| Year |
Citation |
Score |
| 2020 |
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, ... ... Faeder JR, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110. PMID 32845085 DOI: 10.15252/Msb.20199110 |
0.396 |
|
| 2020 |
Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. Journal of Integrative Bioinformatics. PMID 32628633 DOI: 10.1515/Jib-2020-0015 |
0.352 |
|
| 2020 |
Gupta S, Lee REC, Faeder JR. Parallel Tempering with Lasso for model reduction in systems biology. Plos Computational Biology. 16: e1007669. PMID 32150537 DOI: 10.1371/Journal.Pcbi.1007669 |
0.392 |
|
| 2019 |
Tapia JJ, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. Methods in Molecular Biology (Clifton, N.J.). 1945: 203-229. PMID 30945248 DOI: 10.1007/978-1-4939-9102-0_9 |
0.391 |
|
| 2017 |
Sekar JAP, Tapia JJ, Faeder JR. Automated visualization of rule-based models. Plos Computational Biology. 13: e1005857. PMID 29131816 DOI: 10.1371/Journal.Pcbi.1005857 |
0.355 |
|
| 2017 |
Kaya C, Cheng MH, Block ER, Sorkin A, Faeder JR, Bahar I. Effect of Spatial Complexity on Dopaminergic Signaling Revealed from Multiscale Simulations Biophysical Journal. 112: 135a. DOI: 10.1016/J.Bpj.2016.11.751 |
0.323 |
|
| 2016 |
Morel PA, Lee RE, Faeder JR. Demystifying the cytokine network: Mathematical models point the way. Cytokine. PMID 27919524 DOI: 10.1016/J.Cyto.2016.11.013 |
0.371 |
|
| 2016 |
Harris LA, Hogg JS, Tapia JJ, Sekar JA, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR. BioNetGen 2.2: Advances in Rule-Based Modeling. Bioinformatics (Oxford, England). PMID 27402907 DOI: 10.1093/Bioinformatics/Btw469 |
0.371 |
|
| 2016 |
Faeder JR, Morel PA. Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments. Biophysical Journal. 110: 1681-3. PMID 27119628 DOI: 10.1016/J.Bpj.2016.03.025 |
0.367 |
|
| 2016 |
Donovan RM, Tapia JJ, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, Zuckerman DM. Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. Plos Computational Biology. 12: e1004611. PMID 26845334 DOI: 10.1371/Journal.Pcbi.1004611 |
0.333 |
|
| 2015 |
Chylek LA, Harris LA, Faeder JR, Hlavacek WS. Modeling for (physical) biologists: an introduction to the rule-based approach. Physical Biology. 12: 045007. PMID 26178138 DOI: 10.1088/1478-3975/12/4/045007 |
0.359 |
|
| 2014 |
Wenskovitch JE, Harris LA, Tapia JJ, Faeder JR, Marai GE. MOSBIE: a tool for comparison and analysis of rule-based biochemical models. Bmc Bioinformatics. 15: 316. PMID 25253680 DOI: 10.1186/1471-2105-15-316 |
0.374 |
|
| 2014 |
Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR. Exact hybrid particle/population simulation of rule-based models of biochemical systems. Plos Computational Biology. 10: e1003544. PMID 24699269 DOI: 10.1371/Journal.Pcbi.1003544 |
0.364 |
|
| 2014 |
Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 6: 13-36. PMID 24123887 DOI: 10.1002/Wsbm.1245 |
0.407 |
|
| 2013 |
Donovan RM, Sedgewick AJ, Faeder JR, Zuckerman DM. Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. The Journal of Chemical Physics. 139: 115105. PMID 24070313 DOI: 10.1063/1.4821167 |
0.345 |
|
| 2013 |
Sheehan RP, Garg A, Gaffen SL, Faeder JR. 236 Cytokine. 63: 299. DOI: 10.1016/J.Cyto.2013.06.239 |
0.369 |
|
| 2012 |
Sekar JA, Faeder JR. Rule-based modeling of signal transduction: a primer. Methods in Molecular Biology (Clifton, N.J.). 880: 139-218. PMID 23361986 DOI: 10.1007/978-1-61779-833-7_9 |
0.4 |
|
| 2012 |
Smith AM, Xu W, Sun Y, Faeder JR, Marai GE. RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. Bmc Bioinformatics. 13: S3. PMID 22607382 DOI: 10.1186/1471-2105-13-S8-S3 |
0.351 |
|
| 2011 |
Horton AA, Wang B, Camp L, Price MS, Arshi A, Nagy M, Nadler SA, Faeder JR, Luckhart S. The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases. Bmc Genomics. 12: 574. PMID 22111877 DOI: 10.1186/1471-2164-12-574 |
0.307 |
|
| 2011 |
Faeder JR. Toward a comprehensive language for biological systems. Bmc Biology. 9: 68. PMID 22005092 DOI: 10.1186/1741-7007-9-68 |
0.356 |
|
| 2011 |
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models. Molecular Biosystems. 7: 2779-95. PMID 21647530 DOI: 10.1039/C1Mb05077J |
0.379 |
|
| 2011 |
Xu W, Smith AM, Faeder JR, Marai GE. RuleBender: a visual interface for rule-based modeling. Bioinformatics (Oxford, England). 27: 1721-2. PMID 21493655 DOI: 10.1093/Bioinformatics/Btr197 |
0.313 |
|
| 2011 |
Sneddon MW, Faeder JR, Emonet T. Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nature Methods. 8: 177-83. PMID 21186362 DOI: 10.1038/Nmeth.1546 |
0.412 |
|
| 2010 |
Gong H, Zuliani P, Komuravelli A, Faeder JR, Clarke EM. Analysis and verification of the HMGB1 signaling pathway. Bmc Bioinformatics. 11: S10. PMID 21106117 DOI: 10.1186/1471-2105-11-S7-S10 |
0.359 |
|
| 2010 |
Nag A, Faeder JR, Goldstein B. Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling. Iet Systems Biology. 4: 334-47. PMID 21073233 DOI: 10.1049/Iet-Syb.2010.0006 |
0.316 |
|
| 2010 |
Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophysical Journal. 98: 48-56. PMID 20085718 DOI: 10.1016/J.Bpj.2009.09.043 |
0.325 |
|
| 2009 |
Indest KJ, Buchholz WG, Faeder JR, Setlow P. Workshop report: modeling the molecular mechanism of bacterial spore germination and elucidating reasons for germination heterogeneity. Journal of Food Science. 74: R73-8. PMID 19723224 DOI: 10.1111/J.1750-3841.2009.01245.X |
0.325 |
|
| 2009 |
Hlavacek WS, Faeder JR. The complexity of cell signaling and the need for a new mechanics. Science Signaling. 2: pe46. PMID 19638613 DOI: 10.1126/Scisignal.281Pe46 |
0.347 |
|
| 2009 |
Faeder JR, Blinov ML, Hlavacek WS. Rule-based modeling of biochemical systems with BioNetGen. Methods in Molecular Biology (Clifton, N.J.). 500: 113-67. PMID 19399430 DOI: 10.1007/978-1-59745-525-1_5 |
0.405 |
|
| 2009 |
Barua D, Faeder JR, Haugh JM. A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. Plos Computational Biology. 5: e1000364. PMID 19381268 DOI: 10.1371/Journal.Pcbi.1000364 |
0.32 |
|
| 2009 |
Nag A, Monine MI, Faeder JR, Goldstein B. Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophysical Journal. 96: 2604-23. PMID 19348745 DOI: 10.1016/J.Bpj.2009.01.019 |
0.367 |
|
| 2009 |
Hu B, Matthew Fricke G, Faeder JR, Posner RG, Hlavacek WS. GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics (Oxford, England). 25: 1457-60. PMID 19321734 DOI: 10.1093/Bioinformatics/Btp173 |
0.34 |
|
| 2009 |
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG. Simulation of large-scale rule-based models. Bioinformatics (Oxford, England). 25: 910-7. PMID 19213740 DOI: 10.1093/Bioinformatics/Btp066 |
0.389 |
|
| 2009 |
An GC, Faeder JR. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Mathematical Biosciences. 217: 53-63. PMID 18835283 DOI: 10.1016/J.Mbs.2008.08.013 |
0.366 |
|
| 2008 |
Goldstein B, Coombs D, Faeder JR, Hlavacek WS. Kinetic proofreading model. Advances in Experimental Medicine and Biology. 640: 82-94. PMID 19065786 DOI: 10.1007/978-0-387-09789-3_8 |
0.322 |
|
| 2008 |
Borisov NM, Chistopolsky AS, Faeder JR, Kholodenko BN. Domain-oriented reduction of rule-based network models Iet Systems Biology. 2: 342-351. PMID 19045829 DOI: 10.1049/Iet-Syb:20070081 |
0.367 |
|
| 2008 |
Yang J, Monine MI, Faeder JR, Hlavacek WS. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 78: 031910. PMID 18851068 DOI: 10.1103/Physreve.78.031910 |
0.351 |
|
| 2008 |
Lipniacki T, Hat B, Faeder JR, Hlavacek WS. Stochastic effects and bistability in T cell receptor signaling. Journal of Theoretical Biology. 254: 110-22. PMID 18556025 DOI: 10.1016/J.Jtbi.2008.05.001 |
0.385 |
|
| 2008 |
Barua D, Faeder JR, Haugh JM. Computational models of tandem SRC homology 2 domain interactions and application to phosphoinositide 3-kinase. The Journal of Biological Chemistry. 283: 7338-45. PMID 18204097 DOI: 10.1074/Jbc.M708359200 |
0.304 |
|
| 2007 |
Torigoe C, Faeder JR, Oliver JM, Goldstein B. Kinetic proofreading of ligand-FcepsilonRI interactions may persist beyond LAT phosphorylation. Journal of Immunology (Baltimore, Md. : 1950). 178: 3530-5. PMID 17339448 DOI: 10.4049/Jimmunol.178.6.3530 |
0.337 |
|
| 2007 |
Barua D, Faeder JR, Haugh JM. Structure-based kinetic models of modular signaling protein function: focus on Shp2. Biophysical Journal. 92: 2290-300. PMID 17208977 DOI: 10.1529/Biophysj.106.093484 |
0.387 |
|
| 2007 |
Faeder J, Monine M, Nag A, Goldstein B, Hlavacek W. Rule-based modeling of signal transduction Journal of Critical Care. 22: 349-350. DOI: 10.1016/J.Jcrc.2007.10.033 |
0.346 |
|
| 2006 |
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. Rules for modeling signal-transduction systems. Science's Stke : Signal Transduction Knowledge Environment. 2006: re6. PMID 16849649 DOI: 10.1126/Stke.3442006Re6 |
0.377 |
|
| 2006 |
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Bio Systems. 83: 136-51. PMID 16233948 DOI: 10.1016/J.Biosystems.2005.06.014 |
0.389 |
|
| 2005 |
Faeder J, Ladanyi BM. Solvation dynamics in reverse micelles: the role of headgroup-solute interactions. The Journal of Physical Chemistry. B. 109: 6732-40. PMID 16851757 DOI: 10.1021/Jp045202M |
0.586 |
|
| 2005 |
Blinov ML, Faeder JR, Yang J, Goldstein B, Hlavacek WS. 'On-the-fly' or 'generate-first' modeling? Nature Biotechnology. 23: 1344-5; author reply. PMID 16273053 DOI: 10.1038/Nbt1105-1344 |
0.312 |
|
| 2004 |
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics (Oxford, England). 20: 3289-91. PMID 15217809 DOI: 10.1093/Bioinformatics/Bth378 |
0.404 |
|
| 2004 |
Goldstein B, Faeder JR, Hlavacek WS. Mathematical and computational models of immune-receptor signalling. Nature Reviews. Immunology. 4: 445-56. PMID 15173833 DOI: 10.1038/Nri1374 |
0.387 |
|
| 2003 |
Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B. The complexity of complexes in signal transduction. Biotechnology and Bioengineering. 84: 783-94. PMID 14708119 DOI: 10.1002/Bit.10842 |
0.353 |
|
| 2003 |
Faeder JR, Hlavacek WS, Reischl I, Blinov ML, Metzger H, Redondo A, Wofsy C, Goldstein B. Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model. Journal of Immunology (Baltimore, Md. : 1950). 170: 3769-81. PMID 12646643 DOI: 10.4049/Jimmunol.170.7.3769 |
0.357 |
|
| 2003 |
Faeder J, Albert MV, Ladanyi BM. Molecular dynamics simulations of the interior of aqueous reverse micelles: A comparison between sodium and potassium counterions Langmuir. 19: 2514-2520. DOI: 10.1021/La026755W |
0.568 |
|
| 2002 |
Goldstein B, Faeder JR, Hlavacek WS, Blinov ML, Redondo A, Wofsy C. Modeling the early signaling events mediated by FcepsilonRI. Molecular Immunology. 38: 1213-9. PMID 12217386 DOI: 10.1016/S0161-5890(02)00066-4 |
0.359 |
|
| 2001 |
Faeder J, Ladanyi BM. Solvation dynamics in aqueous reverse micelles: A computer simulation study Journal of Physical Chemistry B. 105: 11148-11158. DOI: 10.1021/Jp010632N |
0.588 |
|
| 2000 |
Faeder J, Ladanyi BM. Molecular Dynamics Simulations of the Interior of Aqueous Reverse Micelles The Journal of Physical Chemistry B. 104: 1033-1046. DOI: 10.1021/Jp993076U |
0.593 |
|
| 2000 |
Parson R, Faeder J, Delaney N. Charge flow and solvent dynamics in the photodissociation of solvated molecular ions Journal of Physical Chemistry A. 104: 9663-9665. DOI: 10.1021/Jp0019916 |
0.317 |
|
| 1998 |
Maslen PE, Faeder J, Parson R. An effective Hamiltonian for an electronically excited solute in a polarizable molecular solvent Molecular Physics. 94: 693-706. DOI: 10.1080/002689798167854 |
0.314 |
|
| 1998 |
Faeder J, Parson R. Ultrafast reaction dynamics in cluster ions: Simulation of the transient photoelectron spectrum of I- 2 Arn photodissociation Journal of Chemical Physics. 108: 3909-3914. DOI: 10.1063/1.475793 |
0.334 |
|
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