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ORCIDJosé Juan Tapia
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Journal Articles
- 2020
[j7]Fengkai Zhang
, Lucian P. Smith, Michael L. Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia, Sarah M. Keating, Nicolas Rodriguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim:
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J. Integr. Bioinform. 17(2-3) (2020)- 2017
- [j6]John A. P. Sekar, José Juan Tapia, James R. Faeder:
Automated visualization of rule-based models. PLoS Comput. Biol. 13(11) (2017) - 2016
- [j5]Leonard A. Harris, Justin S. Hogg, José Juan Tapia, John A. P. Sekar, Sanjana Gupta, Ilya Korsunsky, Arshi Arora, Dipak Barua, Robert P. Sheehan, James R. Faeder:
BioNetGen 2.2: advances in rule-based modeling. Bioinform. 32(21): 3366-3368 (2016) - [j4]Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman:
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Comput. Biol. 12(2) (2016) - 2014
- [j3]John E. Wenskovitch, Leonard A. Harris, José Juan Tapia, James R. Faeder, G. Elisabeta Marai:
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. BMC Bioinform. 15: 316 (2014) - 2012
- [j2]Denis V. Gladkov, José Juan Tapia, Samuel Alberts, Roshan M. D'Souza:
Graphics processing unit based direct simulation Monte Carlo. Simul. 88(6): 680-693 (2012) - 2011
- [j1]José Juan Tapia, Roshan M. D'Souza:
Parallelizing the Cellular Potts Model on graphics processing units. Comput. Phys. Commun. 182(4): 857-865 (2011)
Conference and Workshop Papers
- 2015
- [c6]Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech:
Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity. ACM Great Lakes Symposium on VLSI 2015: 321-323 - 2013
- [c5]José Juan Tapia, James R. Faeder:
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. BCB 2013: 726 - 2012
- [c4]José Juan Tapia, James R. Faeder, Brian Munsky:
Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation. CDC 2012: 5361-5366 - 2009
- [c3]José Juan Tapia, Edgar E. Vallejo, Enrique Morett:
MOCEA: a multi-objective clustering evolutionary algorithm for inferring protein-protein functional interactions. GECCO 2009: 1793-1794 - [c2]José Juan Tapia, Roshan M. D'Souza:
Data-Parallel Algorithms for Large-Scale Real-Time Simulation of the Cellular Potts Model on Graphics Processing Units. SMC 2009: 1411-1418 - 2008
- [c1]José Juan Tapia, Edgar E. Vallejo:
A clustering genetic algorithm for inferring protein-protein functional interactions from phylogenetic profiles. IEEE Congress on Evolutionary Computation 2008: 2757-2763
Parts in Books or Collections
- 2009
- [p1]José Juan Tapia, Enrique Morett, Edgar E. Vallejo:
A Clustering Genetic Algorithm for Genomic Data Mining. Foundations of Computational Intelligence (4) 2009: 249-275
Coauthor Index
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