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Jose Juan Tapia
Jose Juan Tapia
Data Scientist, Monsanto Company
Bestätigte E-Mail-Adresse bei pitt.edu
Titel
Zitiert von
Zitiert von
Jahr
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
2292016
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
442016
Parallelizing the cellular potts model on graphics processing units
JJ Tapia, RM D'Souza
Computer Physics Communications 182 (4), 857-865, 2011
262011
Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units
I Komarov, RM D’Souza, JJ Tapia
PloS one 7 (6), e37370, 2012
252012
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
212014
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
212009
Graphics processing unit based direct simulation Monte Carlo
D Gladkov, JJ Tapia, S Alberts, RM D’Souza
Simulation 88 (6), 680-693, 2012
202012
Automated visualization of rule-based models
JAP Sekar, JJ Tapia, JR Faeder
PLoS computational biology 13 (11), e1005857, 2017
172017
The Atomizer: extracting implicit molecular structure from reaction network models
JJ Tapia, JR Faeder
Proceedings of the International Conference on Bioinformatics, Computational …, 2013
172013
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
172012
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
162019
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
112020
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
82009
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
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
Visualizing regulation in rule-based models
JAP Sekar, JJ Tapia, JR Faeder
arXiv preprint arXiv:1509.00896, 2015
32015
QB1-Stochastic Gene Regulation
B Munsky
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
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
12014
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