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
244 2016 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
225 2020 Molecular Chemisorption as the Theoretically Preferred Pathway <?format ?>for Water Adsorption on Ideal Rutile LA Harris, AA Quong
Physical review letters 93 (8), 086105, 2004
188 2004 Quantifying drug combination synergy along potency and efficacy axes CT Meyer, DJ Wooten, BB Paudel, J Bauer, KN Hardeman, D Westover, ...
Cell systems 8 (2), 97-108. e16, 2019
163 2019 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
161 2014 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
142 2008 An unbiased metric of antiproliferative drug effect in vitro LA Harris, PL Frick, SP Garbett, KN Hardeman, BB Paudel, CF Lopez, ...
Nature methods 13 (6), 497-500, 2016
114 2016 A “partitioned leaping” approach for multiscale modeling of chemical reaction dynamics LA Harris, P Clancy
The Journal of chemical physics 125 (14), 2006
95 2006 Modeling for (physical) biologists: an introduction to the rule-based approach LA Chylek, LA Harris, JR Faeder, WS Hlavacek
Physical biology 12 (4), 045007, 2015
72 2015 Compartmental rule-based modeling of biochemical systems LA Harris, JS Hogg, JR Faeder
Proceedings of the 2009 Winter Simulation Conference (WSC), 908-919, 2009
59 2009 Exact hybrid particle/population simulation of rule-based models of biochemical systems JS Hogg, LA Harris, LJ Stover, NS Nair, JR Faeder
PLoS computational biology 10 (4), e1003544, 2014
54 2014 A nonquiescent “idling” population state in drug-treated, BRAF-mutated melanoma BB Paudel, LA Harris, KN Hardeman, AA Abugable, CE Hayford, ...
Biophysical journal 114 (6), 1499-1511, 2018
39 2018 Modeling heterogeneous tumor growth dynamics and cell–cell interactions at single-cell and cell-population resolution LA Harris, S Beik, PMM Ozawa, L Jimenez, AM Weaver
Current opinion in systems biology 17, 24-34, 2019
37 2019 Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm KA Iyengar, LA Harris, P Clancy
The Journal of chemical physics 132 (9), 2010
36 2010 An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability CE Hayford, DR Tyson, CJ Robbins III, PL Frick, V Quaranta, LA Harris
PLoS Biology 19 (6), e3000797, 2021
31 2021 Activated oncogenic pathway modifies iron network in breast epithelial cells: a dynamic modeling perspective J Chifman, S Arat, Z Deng, E Lemler, JC Pino, LA Harris, MA Kochen, ...
PLoS computational biology 13 (2), e1005352, 2017
28 2017 Harris and quong reply LA Harris, AA Quong
Physical Review Letters 95 (2), 029602, 2005
23 2005 GPU-powered model analysis with PySB/cupSODA LA Harris, MS Nobile, JC Pino, ALR Lubbock, D Besozzi, G Mauri, ...
Bioinformatics 33 (21), 3492-3494, 2017
22 2017 MOSBIE: a tool for comparison and analysis of rule-based biochemical models JE Wenskovitch, LA Harris, JJ Tapia, JR Faeder, GE Marai
BMC bioinformatics 15, 1-16, 2014
21 2014 Quantifying stochastic effects in biochemical reaction networks using partitioned leaping LA Harris, AM Piccirilli, ER Majusiak, P Clancy
Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 79 (5 …, 2009
20 2009 