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James R Faeder
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Rule-based modeling of biochemical systems with BioNetGen
JR Faeder, ML Blinov, WS Hlavacek
Systems biology, 113-167, 2009
5592009
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains
ML Blinov, JR Faeder, B Goldstein, WS Hlavacek
Bioinformatics 20 (17), 3289-3291, 2004
5252004
Molecular dynamics simulations of the interior of aqueous reverse micelles
J Faeder, BM Ladanyi
The Journal of Physical Chemistry B 104 (5), 1033-1046, 2000
5072000
Rules for modeling signal-transduction systems
WS Hlavacek, JR Faeder, ML Blinov, RG Posner, M Hucka, W Fontana
Science's STKE 2006 (344), re6-re6, 2006
4632006
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
MW Sneddon, JR Faeder, T Emonet
Nature methods 8 (2), 177-183, 2011
3802011
The complexity of complexes in signal transduction
WS Hlavacek, JR Faeder, ML Blinov, AS Perelson, B Goldstein
Biotechnology and bioengineering 84 (7), 783-794, 2003
2682003
Mathematical and computational models of immune-receptor signalling
B Goldstein, JR Faeder, WS Hlavacek
Nature Reviews Immunology 4 (6), 445-456, 2004
2662004
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
2572020
BioNetGen 2.2: advances in rule-based modeling
LA Harris, JS Hogg, JJ Tapia, JAP Sekar, S Gupta, I Korsunsky, A Arora, ...
Bioinformatics 32 (21), 3366-3368, 2016
2552016
Investigation of early events in FcεRI-mediated signaling using a detailed mathematical model
JR Faeder, WS Hlavacek, I Reischl, ML Blinov, H Metzger, A Redondo, ...
The Journal of Immunology 170 (7), 3769-3781, 2003
2202003
A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity
ML Blinov, JR Faeder, B Goldstein, WS Hlavacek
Biosystems 83 (2-3), 136-151, 2006
2112006
Solvation dynamics in aqueous reverse micelles: a computer simulation study
J Faeder, BM Ladanyi
The Journal of Physical Chemistry B 105 (45), 11148-11158, 2001
1902001
Rule‐based modeling of biochemical networks
JR Faeder, ML Blinov, B Goldstein, WS Hlavacek
Complexity 10 (4), 22-41, 2005
1782005
Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems
LA Chylek, LA Harris, CS Tung, JR Faeder, CF Lopez, WS Hlavacek
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 6 (1), 13-36, 2014
1682014
Kinetic Monte Carlo method for rule-based modeling of biochemical networks
J Yang, MI Monine, JR Faeder, WS Hlavacek
Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 78 (3 …, 2008
1542008
Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway
EM Clarke, JR Faeder, CJ Langmead, LA Harris, SK Jha, A Legay
Computational Methods in Systems Biology: 6th International Conference CMSB …, 2008
1452008
The duration of T cell stimulation is a critical determinant of cell fate and plasticity
N Miskov-Zivanov, MS Turner, LP Kane, PA Morel, JR Faeder
Science signaling 6 (300), ra97-ra97, 2013
1442013
Solvation dynamics in reverse micelles: the role of headgroup− solute interactions
J Faeder, BM Ladanyi
The Journal of Physical Chemistry B 109 (14), 6732-6740, 2005
1322005
Molecular dynamics simulations of the interior of aqueous reverse micelles: A comparison between sodium and potassium counterions
J Faeder, MV Albert, BM Ladanyi
Langmuir 19 (6), 2514-2520, 2003
1292003
Toward a quantitative theory of intrinsically disordered proteins and their function
J Liu, JR Faeder, CJ Camacho
Proceedings of the National Academy of Sciences 106 (47), 19819-19823, 2009
1212009
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