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BioNetGen 2.2: advances in rule-based modeling

Bioinformatics (Oxford, England), 2016-11, Vol.32 (21), p.3366-3368

2016

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Parallel Tempering with Lasso for model reduction in systems biology

PLoS computational biology, 2020-03, Vol.16 (3), p.e1007669-e1007669

2020

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Automated visualization of rule-based models

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005857-e1005857

2017

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MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface

PLoS computational biology, 2024-04, Vol.20 (4), p.e1011800-e1011800

2024

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Toward a quantitative theory of intrinsically disordered proteins and their function

Proceedings of the National Academy of Sciences - PNAS, 2009-11, Vol.106 (47), p.19819-19823

2009

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BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

Bioinformatics, 2004-11, Vol.20 (17), p.3289-3291

2004

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Toward a comprehensive language for biological systems

BMC biology, 2011-10, Vol.9 (1), p.68-68, Article 68

Faeder, James R

2011

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Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments

Biophysical journal, 2016-04, Vol.110 (8), p.1681-1683

2016

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Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

PLoS computational biology, 2016-02, Vol.12 (2), p.e1004611-e1004611

2016

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The interplay of double phosphorylation and scaffolding in MAPK pathways

Journal of theoretical biology, 2012-02, Vol.295, p.116-124

2012

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Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors

Scientific reports, 2018-06, Vol.8 (1), p.9388-12, Article 9388

2018

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Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System

Biophysical journal, 2009-04, Vol.96 (7), p.2604-2623

2009

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Exact hybrid particle/population simulation of rule-based models of biochemical systems

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003544-e1003544

2014

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The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases

BMC genomics, 2011-11, Vol.12 (1), p.574-574, Article 574

2011

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Memory of Germinant Stimuli in Bacterial Spores

mBio, 2015-11, Vol.6 (6), p.e01859-e01815

2015

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Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

Nature methods, 2011-02, Vol.8 (2), p.177-183

2011

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Synergism between Different Germinant Receptors in the Germination of Bacillus subtilis Spores

Journal of Bacteriology, 2011-09, Vol.193 (18), p.4664-4671

2011

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The complexity of complexes in signal transduction

Biotechnology and bioengineering, 2003-12, Vol.84 (7), p.783-794

2003

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The duration of T cell stimulation is a critical determinant of cell fate and plasticity

Science signaling, 2013-11, Vol.6 (300), p.ra97

2013

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A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases

PLoS computational biology, 2009-04, Vol.5 (4), p.e1000364-e1000364

2009

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RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

BMC bioinformatics, 2012, Vol.13 Suppl 8 (Suppl 8), p.S3-S3, Article S3

2012

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Rule-based modeling of biochemical systems with BioNetGen

Methods in molecular biology (Clifton, N.J.), 2009, Vol.500, p.113

2009

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Computational Models of Tandem Src Homology 2 Domain Interactions and Application to Phosphoinositide 3-Kinase

The Journal of biological chemistry, 2008-03, Vol.283 (12), p.7338-7345

2008

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Multiview learning for understanding functional multiomics

PLoS computational biology, 2020-04, Vol.16 (4), p.e1007677-e1007677

2020

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Demystifying the cytokine network: Mathematical models point the way

Cytokine (Philadelphia, Pa.), 2017-10, Vol.98, p.115-123

2017

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BioNetGen 2.2: advances in rule-based modeling

Parallel Tempering with Lasso for model reduction in systems biology

Automated visualization of rule-based models

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface

Toward a quantitative theory of intrinsically disordered proteins and their function

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

Toward a comprehensive language for biological systems

Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

The interplay of double phosphorylation and scaffolding in MAPK pathways

Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors

Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System

Exact hybrid particle/population simulation of rule-based models of biochemical systems

The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases

Memory of Germinant Stimuli in Bacterial Spores

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

Synergism between Different Germinant Receptors in the Germination of Bacillus subtilis Spores

The complexity of complexes in signal transduction

The duration of T cell stimulation is a critical determinant of cell fate and plasticity

A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

Rule-based modeling of biochemical systems with BioNetGen

Computational Models of Tandem Src Homology 2 Domain Interactions and Application to Phosphoinositide 3-Kinase

Multiview learning for understanding functional multiomics

Demystifying the cytokine network: Mathematical models point the way

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