BioNetGen 2.2: advances in rule-based modeling von Harris, Leonard A, Hogg, Justin S, Tapia, José-Juan, Sekar, John A P, Gupta, Sanjana, Korsunsky, Ilya, Arora, Arshi, Barua, Dipak, Sheehan, Robert P, Faeder, James R

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Parallel Tempering with Lasso for model reduction in systems biology von Gupta, Sanjana, Lee, Robin E C, Faeder, James R

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Automated visualization of rule-based models von Sekar, John Arul Prakash, Tapia, Jose-Juan, Faeder, James R

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MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface von Husar, Adam, Ordyan, Mariam, Garcia, Guadalupe C, Yancey, Joel G, Saglam, Ali S, Faeder, James R, Bartol, Thomas M, Kennedy, Mary B, Sejnowski, Terrence J

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Toward a quantitative theory of intrinsically disordered proteins and their function von Liu, Jintao, Faeder, James R, Camacho, Carlos J

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BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains von Blinov, Michael L., Faeder, James R., Goldstein, Byron, Hlavacek, William S.

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Toward a comprehensive language for biological systems von Faeder, James R

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Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments von Faeder, James R., Morel, Penelope A.

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Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories von Donovan, Rory M, Tapia, Jose-Juan, Sullivan, Devin P, Faeder, James R, Murphy, Robert F, Dittrich, Markus, Zuckerman, Daniel M

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The interplay of double phosphorylation and scaffolding in MAPK pathways von Kocieniewski, PaweŁ, Faeder, James R., Lipniacki, Tomasz

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Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors von Singh, Manjulata, Warita, Katsuhiko, Warita, Tomoko, Faeder, James R., Lee, Robin E. C., Sant, Shilpa, Oltvai, Zoltán N.

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Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System von Nag, Ambarish, Monine, Michael I., Faeder, James R., Goldstein, Byron

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Exact hybrid particle/population simulation of rule-based models of biochemical systems von Hogg, Justin S, Harris, Leonard A, Stover, Lori J, Nair, Niketh S, Faeder, James R

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The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases von Horton, Ashley A, Wang, Bo, Camp, Lauren, Price, Mark S, Arshi, Arora, Nagy, Mate, Nadler, Steven A, Faeder, James R, Luckhart, Shirley

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Memory of Germinant Stimuli in Bacterial Spores von Wang, Shiwei, Faeder, James R, Setlow, Peter, Li, Yong-qing

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Efficient modeling, simulation and coarse-graining of biological complexity with NFsim von Emonet, Thierry, Sneddon, Michael W, Faeder, James R

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Synergism between Different Germinant Receptors in the Germination of Bacillus subtilis Spores von Yi, Xuan, Liu, Jintao, Faeder, James R, Setlow, Peter

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The complexity of complexes in signal transduction von Hlavacek, William S., Faeder, James R., Blinov, Michael L., Perelson, Alan S., Goldstein, Byron

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The duration of T cell stimulation is a critical determinant of cell fate and plasticity von Miskov-Zivanov, Natasa, Turner, Michael S, Kane, Lawrence P, Morel, Penelope A, Faeder, James R

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A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases von Barua, Dipak, Faeder, James R, Haugh, Jason M

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