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José Juan Tapia
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2020 – today
- 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)
2010 – 2019
- 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) - 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 - 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) - 2013
- [c5]José Juan Tapia, James R. Faeder
:
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. BCB 2013: 726 - 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) - [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 - 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)
2000 – 2009
- 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 - [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 - 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
Coauthor Index
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