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

Preservation of dynamic properties in qualitative modeling frameworks for gene regulatory networks

(2013) Shahrad Jamshidi et al.   BIOSYSTEMS

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

(2012) Jérémy Huard et al.   FEBS Journal

State–time spectrum of signal transduction logic models

(2012) Aidan MacNamara et al.   PHYSICAL BIOLOGY

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Elementary signaling modes predict the essentiality of signal transduction network components

(2011) Rui-Sheng Wang et al.   BMC Systems Biology

Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

(2011) Oliver Hädicke et al.   BMC Systems Biology

Multistationarity in mass action networks with applications to ERK activation

(2011) Carsten Conradi et al.   JOURNAL OF MATHEMATICAL BIOLOGY

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

(2011) Anke Ryll et al.   Molecular BioSystems

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation

(2011) Michelle C. Mendoza et al.   TRENDS IN BIOCHEMICAL SCIENCES

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

(2011) Melody K. Morris et al.   PLoS Computational Biology

Comparing Boolean and Piecewise Affine Differential Models for Genetic Networks

(2010) Madalena Chaves et al.   ACTA BIOTHEORETICA

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks

(2010) Regina Samaga et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Attractor analysis of asynchronous Boolean models of signal transduction networks

(2010) Assieh Saadatpour et al.   JOURNAL OF THEORETICAL BIOLOGY

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

(2010) Aurélien Naldi et al.   PLoS Computational Biology

A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development

(2010) Clare E. Giacomantonio et al.   PLoS Computational Biology

ProMoT: modular modeling for systems biology

(2009) Sebastian Mirschel et al.   BIOINFORMATICS

On the robustness of update schedules in Boolean networks

(2009) J. Aracena et al.   BIOSYSTEMS

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

(2009) Carito Guziolowski et al.   BMC GENOMICS

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

(2009) Tobias S Christensen et al.   BMC Systems Biology

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

(2009) Tomáš Helikar et al.   BMC Systems Biology

Recent Advances in Intervention in Markovian Regulatory Networks

(2009) Babak Faryabi et al.   CURRENT GENOMICS

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

(2009) Regina Samaga et al.   PLoS Computational Biology

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling

(2009) Bree B. Aldridge et al.   PLoS Computational Biology

Hypergraphs and Cellular Networks

(2009) Steffen Klamt et al.   PLoS Computational Biology

ON/OFF and Beyond - A Boolean Model of Apoptosis

(2009) Rebekka Schlatter et al.   PLoS Computational Biology

Network modeling of signal transduction: establishing the global view

(2008) Hans A. Kestler et al.   BIOESSAYS

Synchronous versus asynchronous modeling of gene regulatory networks

(2008) A. Garg et al.   BIOINFORMATICS

Constraint-based network model of pathogen-immune system interactions

(2008) J. Thakar et al.   Journal of the Royal Society Interface

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Network model of survival signaling in large granular lymphocyte leukemia

(2008) R. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feedback Loops Shape Cellular Signals in Space and Time

(2008) O. Brandman et al.   SCIENCE

Fault Diagnosis Engineering of Digital Circuits Can Identify Vulnerable Molecules in Complex Cellular Pathways

(2008) A. Abdi et al.   Science Signaling