| 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 | 230 | 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 | 203 | 2020 |
| Molecular Chemisorption as the Theoretically Preferred Pathway for Water Adsorption on Ideal Rutile T i O 2 (110) LA Harris, AA Quong Physical review letters 93 (8), 086105, 2004 | 188 | 2004 |
| 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 | 157 | 2014 |
| 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 | 150 | 2019 |
| 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 | 141 | 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 | 109 | 2016 |
| A “partitioned leaping” approach for multiscale modeling of chemical reaction dynamics LA Harris, P Clancy The Journal of chemical physics 125 (14), 2006 | 93 | 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 | 69 | 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 | 56 | 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 | 52 | 2014 |
| 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 | 36 | 2019 |
| 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 | 36 | 2018 |
| 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 | 28 | 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 | 25 | 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 79 (5), 051906, 2009 | 21 | 2009 |
