M-BISON: Microarray-based integration of data sources using networks. - Bernie J. Daigle Jr.; Russ B. Altman (BMC Bioinform., 2008)

Independent component analysis: Mining microarray data for fundamental human gene expression modules. - Jesse M. Engreitz; Bernie J. Daigle Jr.; Jonathan J. Marshall; Russ B. Altman (J. Biomed. Informatics, 2010)

Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance. - Bernie J. Daigle Jr.; Alicia Deng; Tracey McLaughlin; Samuel W. Cushman; Margaret C. Cam; Gerald Reaven; Philip S. Tsao; Russ B. Altman (PLoS Comput. Biol., 2010)

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. - Bernie J. Daigle Jr.; Min K. Roh; Linda R. Petzold; Jarad Niemi (BMC Bioinform., 2012)

Core module biomarker identification with network exploration for breast cancer metastasis. - Ruoting Yang; Bernie J. Daigle Jr.; Linda R. Petzold; Francis J. Doyle III (BMC Bioinform., 2012)

Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder. - Ruoting Yang; Bernie J. Daigle Jr.; Seid Y. Muhie; Rasha Hammamieh; Marti Jett; Linda R. Petzold; Francis J. Doyle III (BMC Syst. Biol., 2013)

A Cure Time Model for Joint Prediction of Outcome and Time-to-Outcome. - Yuanyang Zhang; Bernie J. Daigle Jr.; Mitchell J. Cohen; Linda R. Petzold (ICDM, 2015)

Inferring single-cell gene expression mechanisms using stochastic simulation. - Bernie J. Daigle Jr.; Mohammad Soltani; Linda R. Petzold; Abhyudai Singh (Bioinform., 2015)

SParSE++: improved event-based stochastic parameter search. - Min K. Roh; Bernie J. Daigle Jr. (BMC Syst. Biol., 2016)

Identification of disease states associated with coagulopathy in trauma. - Yuanyang Zhang; Tie Bo Wu; Bernie J. Daigle Jr.; Mitchell J. Cohen; Linda R. Petzold (BMC Medical Informatics Decis. Mak., 2016)

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. - Brian Drawert; Andreas Hellander; Benjamin B. Bales; Debjani Banerjee; Giovanni Bellesia; Bernie J. Daigle Jr.; Geoffrey Douglas; Mengyuan Gu; Anand Gupta; Stefan Hellander; Christopher B. Horuk; Dibyendu Nath; et al. (PLoS Comput. Biol., 2016)

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016. - Eric C. Rouchka; Julia H. Chariker; Benjamin J. Harrison; Juw Won Park; Xueyuan Cao; Stanley Pounds; Susana C. Raimondi; James R. Downing; Raul C. Ribeiro; Jeffrey Rubnitz; Jatinder Lamba; Bernie J. Daigle Jr.; et al. (BMC Bioinform., 2016)

Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics: Burns, TN, USA. April 21-23, 2017. - Eric C. Rouchka; Julia H. Chariker; David Tieri; Juw Won Park; Shreedharkumar D. Rajurkar; Vikas Singh; Nishchal K. Verma; Yan Cui 001; Mark L. Farman; Bradford Condon; Neil Moore; Jerzy W. Jaromczyk; et al. (BMC Bioinform., 2017)

icHET: interactive visualization of cytoplasmic heteroplasmy. - Vinhthuy Phan; Diem-Trang Pham; Caroline Melton; Adam J. Ramsey; Bernie J. Daigle Jr.; Jennifer R. Mandel (Bioinform., 2019)

GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. - Liangqun Lu; Kevin A. Townsend; Bernie J. Daigle Jr. (BMC Bioinform., 2021)