José Juan Tapia

According to our database, José Juan Tapia authored at least 14 papers between 2008 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.

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

J. Integr. Bioinform., 2020

2017

Automated visualization of rule-based models.

John A. P. Sekar, José Juan Tapia, James R. Faeder

PLoS Comput. Biol., 2017

2016

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.

Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman

PLoS Comput. Biol., 2016

BioNetGen 2.2: advances in rule-based modeling.

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

Bioinform., 2016

2015

Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity.

Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech

Proceedings of the 25th edition on Great Lakes Symposium on VLSI, GLVLSI 2015, Pittsburgh, PA, USA, May 20, 2015

2014

MOSBIE: a tool for comparison and analysis of rule-based biochemical models.

John E. Wenskovitch, Leonard A. Harris, José Juan Tapia, James R. Faeder, G. Elisabeta Marai

BMC Bioinform., 2014

2013

The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models.

José Juan Tapia, James R. Faeder

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

Graphics processing unit based direct simulation Monte Carlo.

Denis V. Gladkov, José Juan Tapia, Samuel Alberts, Roshan M. D'Souza

Simul., 2012

Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation.

José Juan Tapia, James R. Faeder, Brian Munsky

Proceedings of the 51th IEEE Conference on Decision and Control, 2012

2011

Parallelizing the Cellular Potts Model on graphics processing units.

José Juan Tapia, Roshan M. D'Souza

Comput. Phys. Commun., 2011

2009

A Clustering Genetic Algorithm for Genomic Data Mining.

José Juan Tapia, Enrique Morett, Edgar E. Vallejo

Proceedings of the Foundations of Computational Intelligence, 2009

Data-Parallel Algorithms for Large-Scale Real-Time Simulation of the Cellular Potts Model on Graphics Processing Units.

José Juan Tapia, Roshan M. D'Souza

Proceedings of the IEEE International Conference on Systems, 2009

MOCEA: a multi-objective clustering evolutionary algorithm for inferring protein-protein functional interactions.

José Juan Tapia, Edgar E. Vallejo, Enrique Morett

Proceedings of the Genetic and Evolutionary Computation Conference, 2009

2008

A clustering genetic algorithm for inferring protein-protein functional interactions from phylogenetic profiles.

José Juan Tapia, Edgar E. Vallejo

Proceedings of the IEEE Congress on Evolutionary Computation, 2008