José Juan Tapia

14 papers A 1B 2Journal 7Unranked 3
YearRankTypeTitle / Venue / Authors
2020 J jnl
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
J. Integr. Bioinform.
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
2017 J jnl
Automated visualization of rule-based models.
PLoS Comput. Biol.
John A. P. Sekar, José Juan Tapia, James R. Faeder
2016 J jnl
BioNetGen 2.2: advances in rule-based modeling.
Bioinform.
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
2016 J jnl
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.
PLoS Comput. Biol.
Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman
2015 — conf
Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity.
ACM Great Lakes Symposium on VLSI
Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech
2014 J jnl
MOSBIE: a tool for comparison and analysis of rule-based biochemical models.
BMC Bioinform.
John E. Wenskovitch, Leonard A. Harris, José Juan Tapia, James R. Faeder, G. Elisabeta Marai
2013 — conf
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models.
BCB
José Juan Tapia, James R. Faeder
2012 — conf
Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation.
CDC
José Juan Tapia, James R. Faeder, Brian Munsky
2012 J jnl
Graphics processing unit based direct simulation Monte Carlo.
Simul.
Denis V. Gladkov, José Juan Tapia, Samuel Alberts, Roshan M. D'Souza
2011 J jnl
Parallelizing the Cellular Potts Model on graphics processing units.
Comput. Phys. Commun.
José Juan Tapia, Roshan M. D'Souza
2009 — ch.
A Clustering Genetic Algorithm for Genomic Data Mining.
Foundations of Computational Intelligence (4)
José Juan Tapia, Enrique Morett, Edgar E. Vallejo
2009 B conf
Data-Parallel Algorithms for Large-Scale Real-Time Simulation of the Cellular Potts Model on Graphics Processing Units.
SMC
José Juan Tapia, Roshan M. D'Souza
2009 A conf
MOCEA: a multi-objective clustering evolutionary algorithm for inferring protein-protein functional interactions.
GECCO
José Juan Tapia, Edgar E. Vallejo, Enrique Morett
2008 B conf
A clustering genetic algorithm for inferring protein-protein functional interactions from phylogenetic profiles.
IEEE Congress on Evolutionary Computation
José Juan Tapia, Edgar E. Vallejo