BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. - Michael L. Blinov; James R. Faeder; Byron Goldstein; William S. Hlavacek (Bioinform., 2004)

Graphical rule-based representation of signal-transduction networks. - James R. Faeder; Michael L. Blinov; William S. Hlavacek (SAC, 2005)

Rule-based modeling of biochemical networks. - James R. Faeder; Michael L. Blinov; Byron Goldstein; William S. Hlavacek (Complex., 2005)

Graph Theory for Rule-Based Modeling of Biochemical Networks. - Michael L. Blinov; Jin Yang; James R. Faeder; William S. Hlavacek (Trans. Comp. Sys. Biology, 2006)

Carbon-fate maps for metabolic reactions. - Fangping Mu; Robert F. Williams; Clifford J. Unkefer; Pat J. Unkefer; James R. Faeder; William S. Hlavacek (Bioinform., 2007)

Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway. - Edmund M. Clarke; James R. Faeder; Christopher James Langmead; Leonard A. Harris; Sumit Kumar Jha 001; Axel Legay (CMSB, 2008)

Compartmental Rule-based Modeling of Biochemical Systems. - Leonard A. Harris; Justin S. Hogg; James R. Faeder (WSC, 2009)

Simulation of large-scale rule-based models. - Joshua Colvin; Michael I. Monine; James R. Faeder; William S. Hlavacek; Daniel D. Von Hoff; Richard G. Posner (Bioinform., 2009)

GetBonNie for building, analyzing and sharing rule-based models. - Bin Hu 025; G. Matthew Fricke; James R. Faeder; Richard G. Posner; William S. Hlavacek (Bioinform., 2009)

A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases. - Dipak Barua; James R. Faeder; Jason M. Haugh (PLoS Comput. Biol., 2009)

Computational Modeling and Verification of Signaling Pathways in Cancer. - Haijun Gong; Paolo Zuliani; Anvesh Komuravelli; James R. Faeder; Edmund M. Clarke (ANB, 2010)

Analysis and verification of the HMGB1 signaling pathway. - Haijun Gong; Paolo Zuliani; Anvesh Komuravelli; James R. Faeder; Edmund M. Clarke (BMC Bioinform., 2010)

Emulation of biological networks in reconfigurable hardware. - Natasa Miskov-Zivanov; Andrew Bresticker; Deepa Krishnaswamy; Sreesan Venkatakrishnan; Diana Marculescu; James R. Faeder (BCB, 2011)

Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer. - Haijun Gong; Qinsi Wang; Paolo Zuliani; James R. Faeder; Michael Lotze (BICoB, 2011)

RuleBender: Integrated visualization for biochemical rule-based modeling. - Adam M. Smith 002; Wen Xu; Yao Sun 009; James R. Faeder; G. Elisabeta Marai (BioVis, 2011)

Regulatory network analysis acceleration with reconfigurable hardware. - Natasa Miskov-Zivanov; Andrew Bresticker; Deepa Krishnaswamy; Sreesan Venkatakrishnan; Prashant Kashinkunti; Diana Marculescu; James R. Faeder (EMBC, 2011)

RuleBender: a visual interface for rule-based modeling. - Wen Xu; Adam M. Smith 002; James R. Faeder; G. Elisabeta Marai (Bioinform., 2011)

Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation. - José Juan Tapia; James R. Faeder; Brian Munsky (CDC, 2012)

Modeling and design automation of biological circuits and systems. - Natasa Miskov-Zivanov; James R. Faeder; Chris J. Myers; Herbert M. Sauro (ICCAD, 2012)

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. - Adam M. Smith 002; Wen Xu; Yao Sun 009; James R. Faeder; G. Elisabeta Marai (BMC Bioinform., 2012)

Studies of biological networks with statistical model checking: application to immune system cells. - Natasa Miskov-Zivanov; Paolo Zuliani; Edmund M. Clarke; James R. Faeder (BCB, 2013)

The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. - José Juan Tapia; James R. Faeder (BCB, 2013)

Dynamic behavior of cell signaling networks: model design and analysis automation. - Natasa Miskov-Zivanov; Diana Marculescu; James R. Faeder (DAC, 2013)

MOSBIE: a tool for comparison and analysis of rule-based biochemical models. - John E. Wenskovitch; Leonard A. Harris; José Juan Tapia; James R. Faeder; G. Elisabeta Marai (BMC Bioinform., 2014)

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. - Justin S. Hogg; Leonard A. Harris; Lori J. Stover; Niketh S. Nair; James R. Faeder (PLoS Comput. Biol., 2014)

MCell. - Thomas M. Bartol; Markus Dittrich; James R. Faeder (Encyclopedia of Computational Neuroscience, 2014)

Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity. - Devin P. Sullivan; Rohan Arepally; Robert F. Murphy; José Juan Tapia; James R. Faeder; Markus Dittrich; Jacob Czech (ACM Great Lakes Symposium on VLSI, 2015)

Parameter estimation of rule-based models using statistical model checking. - Bing Liu 013; James R. Faeder (BIBM, 2016)

Energy-based modeling in BioNetGen. - John A. P. Sekar; Justin S. Hogg; James R. Faeder (BIBM, 2016)

Formal Modeling and Analysis of Pancreatic Cancer Microenvironment. - Qinsi Wang; Natasa Miskov-Zivanov; Bing Liu 013; James R. Faeder; Michael Lotze; Edmund M. Clarke (CMSB, 2016)

High-level modeling and verification of cellular signaling. - Natasa Miskov-Zivanov; Paolo Zuliani; Qinsi Wang; Edmund M. Clarke; James R. Faeder (HLDVT, 2016)

BioNetGen 2.2: advances in rule-based modeling. - Leonard A. Harris; Justin S. Hogg; José Juan Tapia; John A. P. Sekar; Sanjana Gupta; Ilya Korsunsky; Arshi Arora; Dipak Barua; Robert P. Sheehan; James R. Faeder (Bioinform., 2016)

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. - Rory M. Donovan; José Juan Tapia; Devin P. Sullivan; James R. Faeder; Robert F. Murphy; Markus Dittrich; Daniel M. Zuckerman (PLoS Comput. Biol., 2016)

Automated visualization of rule-based models. - John A. P. Sekar; José Juan Tapia; James R. Faeder (PLoS Comput. Biol., 2017)

Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. - Sanjana Gupta; Liam Hainsworth; Justin S. Hogg; Robin Lee; James R. Faeder (PDP, 2018)

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. - Fengkai Zhang; Lucian P. Smith; Michael L. Blinov; James R. Faeder; William S. Hlavacek; José Juan Tapia; Sarah M. Keating; Nicolas Rodriguez 001; Andreas Dräger; Leonard A. Harris; Andrew Finney; Bin Hu 025; et al. (J. Integr. Bioinform., 2020)

Parallel Tempering with Lasso for model reduction in systems biology. - Sanjana Gupta; Robin E. C. Lee; James R. Faeder (PLoS Comput. Biol., 2020)

Combination treatment optimization using a pan-cancer pathway model. - Robin Schmucker; Gabriele Farina; James R. Faeder; Fabian Fröhlich; Ali Sinan Saglam; Tuomas Sandholm (PLoS Comput. Biol., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. - Adam Husár; Mariam Ordyan; Guadalupe C. Garcia; Joel G. Yancey; Ali Sinan Saglam; James R. Faeder; Thomas M. Bartol; Mary B. Kennedy; Terrence J. Sejnowski (PLoS Comput. Biol., 2024)