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

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

(2013) Carito Guziolowski et al.   BIOINFORMATICS

Precise generation of systems biology models from KEGG pathways

(2013) Clemens Wrzodek et al.   BMC Systems Biology

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

(2013) Finja Büchel et al.   BMC Systems Biology

A Cell Simulator Platform: The Cell Collective

(2013) T Helikar et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

A Comprehensive, Multi-Scale Dynamical Model of ErbB Receptor Signal Transduction in Human Mammary Epithelial Cells

(2013) Tomáš Helikar et al.   PLoS One

Boolean network-based model of the Bcl-2 family mediated MOMP regulation

(2013) Tomas Tokar et al.   Theoretical Biology and Medical Modelling

Integrating literature-constrained and data-driven inference of signalling networks

(2012) Federica Eduati et al.   BIOINFORMATICS

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

The Cell Collective: Toward an open and collaborative approach to systems biology

(2012) Tomáš Helikar et al.   BMC Systems Biology

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

(2012) Alex Madrahimov et al.   BULLETIN OF MATHEMATICAL BIOLOGY

The TOL network ofPseudomonas putidamt-2 processes multiple environmental inputs into a narrowresponse space

(2012) Rafael Silva-Rocha et al.   ENVIRONMENTAL MICROBIOLOGY

HSM — a hybrid system based approach for modelling intracellular networks

(2012) Alvis Brazma et al.   GENE

Digital clocks: simple Boolean models can quantitatively describe circadian systems

(2012) O. E. Akman et al.   Journal of the Royal Society Interface

State–time spectrum of signal transduction logic models

(2012) Aidan MacNamara et al.   PHYSICAL BIOLOGY

A Boolean Model of the Cardiac Gene Regulatory Network Determining First and Second Heart Field Identity

(2012) Franziska Herrmann et al.   PLoS One

Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models

(2012) Tomáš Helikar et al.   PLoS One

Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle

(2012) Robert G. Todd et al.   PLoS One

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions

(2011) Melody K. Morris et al.   Biotechnology Journal

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

(2011) Dagmar Waltemath et al.   BMC Systems Biology

Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models

(2011) J. Saez-Rodriguez et al.   CANCER RESEARCH

Information Routing Driven by Background Chatter in a Signaling Network

(2011) Núria Domedel-Puig et al.   PLoS Computational Biology

Minimum Information About a Simulation Experiment (MIASE)

(2011) Dagmar Waltemath et al.   PLoS Computational Biology

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

(2010) Christoph Müssel et al.   BIOINFORMATICS

Snoopy--a unifying Petri net framework to investigate biomolecular networks

(2010) C. Rohr et al.   BIOINFORMATICS

Attractor analysis of asynchronous Boolean models of signal transduction networks

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

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational 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

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks

(2009) J. Zheng et al.   BIOINFORMATICS

Logical modelling of regulatory networks with GINsim 2.3

(2009) A. Naldi et al.   BIOSYSTEMS

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

(2009) Tomáš Helikar et al.   BMC Systems Biology

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

(2009) Özgür Sahin et al.   BMC Systems Biology

Modular logical modelling of the budding yeast cell cycle

(2009) Adrien Fauré et al.   Molecular BioSystems

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

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

Temporal logic patterns for querying dynamic models of cellular interaction networks

(2008) P. T. Monteiro et al.   BIOINFORMATICS

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

(2008) A. Gonzalez et al.   BIOINFORMATICS

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module

(2008) Lucas Sanchez et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast

(2008) Maria I. Davidich et al.   PLoS One

Emergent decision-making in biological signal transduction networks

(2008) T. Helikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA