A clustering genetic algorithm for inferring protein-protein functional interactions from phylogenetic profiles. - José Juan Tapia; Edgar E. Vallejo (IEEE Congress on Evolutionary Computation, 2008)

MOCEA: a multi-objective clustering evolutionary algorithm for inferring protein-protein functional interactions. - José Juan Tapia; Edgar E. Vallejo; Enrique Morett (GECCO, 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 (SMC, 2009)

A Clustering Genetic Algorithm for Genomic Data Mining. - José Juan Tapia; Enrique Morett; Edgar E. Vallejo (Foundations of Computational Intelligence (4), 2009)

Parallelizing the Cellular Potts Model on graphics processing units. - José Juan Tapia; Roshan M. D'Souza (Comput. Phys. Commun., 2011)

Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation. - José Juan Tapia; James R. Faeder; Brian Munsky (CDC, 2012)

Graphics processing unit based direct simulation Monte Carlo. - Denis V. Gladkov; José Juan Tapia; Samuel Alberts; Roshan M. D'Souza (Simul., 2012)

The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. - José Juan Tapia; James R. Faeder (BCB, 2013)

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)

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 (ACM Great Lakes Symposium on VLSI, 2015)

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)

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)

Automated visualization of rule-based models. - John A. P. Sekar; José Juan Tapia; James R. Faeder (PLoS Comput. Biol., 2017)

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 001; Andreas Dräger; Leonard A. Harris; Andrew Finney; Bin Hu 025; et al. (J. Integr. Bioinform., 2020)