James R. Faeder
Affiliations: | 1998-1999 | Department of Computational Biology | University of Pittsburgh School of Medicine, Pittsburgh, PA, United States |
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Parents
Sign in to add mentor| Branka M. Ladanyi | post-doc | 1998-1999 | University of Pittsburgh School of Medicine |
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Publications
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| Keating SM, Waltemath D, König M, et al. (2020) SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110 |
| Zhang F, Smith LP, Blinov ML, et al. (2020) Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. Journal of Integrative Bioinformatics |
| Gupta S, Lee REC, Faeder JR. (2020) Parallel Tempering with Lasso for model reduction in systems biology. Plos Computational Biology. 16: e1007669 |
| Tapia JJ, Saglam AS, Czech J, et al. (2019) MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. Methods in Molecular Biology (Clifton, N.J.). 1945: 203-229 |
| Sekar JAP, Tapia JJ, Faeder JR. (2017) Automated visualization of rule-based models. Plos Computational Biology. 13: e1005857 |
| Kaya C, Cheng MH, Block ER, et al. (2017) Effect of Spatial Complexity on Dopaminergic Signaling Revealed from Multiscale Simulations Biophysical Journal. 112: 135a |
| Morel PA, Lee RE, Faeder JR. (2016) Demystifying the cytokine network: Mathematical models point the way. Cytokine |
| Harris LA, Hogg JS, Tapia JJ, et al. (2016) BioNetGen 2.2: Advances in Rule-Based Modeling. Bioinformatics (Oxford, England) |
| Faeder JR, Morel PA. (2016) Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments. Biophysical Journal. 110: 1681-3 |
| Donovan RM, Tapia JJ, Sullivan DP, et al. (2016) Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. Plos Computational Biology. 12: e1004611 |