The Genome Reverse Compiler: an explorative annotation tool. - Andrew S. Warren; João Carlos Setubal (BMC Bioinform., 2009)

Missing genes in the annotation of prokaryotic genomes. - Andrew S. Warren; Jeremy S. Archuleta; Wu-chun Feng; João Carlos Setubal (BMC Bioinform., 2010)

Global-scale distributed I/O with ParaMEDIC. - Pavan Balaji; Wu-chun Feng; Heshan Lin; Jeremy S. Archuleta; Satoshi Matsuoka; Andrew S. Warren; João Carlos Setubal; Ewing L. Lusk; Rajeev Thakur; Ian T. Foster; Daniel S. Katz; Shantenu Jha; et al. (Concurr. Comput. Pract. Exp., 2010)

Using Entropy Estimates for DAG-Based Ontologies. - Andrew S. Warren; João C. Setubal (CoRR, 2014)

PATRIC, the bacterial bioinformatics database and analysis resource. - Alice R. Wattam; David Abraham; Oral Dalay; Terry Disz; Timothy Driscoll; Joseph L. Gabbard; Joseph J. Gillespie; Roger Gough; Deborah Hix; Ronald W. Kenyon; Dustin Machi; Chunhong Mao; et al. (Nucleic Acids Res., 2014)

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. - Andrew S. Warren; Cristina Aurrecoechea; Brian P. Brunk; Prerak Desai; Scott J. Emrich; Gloria I. Giraldo-Calderón; Omar S. Harb; Deborah Hix; Daniel Lawson; Dustin Machi; Chunhong Mao; Michael McClelland; et al. (Bioinform., 2015)

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. - Alice R. Wattam; James J. Davis 002; Rida Assaf; Sébastien Boisvert; Thomas S. Brettin; Christopher Bun; Neal Conrad; Emily M. Dietrich; Terry Disz; Joseph L. Gabbard; Svetlana Gerdes; Christopher S. Henry; et al. (Nucleic Acids Res., 2017)

Methods for Analysis of Prokaryotic Genome Architecture. - Andrew S. Warren (2017)

PATRIC as a unique resource for studying antimicrobial resistance. - Dionysios A. Antonopoulos; Rida Assaf; Ramy Karam Aziz; Thomas S. Brettin; Christopher Bun; Neal Conrad; James J. Davis 002; Emily M. Dietrich; Terry Disz; Svetlana Gerdes; Ronald W. Kenyon; Dustin Machi; et al. (Briefings Bioinform., 2019)

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. - James J. Davis 002; Alice R. Wattam; Ramy K. Aziz; Thomas S. Brettin; Ralph Butler; Rory Butler; Philippe Chlenski; Neal Conrad; Allan Dickerman; Emily M. Dietrich; Joseph L. Gabbard; Svetlana Gerdes; et al. (Nucleic Acids Res., 2020)

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. - Margo VanOeffelen; Marcus Nguyen; Derya Aytan-Aktug; Thomas S. Brettin; Emily M. Dietrich; Ronald W. Kenyon; Dustin Machi; Chunhong Mao; Robert Olson; Gordon D. Pusch; Maulik Shukla; Rick Stevens; et al. (Briefings Bioinform., 2021)

Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support. - Parantapa Bhattacharya; Jiangzhuo Chen; Stefan Hoops; Dustin Machi; Bryan L. Lewis; Srinivasan Venkatramanan; Mandy L. Wilson; Brian Klahn; Aniruddha Adiga; Benjamin Hurt; Joseph Outten; Abhijin Adiga; et al. (Int. J. High Perform. Comput. Appl., 2023)

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. - Robert D. Olson; Rida Assaf; Thomas S. Brettin; Neal Conrad; Clark Cucinell; James J. Davis 002; Donald M. Dempsey; Allan Dickerman; Emily M. Dietrich; Ronald W. Kenyon; Mehmet Kuscuoglu; Elliot J. Lefkowitz; et al. (Nucleic Acids Res., 2023)

Agent-Based Simulation Framework for Multi-Variant Surveillance. - Sifat Afroj Moon; Jiangzhuo Chen; Baltazar Espinoza; Bryan Lewis 001; Madhav V. Marathe; Joseph Outten; Srinivasan Venkatramanan; Anil Vullikanti; Andrew S. Warren (WSC, 2024)