John Arul Prakash Sekar

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James R FaederUniversity of PittsburghVerified email at pitt.edu
Jonathan KarrIcahn School of Medicine at Mount SinaiVerified email at mssm.edu
Jose Juan TapiaData Scientist, Monsanto CompanyVerified email at pitt.edu
Arthur GoldbergAssociate Professor of Genetics and Genomic Sciences, Institute for Genomics & Multiscale BiologyVerified email at mssm.edu
Yosef RothResearch Assistant, Mt. Sinai School of Medicine, Department of Genetics and Genomic SciencesVerified email at mssm.edu
Robert P SheehanHarvard Medical SchoolVerified email at hms.harvard.edu
Leonard A. HarrisUniversity of Arkansas, Department of Biomedical EngineeringVerified email at uark.edu
Ilya KorsunskyHarvard Medical SchoolVerified email at bwh.harvard.edu
Arshi AroraMemorial Sloan Kettering Cancer CenterVerified email at mskcc.org
Sanjana GuptaStanford UniversityVerified email at stanford.edu
Bilal ShaikhResearcher, Icahn School of Medicine at Mount SinaiVerified email at mssm.edu
Saahith PochirajuBioinformatician, Icahn School of MedicineVerified email at mssm.edu
Yin Hoon ChewPostdoctoral Research Associate, University of BirminghamVerified email at bham.ac.uk
Wolfram LiebermeisterINRAE Jouy-en-JosasVerified email at inrae.fr
Paul F LangSoftware engineer, BiosimVerified email at deeporigin.com
Yassmine ChebaroCNRSVerified email at igbmc.fr
Natasa Miskov-ZivanovUniversity of Pittsburgh, ECE, BioE, CompBioVerified email at pitt.edu
Penelope MorelProfessor of Immunology, University of PittsburghVerified email at pitt.edu

John Arul Prakash Sekar

Senior Scientist, Mt. Sinai School of Medicine, Department of Genetics and Genomic Sciences

Verified email at mssm.edu

cell modeling machine learning structural bioinformatics


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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	231	2016
A blueprint for human whole-cell modeling B Szigeti, YD Roth, JAP Sekar, AP Goldberg, SC Pochiraju, JR Karr Current opinion in systems biology 7, 8-15, 2018	74	2018
Emerging whole-cell modeling principles and methods AP Goldberg, B Szigeti, YH Chew, JAP Sekar, YD Roth, JR Karr Current opinion in biotechnology 51, 97-102, 2018	69	2018
Rule-based modeling of signal transduction: a primer JAP Sekar, JR Faeder Computational Modeling of Signaling Networks, 139-218, 2012	39	2012
Automated visualization of rule-based models JAP Sekar, JJ Tapia, JR Faeder PLoS computational biology 13 (11), e1005857, 2017	17	2017
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks PF Lang, Y Chebaro, X Zheng, JA P. Sekar, B Shaikh, DA Natale, JR Karr Genome biology 21, 1-21, 2020	13	2020
Energy-based modeling in BioNetGen JAP Sekar, JS Hogg, JR Faeder 2016 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2016	11	2016
Exact parallelization of the stochastic simulation algorithm for scalable simulation of large biochemical networks AP Goldberg, DR Jefferson, JAP Sekar, JR Karr arXiv preprint arXiv:2005.05295, 2020	6	2020
Structured spreadsheets with objtables enable data reuse and integration JR Karr, W Liebermeister, AP Goldberg, JAP Sekar, B Shaikh arXiv preprint arXiv:2005.05227, 2020	5	2020
Visualizing regulation in rule-based models JAP Sekar, JJ Tapia, JR Faeder arXiv preprint arXiv:1509.00896, 2015	3	2015
ObjTables: structured spreadsheets that promote data quality, reuse, and integration JR Karr, W Liebermeister, AP Goldberg, JAP Sekar, B Shaikh arXiv preprint arXiv:2005.05227, 2020	2	2020
An introduction to rule-based modeling of immune receptor signaling JAP Sekar, JR Faeder Systems Immunology, 71-90, 2018	2	2018
Rule-based modeling of cell signaling: Advances in model construction, visualization and simulation JAP Sekar University of Pittsburgh, 2015	2	2015
Modeling the Role of Antigen Stimulation in Treg vs. Teff Fate Selection (36.52) J Sekar, N Miskov-Zivanov, M Turner, P Morel, J Faeder The Journal of Immunology 184 (1_Supplement), 36.52-36.52, 2010		2010
Mechanistic analysis of reaction network models JJ Tapia, JAP Sekar, JR Faeder
Visualizing Rule-based models J Sekar, JR Faeder
Experimental Design in Rule-Based Models JAP Sekar, JR Faeder
Modeling of Peripheral T Cell Differentiation N Miskov-Zivanov, JAP Sekar, MS Turner, LP Kane, PA Morel, JR Faeder
Rule Refinement in BioNetGen JAP Sekar, JR Faeder
Modular Construction of Rule-Based Models JAP Sekar, JR Faeder

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