Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units

Por Komarov, Ivan, D’Souza, Roshan M., Tapia, Jose-Juan
Publicado em 2012

Automated visualization of rule-based models

Por Sekar, John Arul Prakash, Tapia, Jose-Juan, Faeder, James R.
Publicado no PLoS Comput Biol (2017)

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

Por E Wenskovitch, John, Harris, Leonard A, Tapia, Jose-Juan, Faeder, James R, Marai, G Elisabeta
Publicado no BMC Bioinformatics (2014)

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

Por Donovan, Rory M., Tapia, Jose-Juan, Sullivan, Devin P., Faeder, James R., Murphy, Robert F., Dittrich, Markus, Zuckerman, Daniel M.
Publicado no PLoS Comput Biol (2016)

BioNetGen 2.2: advances in rule-based modeling

Por Harris, Leonard A., Hogg, Justin S., Tapia, José-Juan, Sekar, John A. P., Gupta, Sanjana, Korsunsky, Ilya, Arora, Arshi, Barua, Dipak, Sheehan, Robert P., Faeder, James R.
Publicado no Bioinformatics (2016)