James R. Faeder

James R. Faeder, Ph.D.
Associate Professor, Vice Chair for Educational Programs/Initiatives

Ph.D. in Chemical Physics, University of Colorado at Boulder

Phone: (412)-648-8171
E-mail: faeder@pitt.edu
Website: /Faculty/Faeder

Research Summary

I am interested in developing mathematical models of biological regulatory processes that integrate specific knowledge about protein-protein interactions. Together with collaborators as Los Alamos National Laboratory I have developed a simulation framework called BioNetGen that allows rule-based specification of biochemical reaction networks and provides both deterministic and stochastic modeling capabilities. My current research includes the development of specific models of signal transduction and the development of new stochastic simulation algorithms that will greatly broaden the scope of models that can be developed. Other research areas include model reduction, parameter estimation and uncertainty analysis, and automated model construction from databases of protein interactions.

Recent Publications

Harris A, Hogg JS, Tapia JJ, Sekar JAP, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR (2016) “BioNetGen 2.2: Advances in Rule-Based Modeling.” Bioinformatics. doi:10.1093/bioinformatics/btw469.

Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O (2015) The eighth q-bio conference: meeting report and special issue preface Phys Biol. 12(6):060401.

Wang S, Faeder JR, Setlow P, Li YQ (2015) Memory of Germinant Stimuli in Bacterial Spores MBio 24;6(6).


Project title Proj Start Date Proj End Date Funding Source
Negative Control of IL-17R Signaling: Implications for Fungal Immunity 1/17/2014 12/31/2018 NIH-R01
Cardiolipin as a Novel Mediator of Acute Lung Injury 1/3/2014 12/31/2018 NIHLB-P01
High Performance Computing for Multiscale Modeling of Biological Systems 9/24/2012 8/31/2017 NIGMS-P41
High-performance weighted ensemble software for simulation of complex bio-events 8/1/2015 6/30/2019 NIH-R01