This is an archive listing of all publications by groups within the Virtual Liver Network, or through collaborations that have an acknowledged involvement of members of the VLN, arranged as an alphabetical listing by title.

0-9
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
#

4-Aminoethylamino-emodin--a novel potent inhibitor of GSK-3beta--acts as an insulin-sensitizer avoiding downstream effects of activated beta-catenin

Automating Mathematical Modeling of Biochemical Reaction Networks

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

Atypical protein kinase C zeta exhibits a proapoptotic function in ovarian cancer

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

Applications and trends in systems biology in biochemistry

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

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

Analysis of drug metabolism activities in a miniaturized liver cell bioreactor for use in pharmacological studies

Analysis of an apoptotic core model focused on experimental design using artificial data

Analysis and Algorithmic Generation of Hepatic Vascular Systems

An update of MALDI-TOF mass spectrometry in lipid research

An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes

An error model for protein quantification

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

Algorithmically generated rodent hepatic vascular trees in arbitrary detail

Adiponectin upregulates hepatocyte CMKLR1 which is reduced in human fatty liver

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

Addressing parameter identifiability by model-based experimentation

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

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

Accessible methods for the dynamic time-scale decomposition of biochemical systems

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

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

ABCB1 single-nucleotide polymorphisms determine tacrolimus response in patients with ulcerative colitis

A variational approach to parameter estimation in ordinary differential equations

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

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

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

A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes

A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes

A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes

A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts

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

A simple TLC-MALDI method to monitor oxidation products of phosphatidylcholines and -ethanolamines

A rapid screening assay to search for phosphorylated proteins in tissue extracts

A Quick Guide for Building a Successful Bioinformatics Community

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

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

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

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

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

A minimal circadian clock model

A methionine-choline-deficient diet elicits NASH in the immunodeficient mouse featuring a model for hepatic cell transplantation

A mesoscale model of G1/S phase transition in liver regeneration

A Mechanistic, Model-Based Approach to Safety Assessment in Clinical Development

A Lattice-gas Cellular Automaton Model for in Vitro Sprouting Angiogenesis

A hypothetical model of cargo-selective rab recruitment during organelle maturation

A General Theoretical Framework to Infer Endosomal Network Dynamics from Quantitative Image Analysis

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

A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles

A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling

A comparison of sampling strategies for histological image analysis

A community-driven global reconstruction of human metabolism

A cell-based simulation software for multi-cellular systems

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

Bridging from molecular simulation to biochemical networks

BowTieBuilder: modeling signal transduction pathways

Bone morphogenetic protein-9 (BMP-9) induces epithelial to mesenchymal transition (EMT) in hepatocellular carcinoma cells

Biochemical network-based drug-target prediction

Biggest challenges in bioinformatics

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

CySBML: a Cytoscape plugin for SBML

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields

COPASI--a COmplex PAthway SImulator

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

Controlled vocabularies and semantics in systems biology

Concurrent epigenetic silencing of wnt/β-catenin pathway inhibitor genes in B cell chronic lymphocytic leukaemia

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

Computing combinatorial intervention strategies and failure modes in signaling networks

Computer aided optimization of carbon atom labeling for tracer experiments

Computational processing and error reduction strategies for standardized quantitative data in biological networks

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

Computational lipidology: predicting lipoprotein density profiles in human blood plasma

Computational Approaches for Studying Drug Binding Kinetics

Comprehensive estimation of input signals and dynamics in biochemical reaction networks

Competing docking interactions can bring about bistability in the MAPK cascade

Comparison of various approaches to calculating the optimal hematocrit in vertebrates

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

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

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

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

COMBINE analysis of the specificity of binding of Ras proteins to their effectors

Clinical Translation in the Virtual Liver Network

Choline-releasing glycerophosphodiesterase EDI3 drives tumor cell migration and metastasis

ChemSpot: a hybrid system for chemical named entity recognition

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

Characterizing the N-terminal processing motif of MHC class I ligands

Challenges for an enzymatic reaction kinetics database

Central energy metabolism remains robust in acute steatotic hepatocytes challenged by a high free fatty acid load

Cellular ERK Phospho-form Profiles with Conserved Preference for a Switch-like Pattern

Cell therapeutic options in liver diseases: cell types, medical devices and regulatory issues

Caveolin-1 abrogates TGF-β mediated hepatocyte apoptosis

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

Cause and cure of sloppiness in ordinary differential equation models

Caspase-8 activity has an essential role in CD95/Fas-mediated MAPK activation

Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes

CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism

Calculating enzyme kinetic parameters from protein structures

Dysregulated serum response factor triggers formation of hepatocellular carcinoma

Dynamics of VEGF matrix-retention in vascular network patterning

Dynamics and feedback loops in the transforming growth factor β signaling pathway

Dynamical modeling and multi-experiment fitting with PottersWheel

Dynamic pathway modeling: feasibility analysis and optimal experimental design

Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets

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

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

Does hepatic steatosis affect drug metabolizing enzymes in the liver

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

DNA methylation is associated with downregulation of the organic cation transporter OCT1 (SLC22A1) in human hepatocellular carcinoma

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

Distinct dedifferentiation processes affect caveolin-1 expression in hepatocytes

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

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

Digitoxin metabolism by rat liver microsomes

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

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

Development of Human Membrane Transporters: Drug Disposition and Pharmacogenetics

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

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

Detecting and investigating substrate cycles in a genome-scale human metabolic network

Decreased levels of active SMAD2 correlate with poor prognosis in gastric cancer

Data-based mathematical modeling of vectorial transport across double-transfected polarized cells

Data-based identifiability analysis of non-linear dynamical models

Data extraction for the reaction kinetics database SABIO-RK

Data collection as a barrier to personalized medicine

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

Expression of organic cation transporters OCT1 (SLC22A1) and OCT3 (SLC22A3) is affected by genetic factors and cholestasis in human liver

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

Experimental design for parameter estimation of gene regulatory networks

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

Evolutionary game theory: molecules as players

Evolutionary game theory: cells as players

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

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

Estimation of gene induction enables a relevance-based ranking of gene sets

Estimating Dose Painting Effects in Radiotherapy: A Mathematical Model

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

Erythropoietin-receptor gene regulation in neuronal cells

Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes

Enzyme kinetics informatics: from instrument to browser

Enzymatic features of the glucose metabolism in tumor cells

Enabling multiscale modeling in systems medicine

Effects of sequestration on signal transduction cascades

Functional characterization of protein variants of the human multidrug transporter ABCC2 by a novel targeted expression system in fibrosarcoma cells

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

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

Fluxviz - cytoscape plug-in for visualization of flux distributions in networks

Fluorescence based cell counting in collagen monolayer cultures of primary hepatocytes

Finding one's way in proteomics: a protein species nomenclature

FGF acts as a co-transmitter through adenosine A(2A) receptor to regulate synaptic plasticity

Fast and accurate identification of fat droplets in histological images

FASIMU: flexible software for flux-balance computation series in large metabolic networks

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

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

Glucocorticoids increase interleukin-6-dependent gene induction by interfering with the expression of the suppressor of cytokine signaling 3 feedback inhibitor

Germans cook up liver project

Genomics of ADME gene expression: mapping expression quantitative trait loci relevant for absorption, distribution, metabolism and excretion of drugs in human liver

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

Genome-wide comparison between IL-17 and combined TNF-alpha/IL-17 induced genes in primary murine hepatocytes

Genetics, epigenetics and regulation of drug metabolizing cytochrome P450 enzymes

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

Genetic and functional identification of the likely causative variant for cholesterol gallstone disease at the ABCG5/8 lithogenic locus

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

Human pregnane X receptor genotype of the donor but not of the recipient is a risk factor for delayed graft function after renal transplantation

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

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

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

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

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

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

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

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

HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition

High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury

Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration

Heterogeneous expression of suppressor of cytokine signalling 2 (SOCS-2) in liver tissue

Heritability of metoprolol and torsemide pharmacokinetics

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

Hepatocyte-specific Smad7 expression attenuates TGF-beta-mediated fibrogenesis and protects against liver damage

Hepatocyte-specific S100a8 and S100a9 transgene expression in mice causes Cxcl1 induction and systemic neutrophil enrichment

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

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

Hepatic acute phase proteins--regulation by IL-6- and IL-1-type cytokines involving STAT3 and its crosstalk with NF-κB-dependent signaling

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

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

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

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

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

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

Iron regulatory proteins secure mitochondrial iron sufficiency and function

Iron regulatory proteins control a mucosal block to intestinal iron absorption

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

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

Interpretation of non-invasive breath tests using (13)C-labeled substrates--a preliminary report with (13)C-methacetin

Interleukin-22 promotes proliferation of liver stem/progenitor cells in mice and patients with chronic hepatitis B virus infection

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

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

Integration of SABIO-RK in workbenches for kinetic model design

Integration of Boolean models exemplified on hepatocyte signal transduction

Integration of Boolean models exemplified on hepatocyte signal transduction

Integrating Cellular Metabolism into a Multiscale Whole-Body Model

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

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

Insulin/IGF signaling drives cell proliferation in part via Yorkie/YAP

Inhibition of GSK3 differentially modulates NF-kappaB, CREB, AP-1 and beta-catenin signaling in hepatocytes, but fails to promote TNF-alpha-induced apoptosis

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

Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization

Inferring statin-induced gene regulatory relationships in primary human hepatocytes

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0

In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems

In silico evidence for gluconeogenesis from fatty acids in humans

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

Implication of hepatic stem cells in functional liver repopulation

Implementation of systems theory in liver cancer research

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

Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice

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

IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities

Identification of RARRES1 as a core regulator in liver fibrosis

Identifiability and observability analysis for experimental design in nonlinear dynamical models

JSBML: a flexible Java library for working with SBML

JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.

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

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

Kinetic Modeling of Human Hepatic Glucose Metabolism in T2DM Predicts Higher Risk of Hypoglycemic Events in Rigorous Insulin Therapy

Kinetic mechanisms for overexpression insensitivity and oncogene cooperation

Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws--a promising method for speeding up the kinetic modelling of complex metabolic networks

KEGGViewer, a BioJS component to visualize KEGG Pathways

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

Low perforin expression of early differentiated HCV-specific CD8+ T cells limits their hepatotoxic potential

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

Lipid analysis by thin-layer chromatography—A review of the current state

Lipid analysis by thin-layer chromatography--a review of the current state

Likelihood based observability analysis and confidence intervals for predictions of dynamic models

LigDig: a web server for querying ligand-protein interactions

libRoadRunner: A High Performance SBML Simulation and Analysis Library

Lessons learned from quantitative dynamical modeling in systems biology

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

Large-scale phosphosite quantification in tissues by a spike-in SILAC method

Large-scale network models of IL-1 and IL-6 signalling and their hepatocellular specification

MYC-regulated genes involved in liver cell dysplasia identified in a transgenic model of liver cancer

Murine hepatic stellate cells veto CD8 T cell activation by a CD54-dependent mechanism

Multiscale mechanistic modeling in pharmaceutical research and development

Multiparametric image analysis reveals role of Caveolin1 in endosomal progression rather than internalization of EGFR

Multidrug and toxin extrusion proteins as transporters of antimicrobial drugs

Multi-Target Regulation by Small RNAs Synchronizes Gene Expression Thresholds and May Enhance Ultrasensitive Behavior

Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model

Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis

Multi-bio and multi-scale systems biology

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

Mouse granzyme K has pro-inflammatory potential

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

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

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

Molecular Interactions between NAFLD and Xenobiotic Metabolism

ModuleMaster: A new tool to decipher transcriptional regulatory networks

Modulation of glutamine metabolism by the PI(3)K-PKB-FOXO network regulates autophagy

Modelling proteasome and proteasome regulator activities

Modeling Wnt/β-Catenin Target Gene Expression in APC and Wnt Gradients Under Wild Type and Mutant Conditions

Modeling the TNFα-Induced Apoptosis Pathway in Hepatocytes

Modeling the in vitro 20S proteasome activity: the effect of PA28-alphabeta and of the sequence and length of polypeptides on the degradation kinetics

Modeling the impact of granular embedding media, and pulling versus pushing cells on growing cell clones

Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection

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

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

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

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

MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases

Metformin and cancer: from the old medicine cabinet to pharmacological pitfalls and prospects

Metannogen: annotation of biological reaction networks

Metabolic Networks

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

Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore�

Mesenchymal stem cell-derived hepatocytes for functional liver replacement

Mesenchymal stem cell-derived hepatocytes for functional liver replacement

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

Membrane identity and GTPase cascades regulated by toggle and cut-out switches

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

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

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

Mathematical modelling of fluid transport and its regulation at multiple scales

Mathematical Modeling of Regenerative Processes

Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability

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

Mammalian MATE (SLC47A) transport proteins: impact on efflux of endogenous substrates and xenobiotics

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

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

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

Normalization And Matching Of Chemical Compound Names

No activation of human PXR by hyperforin-related phloroglucinols

Nicotinic acid inhibits hepatic APOA gene expression: studies in humans and in transgenic mice

Nicotinamide phosphoribosyltransferase (NAMPT/PBEF/visfatin) is constitutively released from human hepatocytes

Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism

Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development

Oxygen consumption rates during three different neuronal activity states in the hippocampal CA3 network

Oxidative changes of lipids monitored by MALDI MS

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

Organic anion transporters and their implications in pharmacotherapy

Organ patterning in the adult stage: the role of Wnt/beta-catenin signaling in liver zonation and beyond

Optimality in the zonation of ammonia detoxification in rodent liver

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

ON/OFF and beyond--a boolean model of apoptosis

On the use of PIPSA to guide target-selective drug design

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

Omics and Drug Response

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

Proton pump inhibitors inhibit metformin uptake by organic cation transporters (OCTs)

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

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

Protein Domains of GTPases on Membranes: Do They Rely on Turing’s Mechanism?

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

Prominent regulatory but weak antigen-presenting cell function of hepatic stellate cells

Profile likelihood in systems biology

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways

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

Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration

Predicting idiosyncratic drug-induced liver injury - some recent advances

Precise generation of systems biology models from KEGG pathways

Practical quantification of necrosis in histological whole-slide images

PPARA: A Novel Genetic Determinant of CYP3A4 In Vitro and In Vivo

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

Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome

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

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

Phenotype and growth behavior of residual β-catenin-positive hepatocytes in livers of β-catenin-deficient mice

Pharmacogenomics: a key component of personalized therapy

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

Pharmacogenomics of Codeine, Morphine, and Morphine-6-Glucuronide: Model-Based Analysis of the Influence of CYP2D6 Activity, UGT2B7 Activity, Renal Impairment, and CYP3A4 Inhibition

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

Pattern-formation mechanisms in motility mutants of Myxococcus xanthus

Pathway-Targeted Pharmacogenomics of CYP1A2 in Human Liver

Pathological implications of cadherin zonation in mouse liver

Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice

Path2Models: large-scale generation of computational models from biochemical pathway maps

Path2Models: large-scale generation of computational models from biochemical pathway maps

Paraoxonase (PON1 and PON3) Polymorphisms: Impact on Liver Expression and Atorvastatin-Lactone Hydrolysis

Parameter Estimation, Metabolic Network Modeling

Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting

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

Quantitative kinetic analysis of BMP2 uptake into cells and its modulation by BMP-antagonists

Quantitative Evaluation and Prediction of Drug Effects and Toxicological Risk Using Mechanistic Multiscale Models

Quantitative analysis of ultrasensitive responses

Quantifying the contribution of the liver to glucose homeostasis: a detailed kinetic model of human hepatic glucose metabolism

Quantification of Hepatic Vascular and Parenchymal Regeneration in Mice

Qualitative translation of relations from BioPAX to SBML qual

qPIPSA: relating enzymatic kinetic parameters and interaction fields

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

Role of ABC transporters in fluoropyrimidine-based chemotherapy response

Rodent animal models for surrogate analysis of cell therapy in acute liver failure

Rodent animal models for surrogate analysis of cell therapy in acute liver failure

Robustness of signal transduction pathways

RNA-binding proteins in Mendelian disease

Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS

Response of sinusoidal mouse liver cells to choline-deficient ethionine-supplemented diet

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

Representative Sinusoids for Hepatic Four-Scale Pharmacokinetics Simulations

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

Reduced modeling of signal transduction - a modular approach

Recurrent design patterns in the feedback regulation of the mammalian signalling network

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

Recent advances in live cell imaging of hepatoma cells

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

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

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

Rab5 is necessary for the biogenesis of the endolysosomal system in vivo

Systems-level interactions between insulin-EGF networks amplify mitogenic signaling

Systems survey of endocytosis by multiparametric image analysis

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

Systems biology: experimental design

Systems Biology of Cell Death in Hepatocytes

Systems Biology of Cell Death in Hepatocytes

Systems analysis of MAPK signal transduction

Systems analysis of iron metabolism: the network of iron pools and fluxes

Systemic iron homeostasis and the iron-responsive element/iron-regulatory protein (IRE/IRP) regulatory network

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

Synchrotron infrared spectroscopic ellipsometry for characterization of biofunctional surfaces

SYCAMORE--a systems biology computational analysis and modeling research environment

Switch from type II to I Fas/CD95 death signaling on in vitro culturing of primary hepatocytes

Sustained submicromolar H2O2 levels induce hepcidin via signal transducer and activator of transcription 3 (STAT3)

Sustained liver regeneration after portal vein embolization --a human molecular pilot study

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

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

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

Storing and annotating of kinetic data

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

Specifications of Standards in Systems and Synthetic Biology

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

Snapshots of protein dynamics and post-translational modifications in one experiment--beta-catenin and its functions

Small RNAs establish delays and temporal thresholds in gene expression

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

SMAD7 controls iron metabolism as a potent inhibitor of hepcidin expression

Smad6 and Smad7 are co-regulated with hepcidin in mouse models of iron overload

SIRT7 oncogenic potential in human hepatocellular carcinoma and its regulation by the tumor suppressors mir-125a-5p and mir-125b

Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics

SFRS10--a splicing factor gene reduced in human obesity

Serum-free culture of primary human hepatocytes in a miniaturized hollow-fibre membrane bioreactor for pharmacological in vitro studies

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

Selective Protection of Human Liver Tissue in TNF-Targeting of Cancers of the Liver by Transient Depletion of Adenosine Triphosphate

SEEK: a systems biology data and model management platform

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

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

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

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

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

SABIO-RK: Integration and Curation of Reaction Kinetics Data

SABIO-RK: Access to Biochemical Reaction Kinetics Data

SABIO-RK: a database for biochemical reactions and their kinetics

SABIO-RK--database for biochemical reaction kinetics

Two to tango: regulation of Mammalian iron metabolism

Tumor necrosis factor α sensitizes primary murine hepatocytes to Fas/CD95-induced apoptosis in a Bim- and Bid-dependent manner

TSSi--an R package for transcription start site identification from 5' mRNA tag data

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

Transcriptional regulators in hepatocarcinogenesis--key integrators of malignant transformation

Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease

Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes

Tracing Fatty Acid Metabolism by Click Chemistry

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

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

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

Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification

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

The virtual liver: state of the art and future perspectives

The virtual liver: a multidisciplinary, multilevel challenge for systems biology

The Virtual Liver Network: systems understanding from bench to bedside

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

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

The Therapeutic Promise of Mesenchymal Stem Cells for Liver Restoration

The systems biology simulation core algorithm

The speciation of the proteome

The promise and challenge of personalized medicine: aging populations, complex diseases, and unmet medical need

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail

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

The macrophage response towards LPS and its control through the p38(MAPK)-STAT3 axis

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice

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

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity

The influence of the chloride currents on action potential firing and volume regulation of excitable cells studied by a kinetic model

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

The generation of hepatocytes from mesenchymal stem cells and engraftment into murine liver

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

The evolution of standards and data management practices in systems biology

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

TGF-β in progression of liver disease

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

Ten Simple Rules for Organizing an Unconference

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

Using Mean Field Theory to Guide Biofunctional Materials Design

Using expression data for quantification of active processes in physiologically based pharmacokinetic modeling

Using Bayesian-PBPK modeling for assessment of inter-individual variability and subgroup stratification

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

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

Uncovering metabolic objectives pursued by changes of enzyme levels

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

Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction

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

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

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

WISP1 is a novel adipokine linked to inflammation in obesity

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

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

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

What mRNA Abundances Can Tell us about Metabolism

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

webSDA: a web server to simulate macromolecular diffusional association

webPIPSA: a web server for the comparison of protein interaction properties

Web-links as a means to document annotated sequence and 3D-structure alignments in systems biology

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

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

Zonated Quantification of Steatosis in an Entire Mouse Liver

[Pharmacogenomics: hype or hope?]