James R. Faeder

According to our database1, James R. Faeder authored at least 37 papers between 2004 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:

On csauthors.net:


Parallel Tempering with Lasso for model reduction in systems biology.
PLoS Comput. Biol., 2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
J. Integr. Bioinform., 2020

Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology.
Proceedings of the 26th Euromicro International Conference on Parallel, 2018

Automated visualization of rule-based models.
PLoS Comput. Biol., 2017

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.
PLoS Comput. Biol., 2016

BioNetGen 2.2: advances in rule-based modeling.
Bioinform., 2016

High-level 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

Energy-based modeling in BioNetGen.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Parameter estimation of rule-based models using statistical model checking.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

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

Proceedings of the Encyclopedia of Computational Neuroscience, 2014

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems.
PLoS Comput. Biol., 2014

MOSBIE: a tool for comparison and analysis of rule-based biochemical models.
BMC Bioinform., 2014

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

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.
BMC Bioinform., 2012

Modeling and design automation of biological circuits and systems.
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.
Proceedings of the 51th IEEE Conference on Decision and Control, 2012

RuleBender: a visual interface for rule-based modeling.
Bioinform., 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 rule-based 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

Analysis and verification of the HMGB1 signaling pathway.
BMC Bioinform., 2010

Computational Modeling and Verification of Signaling Pathways in Cancer.
Proceedings of the Algebraic and Numeric Biology - 4th International Conference, 2010

A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases.
PLoS Comput. Biol., 2009

GetBonNie for building, analyzing and sharing rule-based models.
Bioinform., 2009

Simulation of large-scale rule-based models.
Bioinform., 2009

Compartmental Rule-based Modeling of Biochemical Systems.
Proceedings of the 2009 Winter Simulation Conference, 2009

Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway.
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

Carbon-fate maps for metabolic reactions.
Bioinform., 2007

Graph Theory for Rule-Based Modeling of Biochemical Networks.
Trans. Comp. Sys. Biology, 2006

Rule-based modeling of biochemical networks.
Complex., 2005

Graphical rule-based representation of signal-transduction networks.
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
Bioinform., 2004