James R. Faeder

Publication Activity (10 Years)

Years Active: 2004-2022
Publications (10 Years): 13

Top Topics

Statistical Models

Parameter Estimation

Systems Biology

Document Management

Top Venues

PLoS Comput. Biol.

Publications

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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David 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) (2022)
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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David 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 (2022)
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)
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)
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)
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)
John A. P. Sekar, José Juan Tapia, James R. Faeder
Automated visualization of rule-based models. PLoS Comput. Biol. 13 (11) (2017)
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)
Natasa Miskov-Zivanov, Paolo Zuliani, Qinsi Wang, Edmund M. Clarke, James R. Faeder
High-level modeling and verification of cellular signaling. HLDVT (2016)
John A. P. Sekar, Justin S. Hogg, James R. Faeder
Energy-based modeling in BioNetGen. BIBM (2016)
Bing Liu, James R. Faeder
Parameter estimation of rule-based models using statistical model checking. BIBM (2016)
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) (2016)
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)
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)
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 (2014)
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)
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)
Natasa Miskov-Zivanov, Diana Marculescu, James R. Faeder
Dynamic behavior of cell signaling networks: model design and analysis automation. DAC (2013)
José Juan Tapia, James R. Faeder
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. BCB (2013)
Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro
Modeling and design automation of biological circuits and systems. ICCAD (2012)
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) (2012)
José Juan Tapia, James R. Faeder, Brian Munsky
Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation. CDC (2012)
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)
Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Diana Marculescu, James R. Faeder
Emulation of biological networks in reconfigurable hardware. BCB (2011)
Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai
RuleBender: Integrated visualization for biochemical rule-based modeling. BioVis (2011)
Wen Xu, Adam M. Smith, James R. Faeder, G. Elisabeta Marai
RuleBender: a visual interface for rule-based modeling. Bioinform. 27 (12) (2011)
Haijun Gong, Qinsi Wang, Paolo Zuliani, James R. Faeder, Michael Lotze
Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer. BICoB (2011)
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) (2010)
Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke
Computational Modeling and Verification of Signaling Pathways in Cancer. ANB (2010)
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)
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) (2009)
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) (2009)
Leonard A. Harris, Justin S. Hogg, James R. Faeder
Compartmental Rule-based Modeling of Biochemical Systems. WSC (2009)
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)
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) (2007)
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 (2006)
James R. Faeder, Michael L. Blinov, William S. Hlavacek
Graphical rule-based representation of signal-transduction networks. SAC (2005)
James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek
Rule-based modeling of biochemical networks. Complex. 10 (4) (2005)
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) (2004)