| 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 | 255 | 2016 |
| Unbiased rare event sampling in spatial stochastic systems biology models using a weighted ensemble of trajectories RM Donovan, JJ Tapia, DP Sullivan, JR Faeder, RF Murphy, M Dittrich, ... PLoS computational biology 12 (2), e1004611, 2016 | 45 | 2016 |
| Parallelizing the cellular potts model on graphics processing units JJ Tapia, RM D'Souza Computer Physics Communications 182 (4), 857-865, 2011 | 30 | 2011 |
| Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units I Komarov, RM D’Souza, JJ Tapia PLoS One 7 (6), e37370, 2012 | 25 | 2012 |
| A clustering genetic algorithm for genomic data mining JJ Tapia, E Morett, EE Vallejo Foundations of Computational Intelligence Volume 4: Bio-Inspired Data Mining …, 2009 | 23 | 2009 |
| 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 |
| Graphics processing unit based direct simulation Monte Carlo D Gladkov, JJ Tapia, S Alberts, RM D’Souza Simulation 88 (6), 680-693, 2012 | 21 | 2012 |
| MCell-R: A particle-resolution network-free spatial modeling framework JJ Tapia, AS Saglam, J Czech, R Kuczewski, TM Bartol, TJ Sejnowski, ... Modeling Biomolecular Site Dynamics: Methods and Protocols, 203-229, 2019 | 18 | 2019 |
| Automated visualization of rule-based models JAP Sekar, JJ Tapia, JR Faeder PLoS computational biology 13 (11), e1005857, 2017 | 18 | 2017 |
| The Atomizer: extracting implicit molecular structure from reaction network models JJ Tapia, JR Faeder Proceedings of the International Conference on Bioinformatics, Computational …, 2013 | 18 | 2013 |
| Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation JJ Tapia, JR Faeder, B Munsky 2012 IEEE 51st IEEE Conference on Decision and Control (CDC), 5361-5366, 2012 | 16 | 2012 |
| Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2 F Zhang, LP Smith, ML Blinov, J Faeder, WS Hlavacek, J Juan Tapia, ... Journal of Integrative Bioinformatics 17 (2-3), 20200015, 2020 | 14 | 2020 |
| Data-parallel algorithms for large-scale real-time simulation of the cellular Potts model on graphics processing units JJ Tapia, R D'Souza 2009 IEEE International Conference on Systems, Man and Cybernetics, 1411-1418, 2009 | 8 | 2009 |
| Design automation for biological models: a pipeline that incorporates spatial and molecular complexity DP Sullivan, R Arepally, RF Murphy, JJ Tapia, JR Faeder, M Dittrich, ... Proceedings of the 25th edition on Great Lakes Symposium on VLSI, 321-323, 2015 | 6 | 2015 |
| A clustering genetic algorithm for inferring protein-protein functional interactions from phylogenetic profiles JJ Tapia, EE Vallejo Evolutionary Computation, 2008. CEC 2008.(IEEE World Congress on …, 2008 | 5 | 2008 |
| MOCEA: A multi-objective clustering evolutionary algorithm for inferring protein-protein functional interactions JJ Tapia, EE Vallejo, E Morett Proceedings of the 11th Annual conference on Genetic and evolutionary …, 2009 | 4 | 2009 |
| Visualizing regulation in rule-based models JAP Sekar, JJ Tapia, JR Faeder arXiv preprint arXiv:1509.00896, 2015 | 3 | 2015 |
| QB1-Stochastic Gene Regulation B Munsky Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2012 | 3 | 2012 |
| Preliminary work on graphics processing unit based direct simulation Monte Carlo D Gladkov, JJ Tapia, RM D'Souza Proceedings of the 2010 Conference on Grand Challenges in Modeling …, 2010 | 2 | 2010 |
| RuleHub: an environment for developing and sharing rule-based models JJ Tapia, JR Faeder Proceedings of 8th Annual q-bio Conference on Cellular Information Processing, 2014 | 1 | 2014 |
James R FaederUniversity of PittsburghZweryfikowany adres z pitt.edu