Related references
Note: Only part of the references are listed.Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming
Carito Guziolowski et al.
BIOINFORMATICS (2013)
Precise generation of systems biology models from KEGG pathways
Clemens Wrzodek et al.
BMC SYSTEMS BIOLOGY (2013)
Path2Models: large-scale generation of computational models from biochemical pathway maps
Finja Buechel et al.
BMC SYSTEMS BIOLOGY (2013)
Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle
Alex Madrahimov et al.
BULLETIN OF MATHEMATICAL BIOLOGY (2013)
A Cell Simulator Platform: The Cell Collective
T. Helikar et al.
CLINICAL PHARMACOLOGY & THERAPEUTICS (2013)
The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space
Rafael Silva-Rocha et al.
ENVIRONMENTAL MICROBIOLOGY (2013)
HSM - a hybrid system based approach for modelling intracellular networks
Alvis Brazma et al.
GENE (2013)
A Comprehensive, Multi-Scale Dynamical Model of ErbB Receptor Signal Transduction in Human Mammary Epithelial Cells
Tomas Helikar et al.
PLOS ONE (2013)
Boolean network-based model of the Bcl-2 family mediated MOMP regulation
Tomas Tokar et al.
THEORETICAL BIOLOGY AND MEDICAL MODELLING (2013)
Integrating literature-constrained and data-driven inference of signalling networks
Federica Eduati et al.
BIOINFORMATICS (2012)
Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions
Melody K. Morris et al.
BIOTECHNOLOGY JOURNAL (2012)
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
Camille Terfve et al.
BMC SYSTEMS BIOLOGY (2012)
The Cell Collective: Toward an open and collaborative approach to systems biology
Tomas Helikar et al.
BMC SYSTEMS BIOLOGY (2012)
Digital clocks: simple Boolean models can quantitatively describe circadian systems
Ozgur E. Akman et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2012)
State-time spectrum of signal transduction logic models
Aidan MacNamara et al.
PHYSICAL BIOLOGY (2012)
A Boolean Model of the Cardiac Gene Regulatory Network Determining First and Second Heart Field Identity
Franziska Herrmann et al.
PLOS ONE (2012)
Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models
Tomas Helikar et al.
PLOS ONE (2012)
Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle
Robert G. Todd et al.
PLOS ONE (2012)
Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol
Ronny Feuer et al.
EURASIP JOURNAL ON BIOINFORMATICS AND SYSTEMS BIOLOGY (2012)
JSBML: a flexible Java library for working with SBML
Andreas Draeger et al.
BIOINFORMATICS (2011)
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
Dagmar Waltemath et al.
BMC SYSTEMS BIOLOGY (2011)
Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models
Julio Saez-Rodriguez et al.
CANCER RESEARCH (2011)
Information Routing Driven by Background Chatter in a Signaling Network
Nuria Domedel-Puig et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Minimum Information About a Simulation Experiment (MIASE)
Dagmar Waltemath et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
SimBoolNet-a Cytoscape plugin for dynamic simulation of signaling networks
Jie Zheng et al.
BIOINFORMATICS (2010)
BoolNet-an R package for generation, reconstruction and analysis of Boolean networks
Christoph Muessel et al.
BIOINFORMATICS (2010)
Snoopy-a unifying Petri net framework to investigate biomolecular networks
Christian Rohr et al.
BIOINFORMATICS (2010)
Attractor analysis of asynchronous Boolean models of signal transduction networks
Assieh Saadatpour et al.
JOURNAL OF THEORETICAL BIOLOGY (2010)
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement
Laurence Calzone et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling
Aurelien Naldi et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development
Clare E. Giacomantonio et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Logical modelling of regulatory networks with GINsim 2.3
A. Naldi et al.
BIOSYSTEMS (2009)
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
Tomas Helikar et al.
BMC SYSTEMS BIOLOGY (2009)
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance
Oezguer Sahin et al.
BMC SYSTEMS BIOLOGY (2009)
Modular logical modelling of the budding yeast cell cycle
Adrien Faure et al.
MOLECULAR BIOSYSTEMS (2009)
The Systems Biology Graphical Notation
Nicolas Le Novere et al.
NATURE BIOTECHNOLOGY (2009)
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
Regina Samaga et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
Bree B. Aldridge et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Temporal logic patterns for querying dynamic models of cellular interaction networks
Pedro T. Monteiro et al.
BIOINFORMATICS (2008)
Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc
Aitor Gonzalez et al.
BIOINFORMATICS (2008)
LibSBML: an API library for SBML
Benjamin J. Bornstein et al.
BIOINFORMATICS (2008)
Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module
Lucas Sanchez et al.
INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY (2008)
Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast
Maria I. Davidich et al.
PLOS ONE (2008)
Emergent decision-making in biological signal transduction networks
Tomas Helikar et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Boolean network simulations for life scientists
Istvan Albert et al.
SOURCE CODE FOR BIOLOGY AND MEDICINE (2008)
Dynamical roles of biological regulatory circuits
Denis Thieffry
BRIEFINGS IN BIOINFORMATICS (2007)
Petri net modelling of biological networks
Claudine Chaouiya
BRIEFINGS IN BIOINFORMATICS (2007)
Structural and functional analysis of cellular networks with CellNetAnalyzer
Steffen Klamt et al.
BMC SYSTEMS BIOLOGY (2007)
Predicting essential components of signal transduction networks: A dynamic model of guard cell abscisic acid signaling
Song Li et al.
PLOS BIOLOGY (2006)
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Adrien Faure et al.
BIOINFORMATICS (2006)
Validation of qualitative models of genetic regulatory networks by model checking:: analysis of the nutritional stress response in Escherichia coli
G Batt et al.
BIOINFORMATICS (2005)
The yeast cell-cycle network is robustly designed
FT Li et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic
G Bernot et al.
JOURNAL OF THEORETICAL BIOLOGY (2004)
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
R Albert et al.
JOURNAL OF THEORETICAL BIOLOGY (2003)
The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models
M Hucka et al.
BIOINFORMATICS (2003)
Share Paper
