Jose Juan Tapia
Jose Juan Tapia
Data Scientist, Monsanto Company
Verified email at pitt.edu
Title
Cited by
Cited by
Year
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
1092016
Germination studies in endemic plant species of the Iberian Peninsula
F Pérez-García, JM Iriondo, ME González-Benito, LF Carnes, J Tapia, ...
Israel Journal of Plant Sciences 43 (3), 239-247, 1995
481995
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
242016
Parallelizing the cellular potts model on graphics processing units
JJ Tapia, RM D'Souza
Computer Physics Communications 182 (4), 857-865, 2011
212011
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), 1-16, 2014
172014
Accelerating the Gillespie τ-leaping method using graphics processing units
I Komarov, RM D’Souza, JJ Tapia
PloS one 7 (6), e37370, 2012
172012
Graphics processing unit based direct simulation Monte Carlo
D Gladkov, JJ Tapia, S Alberts, RM D’Souza
Simulation 88 (6), 680-693, 2012
172012
A clustering genetic algorithm for genomic data mining
JJ Tapia, E Morett, EE Vallejo
Foundations of Computational Intelligence Volume 4, 249-275, 2009
172009
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
152012
The Atomizer: extracting implicit molecular structure from reaction network models
JJ Tapia, JR Faeder
Proceedings of the International Conference on Bioinformatics, Computational …, 2013
132013
Automated visualization of rule-based models
JAP Sekar, JJ Tapia, JR Faeder
PLoS computational biology 13 (11), e1005857, 2017
122017
Micropropagation of commercial and wild genotypes of snapdragon (Antirrhinum spp.)
M Elena Gonzalez-Benito, J Tapia, N Rodriguez, JM Iriondo
Journal of Horticultural science 71 (1), 11-15, 1996
121996
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
62015
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
52009
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
52008
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
42009
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, 203-229, 2019
32019
Visualizing regulation in rule-based models
JAP Sekar, JJ Tapia, JR Faeder
arXiv preprint arXiv:1509.00896, 2015
32015
Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation
B Munsky, JJ Tapia, J Faeder
Los Alamos National Lab.(LANL), Los Alamos, NM (United States), 2012
32012
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
22010
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Articles 1–20