José Juan Tapia

Publication Activity (10 Years)

Years Active: 2008-2020
Publications (10 Years): 5

Top Topics

Design Automation

Markovian Decision

Molecular Structure

Top Venues

PLoS Comput. Biol.

Publications

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)
John A. P. Sekar, José Juan Tapia, James R. Faeder
Automated visualization of rule-based models. PLoS Comput. Biol. 13 (11) (2017)
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) (2016)
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)
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)
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 (2014)
José Juan Tapia, James R. Faeder
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. BCB (2013)
José Juan Tapia, James R. Faeder, Brian Munsky
Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation. CDC (2012)
Denis V. Gladkov, José Juan Tapia, Samuel Alberts, Roshan M. D'Souza
Graphics processing unit based direct simulation Monte Carlo. Simul. 88 (6) (2012)
José Juan Tapia, Roshan M. D'Souza
Parallelizing the Cellular Potts Model on graphics processing units. Comput. Phys. Commun. 182 (4) (2011)
José Juan Tapia, Edgar E. Vallejo, Enrique Morett
MOCEA: a multi-objective clustering evolutionary algorithm for inferring protein-protein functional interactions. GECCO (2009)
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)
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)