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2020 – today
- 2024
[j20]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:
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. PLoS Comput. Biol. 20(4): 1011800 (2024)- 2022
- [j19]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i1]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j18]Robin Schmucker, Gabriele Farina, James R. Faeder, Fabian Fröhlich, Ali Sinan Saglam, Tuomas Sandholm:
Combination treatment optimization using a pan-cancer pathway model. PLoS Comput. Biol. 17(12) (2021) - 2020
- [j17]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:
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J. Integr. Bioinform. 17(2-3) (2020) - [j16]Sanjana Gupta, Robin E. C. Lee, James R. Faeder:
Parallel Tempering with Lasso for model reduction in systems biology. PLoS Comput. Biol. 16(3) (2020)
2010 – 2019
- 2018
- [c19]Sanjana Gupta, Liam Hainsworth, Justin S. Hogg, Robin Lee, James R. Faeder:
Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. PDP 2018: 690-697 - 2017
- [j15]John A. P. Sekar, José Juan Tapia, James R. Faeder:
Automated visualization of rule-based models. PLoS Comput. Biol. 13(11) (2017) - 2016
- [j14]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:
BioNetGen 2.2: advances in rule-based modeling. Bioinform. 32(21): 3366-3368 (2016) - [j13]Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman:
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Comput. Biol. 12(2) (2016) - [c18]Bing Liu, James R. Faeder:
Parameter estimation of rule-based models using statistical model checking. BIBM 2016: 1453-1459 - [c17]John A. P. Sekar, Justin S. Hogg, James R. Faeder:
Energy-based modeling in BioNetGen. BIBM 2016: 1460-1467 - [c16]Qinsi Wang, Natasa Miskov-Zivanov, Bing Liu, James R. Faeder, Michael Lotze, Edmund M. Clarke:
Formal Modeling and Analysis of Pancreatic Cancer Microenvironment. CMSB 2016: 289-305 - [c15]Natasa Miskov-Zivanov, Paolo Zuliani, Qinsi Wang, Edmund M. Clarke, James R. Faeder:
High-level modeling and verification of cellular signaling. HLDVT 2016: 162-169 - 2015
- [c14]Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech:
Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity. ACM Great Lakes Symposium on VLSI 2015: 321-323 - 2014
- [j12]John E. Wenskovitch, Leonard A. Harris, José Juan Tapia, James R. Faeder, G. Elisabeta Marai:
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. BMC Bioinform. 15: 316 (2014) - [j11]Justin S. Hogg, Leonard A. Harris, Lori J. Stover, Niketh S. Nair, James R. Faeder:
Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. PLoS Comput. Biol. 10(4) (2014) - [r1]Thomas M. Bartol, Markus Dittrich, James R. Faeder:
MCell. Encyclopedia of Computational Neuroscience 2014 - 2013
- [c13]José Juan Tapia, James R. Faeder:
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. BCB 2013: 726 - [c12]Natasa Miskov-Zivanov, Paolo Zuliani, Edmund M. Clarke, James R. Faeder:
Studies of biological networks with statistical model checking: application to immune system cells. BCB 2013: 728 - [c11]Natasa Miskov-Zivanov, Diana Marculescu, James R. Faeder:
Dynamic behavior of cell signaling networks: model design and analysis automation. DAC 2013: 8:1-8:6 - 2012
- [j10]Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai:
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinform. 13(S-8): S3 (2012) - [c10]José Juan Tapia, James R. Faeder, Brian Munsky:
Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation. CDC 2012: 5361-5366 - [c9]Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro:
Modeling and design automation of biological circuits and systems. ICCAD 2012: 291-293 - 2011
- [j9]Wen Xu, Adam M. Smith, James R. Faeder, G. Elisabeta Marai:
RuleBender: a visual interface for rule-based modeling. Bioinform. 27(12): 1721-1722 (2011) - [c8]Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Diana Marculescu, James R. Faeder:
Emulation of biological networks in reconfigurable hardware. BCB 2011: 536-540 - [c7]Haijun Gong, Qinsi Wang, Paolo Zuliani, James R. Faeder, Michael Lotze:
Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer. BICoB 2011: 245- - [c6]Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai:
RuleBender: Integrated visualization for biochemical rule-based modeling. BioVis 2011: 103-110 - [c5]Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Prashant Kashinkunti, Diana Marculescu, James R. Faeder:
Regulatory network analysis acceleration with reconfigurable hardware. EMBC 2011: 149-152 - 2010
- [j8]Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke:
Analysis and verification of the HMGB1 signaling pathway. BMC Bioinform. 11(S-7): S10 (2010) - [c4]Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke:
Computational Modeling and Verification of Signaling Pathways in Cancer. ANB 2010: 117-135
2000 – 2009
- 2009
- [j7]Joshua Colvin, Michael I. Monine, James R. Faeder, William S. Hlavacek, Daniel D. Von Hoff, Richard G. Posner:
Simulation of large-scale rule-based models. Bioinform. 25(7): 910-917 (2009) - [j6]Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek:
GetBonNie for building, analyzing and sharing rule-based models. Bioinform. 25(11): 1457-1460 (2009) - [j5]Dipak Barua, James R. Faeder, Jason M. Haugh:
A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases. PLoS Comput. Biol. 5(4) (2009) - [c3]Leonard A. Harris, Justin S. Hogg, James R. Faeder:
Compartmental Rule-based Modeling of Biochemical Systems. WSC 2009: 908-919 - 2008
- [c2]Edmund M. Clarke, James R. Faeder, Christopher James Langmead, Leonard A. Harris, Sumit Kumar Jha, Axel Legay:
Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway. CMSB 2008: 231-250 - 2007
- [j4]Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek:
Carbon-fate maps for metabolic reactions. Bioinform. 23(23): 3193-3199 (2007) - 2006
- [j3]Michael L. Blinov, Jin Yang, James R. Faeder, William S. Hlavacek:
Graph Theory for Rule-Based Modeling of Biochemical Networks. Trans. Comp. Sys. Biology 7: 89-106 (2006) - 2005
- [j2]James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek:
Rule-based modeling of biochemical networks. Complex. 10(4): 22-41 (2005) - [c1]James R. Faeder, Michael L. Blinov, William S. Hlavacek:
Graphical rule-based representation of signal-transduction networks. SAC 2005: 133-140 - 2004
- [j1]Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek:
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinform. 20(17): 3289-3291 (2004)
Coauthor Index
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