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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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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