James R. Faeder
According to our database^{1},
James R. Faeder
authored at least 35 papers
between 2004 and 2018.
Collaborative distances:
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Bibliography
2018
Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology.
Proceedings of the 26th Euromicro International Conference on Parallel, 2018
2017
Automated visualization of rulebased models.
PLoS Computational Biology, 2017
2016
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.
PLoS Computational Biology, 2016
BioNetGen 2.2: advances in rulebased modeling.
Bioinformatics, 2016
Highlevel modeling and verification of cellular signaling.
Proceedings of the IEEE International High Level Design Validation and Test Workshop, 2016
Formal Modeling and Analysis of Pancreatic Cancer Microenvironment.
Proceedings of the Computational Methods in Systems Biology, 2016
Energybased modeling in BioNetGen.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
Parameter estimation of rulebased models using statistical model checking.
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.
Proceedings of the 25th edition on Great Lakes Symposium on VLSI, GLVLSI 2015, Pittsburgh, PA, USA, May 20, 2015
2014
MCell.
Proceedings of the Encyclopedia of Computational Neuroscience, 2014
Exact Hybrid Particle/Population Simulation of RuleBased Models of Biochemical Systems.
PLoS Computational Biology, 2014
MOSBIE: a tool for comparison and analysis of rulebased biochemical models.
BMC Bioinformatics, 2014
2013
Dynamic behavior of cell signaling networks: model design and analysis automation.
Proceedings of the 50th Annual Design Automation Conference 2013, 2013
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models.
Proceedings of the ACM Conference on Bioinformatics, 2013
Studies of biological networks with statistical model checking: application to immune system cells.
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
RuleBender: integrated modeling, simulation and visualization for rulebased intracellular biochemistry.
BMC Bioinformatics, 2012
Modeling and design automation of biological circuits and systems.
Proceedings of the 2012 IEEE/ACM International Conference on ComputerAided Design, 2012
Adaptive coarsegraining for transient and quasiequilibrium analyses of stochastic gene regulation.
Proceedings of the 51th IEEE Conference on Decision and Control, 2012
2011
RuleBender: a visual interface for rulebased modeling.
Bioinformatics, 2011
Regulatory network analysis acceleration with reconfigurable hardware.
Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011
RuleBender: Integrated visualization for biochemical rulebased modeling.
Proceedings of the 2011 IEEE Symposium on Biological Data Visualization, 2011
Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer.
Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology, 2011
Emulation of biological networks in reconfigurable hardware.
Proceedings of the ACM International Conference on Bioinformatics, 2011
2010
Analysis and verification of the HMGB1 signaling pathway.
BMC Bioinformatics, 2010
Computational Modeling and Verification of Signaling Pathways in Cancer.
Proceedings of the Algebraic and Numeric Biology  4th International Conference, 2010
2009
A Bipolar Clamp Mechanism for Activation of JakFamily Protein Tyrosine Kinases.
PLoS Computational Biology, 2009
GetBonNie for building, analyzing and sharing rulebased models.
Bioinformatics, 2009
Simulation of largescale rulebased models.
Bioinformatics, 2009
Compartmental Rulebased Modeling of Biochemical Systems.
Proceedings of the 2009 Winter Simulation Conference, 2009
2008
Statistical Model Checking in BioLab: Applications to the Automated Analysis of TCell Receptor Signaling Pathway.
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008
2007
Carbonfate maps for metabolic reactions.
Bioinformatics, 2007
2006
Graph Theory for RuleBased Modeling of Biochemical Networks.
, 2006
2005
Rulebased modeling of biochemical networks.
Complexity, 2005
Graphical rulebased representation of signaltransduction networks.
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005
2004
BioNetGen: software for rulebased modeling of signal transduction based on the interactions of molecular domains.
Bioinformatics, 2004