The Texas Advanced Computing Center: A complete scientific discovery environment for biomedical informatics and health science research. - Matthew C. Cowperthwaite; James D. Carson; John M. Fonner; Oscar Jiao; Jawon Song; Matthew W. Vaughn (AMIA, 2014)

Launcher: A Shell-based Framework for Rapid Development of Parallel Parametric Studies. - Lucas A. Wilson; John M. Fonner (XSEDE, 2014)

Leveraging the national cyberinfrastructure for biomedical research. - Richard D. LeDuc; Matthew Vaughn; John M. Fonner; Michael Sullivan; James G. Williams 003; Philip D. Blood; James Taylor 001; William K. Barnett (J. Am. Medical Informatics Assoc., 2014)

Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal. - Usha Viswanathan; Suzanne M. Tomlinson; John M. Fonner; Stephen A. Mock; Stanley J. Watowich (J. Chem. Inf. Model., 2014)

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. - Inimary T. Toby; Mikhail K. Levin; Edward Salinas; Scott Christley; Sanchita Bhattacharya; Felix Breden; Adam Buntzman; Brian Corrie; John M. Fonner; Namita T. Gupta; Uri Hershberg; Nishanth Marthandan; et al. (BMC Bioinform., 2016)

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. - Scott Christley; Mikhail K. Levin; Inimary T. Toby; John M. Fonner; Nancy Monson; William Rounds; Florian Rubelt; Walter Scarborough; Richard H. Scheuermann; Lindsay G. Cowell (BMC Bioinform., 2017)

Launcher: A simple tool for executing high throughput computing workloads. - Lucas A. Wilson; John M. Fonner; Jason Allison; Oscar Esteban; Harry Kenya; Marshall Lerner (J. Open Source Softw., 2017)

Building Science Gateway Infrastructure in the Middle of the Pacific and Beyond: Experiences using the Agave Deployer and Agave Platform to Build Science Gateways. - Sean B. Cleveland; Rion Dooley; David Perry; Joe Stubbs; John M. Fonner; Gwen A. Jacobs (PEARC, 2018)

The Agave Platform: An Open, Science-as-a-Service Platform for Digital Science. - Rion Dooley; Steven R. Brandt; John M. Fonner (PEARC, 2018)

Integrating Jupyter into Research Computing Ecosystems: Challenges and Successes in Architecting JupyterHub for Collaborative Research Computing Ecosystems. - Joe Stubbs; Julia Looney; Marjo Poindexter; Elias Chalhoub; Gregory J. Zynda; Erik S. Ferlanti; Matthew Vaughn; John M. Fonner; Maytal Dahan (PEARC, 2020)

RollingGantryCrane: Automation for unpacking containers into HPC environments. - Gregory J. Zynda; Shweta Gopaulakrishnan; John M. Fonner (CANOPIE-HPC@SC, 2021)

Characterizing Containerized HPC Applications Performance at Petascale on CPU and GPU Architectures. - Amit Ruhela; Stephen Lien Harrell; Richard Todd Evans; Gregory J. Zynda; John M. Fonner; Matt Vaughn; Tommy Minyard; John Cazes (ISC, 2021)

Perspectives and Experiences Supporting Containers for Research Computing at the Texas Advanced Computing Center. - Erik S. Ferlanti; William J. Allen; Ernesto A. B. F. Lima; Yinzhi Wang; John M. Fonner (SC Workshops, 2023)

Scalable and Reproducible Virtual Screening through an API-Integrated Workflow. - Tiffany Huff; Austin Darrow; Joshua Medina; Erik S. Ferlanti; James D. Carson; John M. Fonner; Sal Tijerina; Stanley J. Watowich; William J. Allen (PEARC, 2023)