Sep 2012 at 12:58   Last updated: 24th Oct 2013 at 16:22


 

The speciation of the proteome


Authors: Peter R Jungblut, Hermann G Holzhütter, Rolf Apweiler, Hartmut Schlüter

PubMed ID: 18638390

Date Published: 18th Jul 2008

Projects: No Projects

Journal: Chem Cent J

Citation: Chem Cent J 2: 16

Scales: Not specified

Abstract (Expand)

In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the ...

Created: 4th Jan 2013 at 13:00   Last updated: 24th Oct 2013 at 16:22


 

Membrane identity and GTPase cascades regulated by toggle and cut-out switches


Authors: Perla Del Conte-Zerial, Lutz Brusch, Jochen C Rink, Claudio Collinet, Yannis Kalaidzidis, Marino Zerial, Andreas Deutsch

PubMed ID: 18628746

Date Published: 15th Jul 2008

Projects: HepatoSys

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 4: 206

Scales: Not specified

Abstract (Expand)

Key cellular functions and developmental processes rely on cascades of GTPases. GTPases of the Rab family provide a molecular ID code to the generation, maintenance and transport of intracellular ...

Created: 29th Jul 2011 at 16:14   Last updated: 24th Oct 2013 at 16:22


 

Dynamical modeling and multi-experiment fitting with PottersWheel


Authors: Thomas Maiwald, Jens Timmer

PubMed ID: 18614583

Date Published: 9th Jul 2008

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 24(18): 2037-43

Scales: Not specified

Abstract (Expand)

Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. ...

Created: 17th Aug 2012 at 10:13   Last updated: 24th Oct 2013 at 16:22


 

Small RNAs establish delays and temporal thresholds in gene expression


Authors: Stefan Legewie, Dennis Dienst, Annegret Wilde, Hanspeter Herzel, Ilka M Axmann

PubMed ID: 18599624

Date Published: 3rd Jul 2008

Projects: HepatoSys

Journal: Biophys. J.

Citation: Biophys. J. 95(7): 3232-8

Scales: Not specified

Abstract (Expand)

Noncoding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but how they affect the dynamics of transcriptional networks remains poorly understood. We analyzed the temporal ...

Created: 11th Sep 2012 at 13:00   Last updated: 24th Oct 2013 at 16:22


 

A minimal circadian clock model


Authors: Ilka M Axmann, Stefan Legewie, Hanspeter Herzel

PubMed ID: 18546474

Date Published: 12th Jun 2008

Projects: HepatoSys

Journal: Genome Inform

Citation: Genome Inform 18: 54-64

Scales: Not specified

Abstract (Expand)

The coordination of biological activities into daily cycles provides an important advantage for the fitness of diverse organisms. Thereby, an internal circadian oscillator drives gene expression in an ...

Created: 11th Sep 2012 at 13:01   Last updated: 24th Oct 2013 at 16:22


 

Computational lipidology: predicting lipoprotein density profiles in human blood plasma


Authors: Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, Hermann-Georg Holzhütter

PubMed ID: 18497853

Date Published: 24th May 2008

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 4(5): e1000079

Scales: Not specified

Abstract (Expand)

Monitoring cholesterol levels is strongly recommended to identify patients at risk for myocardial infarction. However, clinical markers beyond "bad" and "good" cholesterol are needed ...

Created: 4th Jan 2013 at 12:57   Last updated: 24th Oct 2013 at 16:22


 

Systemic iron homeostasis and the iron-responsive element/iron-regulatory protein (IRE/IRP) regulatory network


Authors: Martina U Muckenthaler, Bruno Galy, Matthias W Hentze

PubMed ID: 18489257

Date Published: 21st May 2008

Projects: HepatoSys

Journal: Annu. Rev. Nutr.

Citation: Annu. Rev. Nutr. 28: 197-213

Scales: Cell

Abstract (Expand)

The regulation and maintenance of systemic iron homeostasis is critical to human health. Iron overload and deficiency diseases belong to the most common nutrition-related pathologies across the globe. ...

Created: 29th Oct 2012 at 11:06   Last updated: 24th Oct 2013 at 16:22


 

Hepatocyte-specific Smad7 expression attenuates TGF-beta-mediated fibrogenesis and protects against liver damage


Authors: Steven Dooley, Jafar Hamzavi, Loredana Ciuclan, Patricio Godoy, Iryna Ilkavets, Sabrina Ehnert, Elke Ueberham, Rolf Gebhardt, Stephan Kanzler, Andreas Geier, Katja Breitkopf, Honglei Weng, Peter R Mertens

PubMed ID: 18602923

Date Published: 15th May 2008

Projects: A3.3: Hepatocyte polarity, HepatoSys

Journal: Gastroenterology

Citation: Gastroenterology 135(2): 642-59

Scales: Not specified

Abstract (Expand)

The profibrogenic role of transforming growth factor (TGF)-beta in liver has mostly been attributed to hepatic stellate cell activation and excess matrix synthesis. Hepatocytes are believed to contribute ...

Created: 24th Feb 2012 at 17:08   Last updated: 24th Oct 2013 at 16:22


 

SYCAMORE--a systems biology computational analysis and modeling research environment


Authors: Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca Wade, Ursula Kummer

PubMed ID: 18463116

Date Published: 7th May 2008

Projects: F3: Kinetic data handling

Journal: Bioinformatics

Citation: Bioinformatics 24(12): 1463-4

Scales: Not specified

Abstract (Expand)

SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model ...

Created: 11th Nov 2010 at 18:27   Last updated: 24th Oct 2013 at 16:22


 

Recurrent design patterns in the feedback regulation of the mammalian signalling network


Authors: Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff, Nils Blüthgen

PubMed ID: 18463614

Date Published: 6th May 2008

Projects: HepatoSys

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 4: 190

Scales: Not specified

Abstract (Expand)

Biochemical networks are characterized by recurrent patterns and motifs, but the design principles underlying the dynamics of the mammalian intracellular signalling network remain unclear. We systematically ...

Created: 11th Sep 2012 at 13:02   Last updated: 24th Oct 2013 at 16:22


 

webPIPSA: a web server for the comparison of protein interaction properties


Authors: Stefan Richter, Anne Wenzel, Matthias Stein, Razif R Gabdoulline, Rebecca C Wade

PubMed ID: 18420653

Date Published: 17th Apr 2008

Projects: No Projects

Journal: Nucleic Acids Res.

Citation: Nucleic Acids Res. 36(Web Server issue): W276-80

Scales: Not specified

Abstract (Expand)

Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular ...

Created: 31st Oct 2012 at 14:11   Last updated: 24th Oct 2013 at 16:22


 

Characterizing the N-terminal processing motif of MHC class I ligands


Authors: Mark M Schatz, Björn Peters, Nadja Akkad, Nina Ullrich, Alejandra Nacarino Martinez, Oliver Carroll, Sascha Bulik, Hans-Georg Rammensee, Peter van Endert, Hermann-Georg Holzhütter, Stefan Tenzer, Hansjörg Schild

PubMed ID: 18292545

Date Published: 23rd Feb 2008

Projects: No Projects

Journal: J. Immunol.

Citation: J. Immunol. 180(5): 3210-7

Scales: Not specified

Abstract (Expand)

Most peptide ligands presented by MHC class I molecules are the product of an intracellular pathway comprising protein breakdown in the cytosol, transport into the endoplasmic reticulum, and successive ...

Created: 4th Jan 2013 at 11:07   Last updated: 24th Oct 2013 at 16:22


 

Modeling the in vitro 20S proteasome activity: the effect of PA28-alphabeta and of the sequence and length of polypeptides on the degradation kinetics


Authors: Michele Mishto, Fabio Luciani, Hermann-Georg Holzhütter, Elena Bellavista, Aurelia Santoro, Kathrin Textoris-Taube, Claudio Franceschi, Peter M Kloetzel, Alexey Zaikin

PubMed ID: 18336834

Date Published: 8th Feb 2008

Projects: No Projects

Journal: J. Mol. Biol.

Citation: J. Mol. Biol. 377(5): 1607-17

Scales: Not specified

Abstract (Expand)

Proteasomes are fundamental for the degradation of intracellular proteins, having a key role in several important metabolic and signaling pathways, in the cell cycle and in antigen presentation. In ...

Created: 4th Jan 2013 at 13:01   Last updated: 24th Oct 2013 at 16:22


 

A mesoscale model of G1/S phase transition in liver regeneration


Authors: Anuradha Chauhan, Stefan Legewie, Pål O Westermark, Stephan Lorenzen, Hanspeter Herzel

PubMed ID: 18339403

Date Published: 1st Feb 2008

Projects: HepatoSys

Journal: J. Theor. Biol.

Citation: J. Theor. Biol. 252(3): 465-73

Scales: Not specified

Abstract (Expand)

The liver regenerates and maintains its function and size after injury by counterbalancing cell death with compensatory cell division. During liver regeneration, injured sites release cytokines, which ...

Created: 11th Sep 2012 at 13:05   Last updated: 24th Oct 2013 at 16:22


 

Calculating enzyme kinetic parameters from protein structures


Authors: Matthias Stein, Razif R Gabdoulline, Rebecca C Wade

PubMed ID: 18208384

Date Published: 23rd Jan 2008

Projects: HepatoSys

Journal: Biochem. Soc. Trans.

Citation: Biochem. Soc. Trans. 36(Pt 1): 51-4

Scales: Cell

Abstract (Expand)

Enzyme kinetic parameters can differ between different species and isoenzymes for the same catalysed reaction. Computational approaches to calculate enzymatic kinetic parameters from the three-dimensional ...

Created: 31st Oct 2012 at 14:12   Last updated: 24th Oct 2013 at 16:23


 

Web-links as a means to document annotated sequence and 3D-structure alignments in systems biology


Authors: Chirstoph Gille, Andreas Hoppe, Herman-Georg Holzhütter

PubMed ID: 19425142

Date Published: 2008

Projects: F2: The Liver Knowledge Base (LKB)

Journal: Genome Inform

Citation: Genome Inform 20: 277-84

Scales: Not specified

Abstract (Expand)

Reconstructed biological networks are the essence of knowledge originating from experiments, scientific literature, databases and modeling. Proteins are the major players in biological networks. If the ...

Created: 4th Jan 2013 at 10:55   Last updated: 24th Oct 2013 at 16:23


 

Computer aided optimization of carbon atom labeling for tracer experiments


Authors: Benjamin Sefa Menküc, Christoph Gille, Hermann-Georg Holzhütter

PubMed ID: 19425141

Date Published: 2008

Projects: No Projects

Journal: Genome Inform

Citation: Genome Inform 20: 270-6

Scales: Not specified

Abstract (Expand)

Isotopomer tracer experiments are indispensable for the determination of flux rates in already known pathways as well as for the identification of new pathways. The information gained from such experiments ...

Created: 4th Jan 2013 at 13:01   Last updated: 24th Oct 2013 at 16:23


 

Inhibition of GSK3 differentially modulates NF-kappaB, CREB, AP-1 and beta-catenin signaling in hepatocytes, but fails to promote TNF-alpha-induced apoptosis


Authors: Frank Götschel, Claudia Kern, Simona Lang, Titus Sparna, Cordula Markmann, Joseph Schwager, Sabine McNelly, Fritz von Weizsäcker, Stefan Laufer, Andreas Hecht, Irmgard Merfort

PubMed ID: 18261723

Date Published: 31st Dec 2007

Projects: HepatoSys

Journal: Exp. Cell Res.

Citation: Exp. Cell Res. 314(6): 1351-66

Scales: Cell

Abstract (Expand)

Glycogen synthase kinase-3 (GSK-3) is known to modulate cell survival and apoptosis through multiple intracellular signaling pathways. However, its hepatoprotective function and its role in activation ...

Created: 30th Aug 2012 at 12:33   Last updated: 24th Oct 2013 at 16:23


 

On the use of PIPSA to guide target-selective drug design


Authors: Stefan Henrich, Stefan Richter, Rebecca C Wade

PubMed ID: 18061917

Date Published: 7th Dec 2007

Projects: HepatoSys

Journal: ChemMedChem

Citation: ChemMedChem 3(3): 413-7

Scales: Not specified

Abstract:

Not specified

Created: 31st Oct 2012 at 14:20   Last updated: 24th Oct 2013 at 16:23


 

Dynamic pathway modeling: feasibility analysis and optimal experimental design


Authors: Thomas Maiwald, Clemens Kreutz, Andrea C Pfeifer, Sebastian Bohl, Ursula Klingmüller, Jens Timmer

PubMed ID: 18033750

Date Published: 24th Nov 2007

Projects: HepatoSys

Journal: Ann. N. Y. Acad. Sci.

Citation: Ann. N. Y. Acad. Sci. 1115: 212-20

Scales: Not specified

Abstract (Expand)

A major challenge in systems biology is to evaluate the feasibility of a biological research project prior to its realization. Since experiments are animals-, cost- and time-consuming, approaches ...

Created: 17th Aug 2012 at 10:21   Last updated: 24th Oct 2013 at 16:23


 

qPIPSA: relating enzymatic kinetic parameters and interaction fields


Authors: Razif R Gabdoulline, Matthias Stein, Rebecca C Wade

PubMed ID: 17919319

Date Published: 5th Oct 2007

Projects: HepatoSys

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 8: 373

Scales: Not specified

Abstract (Expand)

The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore ...

Created: 31st Oct 2012 at 14:14   Last updated: 24th Oct 2013 at 16:23


 

A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling


Authors: Carola Huthmacher, Christoph Gille, Hermann-Georg Holzhütter

PubMed ID: 17988690

Date Published: 5th Oct 2007

Projects: No Projects

Journal: J. Theor. Biol.

Citation: J. Theor. Biol. 252(3): 456-64

Scales: Not specified

Abstract (Expand)

Protein-protein interactions are operative at almost every level of cell structure and function as, for example, formation of sub-cellular organelles, packaging of chromatin, muscle contraction, signal ...

Created: 4th Jan 2013 at 13:00   Last updated: 24th Oct 2013 at 16:23


 

Storing and annotating of kinetic data


Authors: Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig

PubMed ID: 17822389

Date Published: 14th Sep 2007

Projects: F3: Kinetic data handling

Journal: In Silico Biol. (Gedrukt)

Citation: In Silico Biol. (Gedrukt) 7(2 Suppl): S37-44

Scales: Not specified

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such ...

Created: 5th Nov 2010 at 15:52   Last updated: 24th Oct 2013 at 16:23


 

Reduced modeling of signal transduction - a modular approach


Authors: Markus Koschorreck, Holger Conzelmann, Sybille Ebert, Michael Ederer, Ernst Dieter Gilles

PubMed ID: 17854494

Date Published: 13th Sep 2007

Projects: No Projects

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 8: 336

Scales: Not specified

Abstract (Expand)

Combinatorial complexity is a challenging problem in detailed and mechanistic mathematical modeling of signal transduction. This subject has been discussed intensively and a lot of progress has been ...

Created: 30th Oct 2012 at 09:04   Last updated: 24th Oct 2013 at 16:23


 

An error model for protein quantification


Authors: C Kreutz, M M Bartolome Rodriguez, T Maiwald, M Seidl, H E Blum, L Mohr, J Timmer

PubMed ID: 17768165

Date Published: 3rd Sep 2007

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes

Journal: Bioinformatics

Citation: Bioinformatics 23(20): 2747-53

Scales: Not specified

Abstract (Expand)

MOTIVATION: Quantitative experimental data is the critical bottleneck in the modeling of dynamic cellular processes in systems biology. Here, we present statistical approaches improving reproducibility ...

Created: 10th Dec 2010 at 12:12   Last updated: 24th Oct 2013 at 16:23


 

Data-based identifiability analysis of non-linear dynamical models


Authors: S Hengl, C Kreutz, J Timmer, T Maiwald

PubMed ID: 17660526

Date Published: 28th Jul 2007

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 23(19): 2612-8

Scales: Not specified

Abstract (Expand)

MOTIVATION: Mathematical modelling of biological systems is becoming a standard approach to investigate complex dynamic, non-linear interaction mechanisms in cellular processes. However, models may ...

Created: 17th Aug 2012 at 10:25   Last updated: 24th Oct 2013 at 16:23


 

Data-based mathematical modeling of vectorial transport across double-transfected polarized cells


Authors: Kilian Bartholomé, Maria Rius, Katrin Letschert, Daniela Keller, Jens Timmer, Dietrich Keppler

PubMed ID: 17548463

Date Published: 4th Jun 2007

Projects: HepatoSys

Journal: Drug Metab. Dispos.

Citation: Drug Metab. Dispos. 35(9): 1476-81

Scales: Not specified

Abstract (Expand)

Vectorial transport of endogenous small molecules, toxins, and drugs across polarized epithelial cells contributes to their half-life in the organism and to detoxification. To study vectorial transport ...

Created: 25th Jul 2011 at 16:51   Last updated: 24th Oct 2013 at 16:23


 

Competing docking interactions can bring about bistability in the MAPK cascade


Authors: Stefan Legewie, Birgit Schoeberl, Nils Blüthgen, Hanspeter Herzel

PubMed ID: 17526574

Date Published: 25th May 2007

Projects: HepatoSys

Journal: Biophys. J.

Citation: Biophys. J. 93(7): 2279-88

Scales: Not specified

Abstract (Expand)

Mitogen-activated protein kinases are crucial regulators of various cell fate decisions including proliferation, differentiation, and apoptosis. Depending on the cellular context, the Raf-Mek-Erk ...

Created: 11th Sep 2012 at 13:07   Last updated: 24th Oct 2013 at 16:23


 

Activation of NF-kappaB by IL-1beta blocks IL-6-induced sustained STAT3 activation and STAT3-dependent gene expression of the human gamma-fibrinogen gene


Authors: Ute Albrecht, Xiangping Yang, Rosanna Asselta, Verena Keitel, Maria Luisa Tenchini, Stephan Ludwig, Peter C Heinrich, Dieter Häussinger, Fred Schaper, Johannes G Bode

PubMed ID: 17543500

Date Published: 1st May 2007

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato..., A2.4: Linking signalling pathways regulating liver regeneration and orga..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Cell. Signal.

Citation: Cell. Signal. 19(9): 1866-78

Scales: Not specified

Abstract (Expand)

Despite the essential role of the fibrinogen gamma-chain as a blood clotting factor, the fibrinogen gamma-chain contains a number of interaction sites to recruit other factors such as leukocytes important ...

Created: 31st Aug 2012 at 11:47   Last updated: 24th Oct 2013 at 16:23


 

Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting


Authors: M Peifer, J Timmer

PubMed ID: 17441551

Date Published: 20th Apr 2007

Projects: HepatoSys

Journal: IET Syst Biol

Citation: IET Syst Biol 1(2): 78-88

Scales: Not specified

Abstract (Expand)

In silico investigations by simulating dynamical models of biochemical processes play an important role in systems biology. If the parameters of a model are unknown, results from simulation studies can ...

Created: 17th Aug 2012 at 10:29   Last updated: 24th Oct 2013 at 16:23


 

Bridging from molecular simulation to biochemical networks


Authors: Matthias Stein, Razif R Gabdoulline, Rebecca C Wade

PubMed ID: 17395455

Date Published: 28th Mar 2007

Projects: HepatoSys

Journal: Curr. Opin. Struct. Biol.

Citation: Curr. Opin. Struct. Biol. 17(2): 166-72

Scales: Not specified

Abstract (Expand)

How can we make the connection between the three-dimensional structures of individual proteins and understanding how complex biological systems involving many proteins work? The modelling and simulation ...

Created: 31st Oct 2012 at 14:15   Last updated: 24th Oct 2013 at 16:23


 

COMBINE analysis of the specificity of binding of Ras proteins to their effectors


Authors: Sanja Tomić, Branimir Bertosa, Ting Wang, Rebecca C Wade

PubMed ID: 17295314

Date Published: 14th Feb 2007

Projects: HepatoSys

Journal: Proteins

Citation: Proteins 67(2): 435-47

Scales: Not specified

Abstract (Expand)

The small guanosine triphosphate (GTP)-binding proteins of the Ras family are involved in many cellular pathways leading to cell growth, differentiation, and apoptosis. Understanding the interaction ...

Created: 31st Oct 2012 at 14:17   Last updated: 24th Oct 2013 at 16:23


 

Integration of SABIO-RK in workbenches for kinetic model design


Authors: Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig, Isabel Rojas

DOI: 10.1186/1752-0509-1-S1-P4

Date Published: 2007

Projects: F3: Kinetic data handling

Journal: BMC Syst Biol

Citation: BMC Syst Biol 1(Suppl 1) : P4

Scales: Not specified

Abstract:

Not specified

Created: 11th Nov 2010 at 18:36   Last updated: 24th Oct 2013 at 16:23


 

SABIO-RK: a database for biochemical reactions and their kinetics


Authors: Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig

DOI: 10.1186/1752-0509-1-S1-S6

Date Published: 2007

Projects: F3: Kinetic data handling

Journal: BMC Syst Biol

Citation: BMC Syst Biol 1(Suppl 1) : S6

Scales: Not specified

Abstract:

Not specified

Created: 1st Dec 2010 at 13:43   Last updated: 24th Oct 2013 at 16:23


 

Protein Domains of GTPases on Membranes: Do They Rely on Turing’s Mechanism?


Authors: Lutz Brusch, Perla Del Conte-Zerial, Yannis Kalaidzidis, Jochen Rink, Bianca Habermann, Marino Zerial, Andreas Deutsch

DOI: 10.1007/978-0-8176-4558-8_4

Date Published: 2007

Projects: HepatoSys

Book: Mathematical Modeling of Biological Systems, Volume I

Citation: Modeling and Simulation in Science, Engineering and Technology : 33

Scales: Cell

Abstract (Expand)

We evaluate different mechanisms for spatial domain formation of guanosine triphosphatases (GTPases) on cellular membranes. A kinetic model of the basic guanine-nucleotide cycle common to all GTPases ...

Created: 25th Jul 2011 at 17:22   Last updated: 24th Oct 2013 at 16:23


 

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways


Authors: U Klingmüller, A Bauer, S Bohl, P J Nickel, K Breitkopf, S Dooley, S Zellmer, C Kern, I Merfort, T Sparna, J Donauer, G Walz, M Geyer, C Kreutz, M Hermes, F Götschel, A Hecht, D Walter, L Egger, K Neubert, C Borner, M Brulport, W Schormann, C Sauer, F Baumann, R Preiss, S MacNelly, P Godoy, E Wiercinska, L Ciuclan, J Edelmann, K Zeilinger, M Heinrich, U M Zanger, R Gebhardt, T Maiwald, R Heinrich, J Timmer, F von Weizsäcker, J G Hengstler

PubMed ID: 17186705

Date Published: 26th Dec 2006

Projects: HepatoSys

Journal: Syst Biol (Stevenage)

Citation: Syst Biol (Stevenage) 153(6): 433-47

Scales: Cell

Abstract (Expand)

Complex cellular networks regulate regeneration, detoxification and differentiation of hepatocytes. By combining experimental data with mathematical modelling, systems biology holds great promises to ...

Created: 30th Aug 2012 at 12:39   Last updated: 24th Oct 2013 at 16:24


 

COPASI--a COmplex PAthway SImulator


Authors: Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer

PubMed ID: 17032683

Date Published: 10th Oct 2006

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 22(24): 3067-74

Scales: Not specified

Abstract (Expand)

Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling ...

Created: 11th Sep 2012 at 13:26   Last updated: 24th Oct 2013 at 16:24


 

Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability


Authors: Stefan Legewie, Nils Blüthgen, Hanspeter Herzel

PubMed ID: 16978046

Date Published: 28th Jul 2006

Projects: HepatoSys

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 2(9): e120

Scales: Not specified

Abstract (Expand)

The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether cytochrome ...

Created: 11th Sep 2012 at 13:08   Last updated: 24th Oct 2013 at 16:24


 

Effects of sequestration on signal transduction cascades


Authors: Nils Blüthgen, Frank J Bruggeman, Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff, Boris N Kholodenko

PubMed ID: 16478465

Date Published: 16th Feb 2006

Projects: HepatoSys

Journal: FEBS J.

Citation: FEBS J. 273(5): 895-906

Scales: Not specified

Abstract (Expand)

The building blocks of most signal transduction pathways are pairs of enzymes, such as kinases and phosphatases, that control the activity of protein targets by covalent modification. It has previously ...

Created: 11th Sep 2012 at 13:10   Last updated: 24th Oct 2013 at 16:24


 

SABIO-RK: Integration and Curation of Reaction Kinetics Data


Authors: Ulrike Wittig, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Stefanie Anstein, Jasmin Saric, Isabel Rojas

DOI: 10.1007/11799511_9

Date Published: 2006

Projects: F3: Kinetic data handling

Book: Data Integration in the Life Sciences

Citation: Lecture Notes in Computer Science 4075 : 94

Scales: Not specified

Abstract (Expand)

Simulating networks of biochemical reactions require reliable kinetic data. In order to facilitate the access to such kinetic data we have developed SABIO-RK, a curated database with information about ...

Created: 26th Jul 2011 at 18:33   Last updated: 24th Oct 2013 at 16:24


 

Computational processing and error reduction strategies for standardized quantitative data in biological networks


Authors: Marcel Schilling, Thomas Maiwald, Sebastian Bohl, Markus Kollmann, Clemens Kreutz, Jens Timmer, Ursula Klingmüller

PubMed ID: 16336276

Date Published: 13th Dec 2005

Projects: HepatoSys

Journal: FEBS J.

Citation: FEBS J. 272(24): 6400-11

Scales: Not specified

Abstract (Expand)

High-quality quantitative data generated under standardized conditions is critical for understanding dynamic cellular processes. We report strategies for error reduction, and algorithms for automated ...

Created: 23rd Aug 2012 at 13:22   Last updated: 24th Oct 2013 at 16:24


 

Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction


Authors: Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel

PubMed ID: 16261195

Date Published: 28th Oct 2005

Projects: HepatoSys

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 1(5): e54

Scales: Not specified

Abstract (Expand)

Cellular signaling networks are subject to transcriptional and proteolytic regulation under both physiological and pathological conditions. For example, the expression of proteins subject to covalent ...

Created: 11th Sep 2012 at 13:11   Last updated: 24th Oct 2013 at 16:24


 

Quantitative analysis of ultrasensitive responses


Authors: Stefan Legewie, Nils Blüthgen, Hanspeter Herzel

PubMed ID: 16098190

Date Published: 16th Aug 2005

Projects: HepatoSys

Journal: FEBS J.

Citation: FEBS J. 272(16): 4071-9

Scales: Not specified

Abstract (Expand)

Ultrasensitive responses are common in cellular information transfer because they allow cells to decode extracellular stimuli in an all-or-none manner. Biochemical responses are usually analyzed by ...

Created: 11th Sep 2012 at 13:13   Last updated: 24th Oct 2013 at 16:24


 

Digitoxin metabolism by rat liver microsomes


Authors: A. Schmoldt, H. F. Benthe, G. Haberland

PubMed ID: 10

Date Published: 1st Sep 1975

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: Biochem Pharmacol

Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.

Scales: Not specified

Abstract:

Not specified

Created: 17th Nov 2015 at 12:27


 

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study


Authors: J. M. Villaveces, R. C. Jimenez, P. Porras, N. Del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann, H. Hermjakob

PubMed ID: 25652942

Date Published: No date defined

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Database (Oxford)

Citation: Database (Oxford). 2015 Feb 4;2015. pii: bau131. doi: 10.1093/database/bau131. Print 2015.

Scales: Not specified

Abstract (Expand)

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to ...

Created: 18th Dec 2015 at 12:58



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