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Items: 1 to 50 of 68


Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology.

Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM, Bahar I.

Handb Exp Pharmacol. 2019 Jun 15. doi: 10.1007/164_2019_239. [Epub ahead of print]


MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.

Tapia JJ, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR.

Methods Mol Biol. 2019;1945:203-229. doi: 10.1007/978-1-4939-9102-0_9.


Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology.

Gupta S, Hainsworth L, Hogg JS, Lee REC, Faeder JR.

Proc Euromicro Int Conf Parallel Distrib Netw Based Process. 2018 Mar;2018:690-697. doi: 10.1109/PDP2018.2018.00114. Epub 2018 Jun 7.


Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors.

Singh M, Warita K, Warita T, Faeder JR, Lee REC, Sant S, Oltvai ZN.

Sci Rep. 2018 Jun 20;8(1):9388. doi: 10.1038/s41598-018-27266-8.


Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency.

Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I.

eNeuro. 2018 Feb 5;5(1). pii: ENEURO.0298-17.2017. doi: 10.1523/ENEURO.0298-17.2017. eCollection 2018 Jan-Feb.


Automated visualization of rule-based models.

Sekar JAP, Tapia JJ, Faeder JR.

PLoS Comput Biol. 2017 Nov 13;13(11):e1005857. doi: 10.1371/journal.pcbi.1005857. eCollection 2017 Nov.


NF-κB Dynamics Discriminate between TNF Doses in Single Cells.

Zhang Q, Gupta S, Schipper DL, Kowalczyk GJ, Mancini AE, Faeder JR, Lee REC.

Cell Syst. 2017 Dec 27;5(6):638-645.e5. doi: 10.1016/j.cels.2017.10.011. Epub 2017 Nov 8.


Demystifying the cytokine network: Mathematical models point the way.

Morel PA, Lee REC, Faeder JR.

Cytokine. 2017 Oct;98:115-123. doi: 10.1016/j.cyto.2016.11.013. Epub 2016 Dec 3. Review.


BioNetGen 2.2: advances in rule-based modeling.

Harris LA, Hogg JS, Tapia JJ, Sekar JA, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR.

Bioinformatics. 2016 Nov 1;32(21):3366-3368. Epub 2016 Jul 8.


Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments.

Faeder JR, Morel PA.

Biophys J. 2016 Apr 26;110(8):1681-1683. doi: 10.1016/j.bpj.2016.03.025. No abstract available.


Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.

Donovan RM, Tapia JJ, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, Zuckerman DM.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004611. doi: 10.1371/journal.pcbi.1004611. eCollection 2016 Feb.


The eighth q-bio conference: meeting report and special issue preface.

Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O.

Phys Biol. 2015 Dec 30;12(6):060401. doi: 10.1088/1478-3975/12/6/060401. No abstract available.


Memory of Germinant Stimuli in Bacterial Spores.

Wang S, Faeder JR, Setlow P, Li YQ.

MBio. 2015 Nov 24;6(6):e01859-15. doi: 10.1128/mBio.01859-15.


Modeling for (physical) biologists: an introduction to the rule-based approach.

Chylek LA, Harris LA, Faeder JR, Hlavacek WS.

Phys Biol. 2015 Jul 16;12(4):045007. doi: 10.1088/1478-3975/12/4/045007. Review.


Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions.

Hawse WF, Sheehan RP, Miskov-Zivanov N, Menk AV, Kane LP, Faeder JR, Morel PA.

J Immunol. 2015 May 15;194(10):4615-9. doi: 10.4049/jimmunol.1402554. Epub 2015 Apr 8.


MOSBIE: a tool for comparison and analysis of rule-based biochemical models.

Wenskovitch JE Jr, Harris LA, Tapia JJ, Faeder JR, Marai GE.

BMC Bioinformatics. 2014 Sep 25;15:316. doi: 10.1186/1471-2105-15-316.


Modeling the T cell immune response: a fascinating challenge.

Morel PA, Faeder JR, Hawse WF, Miskov-Zivanov N.

J Pharmacokinet Pharmacodyn. 2014 Oct;41(5):401-13. doi: 10.1007/s10928-014-9376-y. Epub 2014 Aug 26. Review.


The Seventh q-bio Conference: meeting report and preface.

Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y.

Phys Biol. 2014 Aug;11(4):040301. doi: 10.1088/1478-3975/11/4/040301. Epub 2014 Jul 30. No abstract available.


Exact hybrid particle/population simulation of rule-based models of biochemical systems.

Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR.

PLoS Comput Biol. 2014 Apr 3;10(4):e1003544. doi: 10.1371/journal.pcbi.1003544. eCollection 2014 Apr.


The duration of T cell stimulation is a critical determinant of cell fate and plasticity.

Miskov-Zivanov N, Turner MS, Kane LP, Morel PA, Faeder JR.

Sci Signal. 2013 Nov 5;6(300):ra97. doi: 10.1126/scisignal.2004217.


Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):13-36. doi: 10.1002/wsbm.1245. Epub 2013 Sep 30. Review.


Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.

Donovan RM, Sedgewick AJ, Faeder JR, Zuckerman DM.

J Chem Phys. 2013 Sep 21;139(11):115105. doi: 10.1063/1.4821167.


In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes.

Price I, Ermentrout B, Zamora R, Wang B, Azhar N, Mi Q, Constantine G, Faeder JR, Luckhart S, Vodovotz Y.

J Theor Biol. 2013 Oct 7;334:173-86. doi: 10.1016/j.jtbi.2013.05.028. Epub 2013 Jun 11.


Special section dedicated to The Sixth q-bio Conference: meeting report and preface.

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR.

Phys Biol. 2013 Jun;10(3):030301. doi: 10.1088/1478-3975/10/3/030301. Epub 2013 Jun 4. No abstract available.


Rule-based modeling of signal transduction: a primer.

Sekar JA, Faeder JR.

Methods Mol Biol. 2012;880:139-218. doi: 10.1007/978-1-61779-833-7_9. Review.


RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.

Smith AM, Xu W, Sun Y, Faeder JR, Marai GE.

BMC Bioinformatics. 2012;13 Suppl 8:S3. doi: 10.1186/1471-2105-13-S8-S3. Epub 2012 May 18.


Regulatory network analysis acceleration with reconfigurable hardware.

Miskov-Zivanov N, Bresticker A, Krishnaswamy D, Venkatakrishnan S, Kashinkunti P, Marculescu D, Faeder JR.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:149-52. doi: 10.1109/IEMBS.2011.6089916.


The interplay of double phosphorylation and scaffolding in MAPK pathways.

Kocieniewski P, Faeder JR, Lipniacki T.

J Theor Biol. 2012 Feb 21;295:116-24. doi: 10.1016/j.jtbi.2011.11.014. Epub 2011 Nov 25.


The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases.

Horton AA, Wang B, Camp L, Price MS, Arshi A, Nagy M, Nadler SA, Faeder JR, Luckhart S.

BMC Genomics. 2011 Nov 23;12:574. doi: 10.1186/1471-2164-12-574.


Toward a comprehensive language for biological systems.

Faeder JR.

BMC Biol. 2011 Oct 17;9:68. doi: 10.1186/1741-7007-9-68. Review.


Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing.

Nemenman I, Faeder JR, Hlavacek WS, Jiang Y, Wall ME, Zilman A.

Phys Biol. 2011 Oct;8(5):050301. doi: 10.1088/1478-3975/8/5/050301. Epub 2011 Aug 10.


Synergism between different germinant receptors in the germination of Bacillus subtilis spores.

Yi X, Liu J, Faeder JR, Setlow P.

J Bacteriol. 2011 Sep;193(18):4664-71. doi: 10.1128/JB.05343-11. Epub 2011 Jul 1. Erratum in: J Bacteriol. 2011 Nov;193(21):6111.


Guidelines for visualizing and annotating rule-based models.

Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS.

Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7.


RuleBender: a visual interface for rule-based modeling.

Xu W, Smith AM, Faeder JR, Marai GE.

Bioinformatics. 2011 Jun 15;27(12):1721-2. doi: 10.1093/bioinformatics/btr197. Epub 2011 Apr 14.


Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.

Sneddon MW, Faeder JR, Emonet T.

Nat Methods. 2011 Feb;8(2):177-83. doi: 10.1038/nmeth.1546. Epub 2010 Dec 26.


Analysis and verification of the HMGB1 signaling pathway.

Gong H, Zuliani P, Komuravelli A, Faeder JR, Clarke EM.

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S10. doi: 10.1186/1471-2105-11-S7-S10.


Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling.

Nag A, Faeder JR, Goldstein B.

IET Syst Biol. 2010 Nov;4(6):334-47. doi: 10.1049/iet-syb.2010.0006.


Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates.

Monine MI, Posner RG, Savage PB, Faeder JR, Hlavacek WS.

Biophys J. 2010 Jan 6;98(1):48-56. doi: 10.1016/j.bpj.2009.09.043.


Toward a quantitative theory of intrinsically disordered proteins and their function.

Liu J, Faeder JR, Camacho CJ.

Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19819-23. doi: 10.1073/pnas.0907710106. Epub 2009 Nov 10.


Simulations of ICl-(CO2)n photodissociation: effects of structure, excited state charge flow, and solvent dynamics.

Faeder JR, Parson R.

J Phys Chem A. 2010 Jan 28;114(3):1347-56. doi: 10.1021/jp905811t.


Workshop report: modeling the molecular mechanism of bacterial spore germination and elucidating reasons for germination heterogeneity.

Indest KJ, Buchholz WG, Faeder JR, Setlow P.

J Food Sci. 2009 Aug;74(6):R73-8. doi: 10.1111/j.1750-3841.2009.01245.x.


The complexity of cell signaling and the need for a new mechanics.

Hlavacek WS, Faeder JR.

Sci Signal. 2009 Jul 28;2(81):pe46. doi: 10.1126/scisignal.281pe46.


Rule-based modeling of biochemical systems with BioNetGen.

Faeder JR, Blinov ML, Hlavacek WS.

Methods Mol Biol. 2009;500:113-67. doi: 10.1007/978-1-59745-525-1_5.


A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases.

Barua D, Faeder JR, Haugh JM.

PLoS Comput Biol. 2009 Apr;5(4):e1000364. doi: 10.1371/journal.pcbi.1000364. Epub 2009 Apr 17.


Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system.

Nag A, Monine MI, Faeder JR, Goldstein B.

Biophys J. 2009 Apr 8;96(7):2604-23. doi: 10.1016/j.bpj.2009.01.019.


GetBonNie for building, analyzing and sharing rule-based models.

Hu B, Matthew Fricke G, Faeder JR, Posner RG, Hlavacek WS.

Bioinformatics. 2009 Jun 1;25(11):1457-60. doi: 10.1093/bioinformatics/btp173. Epub 2009 Mar 25.


Simulation of large-scale rule-based models.

Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG.

Bioinformatics. 2009 Apr 1;25(7):910-7. doi: 10.1093/bioinformatics/btp066. Epub 2009 Feb 11.


Kinetic proofreading model.

Goldstein B, Coombs D, Faeder JR, Hlavacek WS.

Adv Exp Med Biol. 2008;640:82-94. doi: 10.1007/978-0-387-09789-3_8. Review.


Domain-oriented reduction of rule-based network models.

Borisov NM, Chistopolsky AS, Faeder JR, Kholodenko BN.

IET Syst Biol. 2008 Sep;2(5):342-51. doi: 10.1049/iet-syb:20070081.


Selected papers from the First q-bio Conference on Cellular Information Processing.

Nemenman I, Hlavacek WS, Edwards JS, Faeder JR, Jiang Y, Wall ME.

IET Syst Biol. 2008 Sep;2(5):203-5. doi: 10.1049/iet-syb:20089018. No abstract available.


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