James R. Faeder

According to our database, James R. Faeder authored at least 41 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

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

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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

CoRR, 2022

2021

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

2020

Parallel Tempering with Lasso for model reduction in systems biology.

Sanjana Gupta, Robin E. C. Lee, James R. Faeder

PLoS Comput. Biol., 2020

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, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim

J. Integr. Bioinform., 2020

2018

Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology.

Sanjana Gupta, Liam Hainsworth, Justin S. Hogg, Robin Lee, James R. Faeder

Proceedings of the 26th Euromicro International Conference on Parallel, 2018

2017

Automated visualization of rule-based models.

John A. P. Sekar, José Juan Tapia, James R. Faeder

PLoS Comput. Biol., 2017

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

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

High-level modeling and verification of cellular signaling.

Natasa Miskov-Zivanov, Paolo Zuliani, Qinsi Wang, Edmund M. Clarke, James R. Faeder

Proceedings of the IEEE International High Level Design Validation and Test Workshop, 2016

Formal Modeling and Analysis of Pancreatic Cancer Microenvironment.

Qinsi Wang, Natasa Miskov-Zivanov, Bing Liu, James R. Faeder, Michael Lotze, Edmund M. Clarke

Proceedings of the Computational Methods in Systems Biology, 2016

Energy-based modeling in BioNetGen.

John A. P. Sekar, Justin S. Hogg, James R. Faeder

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Parameter estimation of rule-based models using statistical model checking.

Bing Liu, James R. Faeder

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

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

Proceedings of the 25th edition on Great Lakes Symposium on VLSI, GLVLSI 2015, Pittsburgh, PA, USA, May 20, 2015

2014

MCell.

Thomas M. Bartol, Markus Dittrich, James R. Faeder

Proceedings of the Encyclopedia of Computational Neuroscience, 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

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

2013

Dynamic behavior of cell signaling networks: model design and analysis automation.

Natasa Miskov-Zivanov, Diana Marculescu, James R. Faeder

Proceedings of the 50th Annual Design Automation Conference 2013, 2013

The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models.

José Juan Tapia, James R. Faeder

Proceedings of the ACM Conference on Bioinformatics, 2013

Studies of biological networks with statistical model checking: application to immune system cells.

Natasa Miskov-Zivanov, Paolo Zuliani, Edmund M. Clarke, James R. Faeder

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

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

Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai

BMC Bioinform., 2012

Modeling and design automation of biological circuits and systems.

Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro

Proceedings of the 2012 IEEE/ACM International Conference on Computer-Aided Design, 2012

Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation.

José Juan Tapia, James R. Faeder, Brian Munsky

Proceedings of the 51th IEEE Conference on Decision and Control, 2012

2011

RuleBender: a visual interface for rule-based modeling.

Wen Xu, Adam M. Smith, James R. Faeder, G. Elisabeta Marai

Bioinform., 2011

Regulatory network analysis acceleration with reconfigurable hardware.

Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Prashant Kashinkunti, Diana Marculescu, James R. Faeder

Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

RuleBender: Integrated visualization for biochemical rule-based modeling.

Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai

Proceedings of the 2011 IEEE Symposium on Biological Data Visualization, 2011

Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer.

Haijun Gong, Qinsi Wang, Paolo Zuliani, James R. Faeder, Michael Lotze

Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology, 2011

Emulation of biological networks in reconfigurable hardware.

Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Diana Marculescu, James R. Faeder

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

Analysis and verification of the HMGB1 signaling pathway.

Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke

BMC Bioinform., 2010

Computational Modeling and Verification of Signaling Pathways in Cancer.

Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke

Proceedings of the Algebraic and Numeric Biology - 4th International Conference, 2010

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

GetBonNie for building, analyzing and sharing rule-based models.

Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek

Bioinform., 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

Compartmental Rule-based Modeling of Biochemical Systems.

Leonard A. Harris, Justin S. Hogg, James R. Faeder

Proceedings of the 2009 Winter Simulation Conference, 2009

2008

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, Axel Legay

Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

2007

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

2006

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

2005

Rule-based modeling of biochemical networks.

James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek

Complex., 2005

Graphical rule-based representation of signal-transduction networks.

James R. Faeder, Michael L. Blinov, William S. Hlavacek

Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

2004

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