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2020 – today
- 2025
[j8]Ronald Galiwango, Christopher J. Whalen, Grace Kebirungi, Mugume T. Atwine, Rodgers Kimera, Alfred Ssekagiri, Timothy W. Kimbowa, Edward Lukyamuzi, Mike Nsubuga, Lloyd Ssentongo, Henry Mutegeki, John M. Fonner, Frank Wuerthwein, Ari Berman, Laura B. Okalebo, Meghan Coakley McCarthy, Victor S. Kramer, Mariam Quiñones, Phillip Cruz, Darrell E. Hurt, Maria Y. Giovanni, Nicola J. Mulder, Michael Tartakovsky, Jonathan K. Kayondo, Daudi Jjingo:
Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings. PLoS Comput. Biol. 21(9): 1013481 (2025)- [c11]William J. Allen
, Kelsey M. Beavers, Erik S. Ferlanti, Lorenzo Concia, Joshua Urrutia, Ernesto A. B. F. Lima, John M. Fonner, Felix Zuo, H. E. Duplechin Seymour, Ari B. Kahn, Joe Stubbs, Anagha Jamthe, Stephanie N. Baker, Tabish Khan, James P. Carson:
A Model for Teaching Machine Learning, Deep Learning, and Research Computing to Domain Scientists on HPC Resources. SC Workshops 2025: 401-408 - 2024
- [j7]Tyson L. Swetnam, Parker B. Antin, Ryan Bartelme, Alexander Bucksch, David Camhy, Greg Chism, Illyoung Choi, Amanda M. Cooksey, Michele Cosi, Cindy Cowen, Michael Culshaw-Maurer, Robert Davey, Sean Davey, Upendra Devisetty, Tony Edgin, Andy Edmonds, Dmitry V. Fedorov, Jeremy Frady, John M. Fonner, Jeffrey K. Gillan, Iqbal Hossain, Blake Joyce, Konrad Lang, Tina Lee, Shelley Littin, Ian McEwen, Nirav C. Merchant, David Micklos, Andrew Nelson, Ashley Ramsey, Sarah Roberts, Paul Sarando, Edwin Skidmore, Jawon Song, Mary Margaret Sprinkle, Sriram Srinivasan, Dan Stanzione, Jonathan D. Strootman, Sarah Stryeck, Reetu Tuteja, Matthew Vaughn, Mojib Wali, Mariah Wall, Ramona Walls, Liya Wang, Todd Wickizer, Jason Williams, John Wregglesworth, Eric Lyons:
CyVerse: Cyberinfrastructure for open science. PLoS Comput. Biol. 20(2) (2024) - [c10]Justin Drake, Niall Gaffney, Nathan Dean Freeman, Erik S. Ferlanti, John M. Fonner:
Human-powered AI Gym: Lessons Learned as the Test and Evaluation Team for the DARPA SHADE Program: Human-powered AI Gym. PEARC 2024: 38:1-38:5 - 2023
- [c9]Erik S. Ferlanti, William J. Allen, Ernesto A. B. F. Lima, Yinzhi Wang, John M. Fonner:
Perspectives and Experiences Supporting Containers for Research Computing at the Texas Advanced Computing Center. SC Workshops 2023: 155-164 - [c8]Tiffany Huff, Austin Darrow, Joshua Medina, Erik S. Ferlanti, James D. Carson, John M. Fonner, Sal Tijerina, Stanley J. Watowich, William J. Allen:
Scalable and Reproducible Virtual Screening through an API-Integrated Workflow. PEARC 2023: 196-199 - 2022
- [j6]Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John M. Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung:
Prediction of whole-cell transcriptional response with machine learning. Bioinform. 38(2): 404-409 (2022) - 2021
- [c7]Gregory J. Zynda, Shweta Gopaulakrishnan, John M. Fonner:
RollingGantryCrane: Automation for unpacking containers into HPC environments. CANOPIE-HPC@SC 2021: 29-34 - [c6]Amit Ruhela, Stephen Lien Harrell, Richard Todd Evans, Gregory J. Zynda, John M. Fonner, Matt Vaughn, Tommy Minyard, John Cazes:
Characterizing Containerized HPC Applications Performance at Petascale on CPU and GPU Architectures. ISC 2021: 411-430 - 2020
- [c5]Joe Stubbs, Julia Looney, Marjo Poindexter, Elias Chalhoub, Gregory J. Zynda, Erik S. Ferlanti, Matthew Vaughn, John M. Fonner, Maytal Dahan:
Integrating Jupyter into Research Computing Ecosystems: Challenges and Successes in Architecting JupyterHub for Collaborative Research Computing Ecosystems. PEARC 2020: 91-98
2010 – 2019
- 2018
- [c4]Sean B. Cleveland, Rion Dooley, David Perry, Joe Stubbs, John M. Fonner, Gwen A. Jacobs:
Building Science Gateway Infrastructure in the Middle of the Pacific and Beyond: Experiences using the Agave Deployer and Agave Platform to Build Science Gateways. PEARC 2018: 4:1-4:8 - [c3]Rion Dooley, Steven R. Brandt, John M. Fonner:
The Agave Platform: An Open, Science-as-a-Service Platform for Digital Science. PEARC 2018: 28:1-28:8 - 2017
- [j5]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:
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinform. 18(1): 448:1-448:5 (2017) - [j4]Lucas A. Wilson, John M. Fonner, Jason Allison, Oscar Esteban, Harry Kenya, Marshall Lerner:
Launcher: A simple tool for executing high throughput computing workloads. J. Open Source Softw. 2(16): 289 (2017) - 2016
- [j3]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, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell:
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinform. 17(S-13): 333 (2016) - 2014
- [j2]Richard D. LeDuc, Matthew Vaughn, John M. Fonner, Michael Sullivan, James G. Williams, Philip D. Blood, James Taylor, William K. Barnett:
Leveraging the national cyberinfrastructure for biomedical research. J. Am. Medical Informatics Assoc. 21(2): 195-199 (2014) - [j1]Usha Viswanathan, Suzanne M. Tomlinson, John M. Fonner, Stephen A. Mock, Stanley J. Watowich:
Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal. J. Chem. Inf. Model. 54(10): 2816-2825 (2014) - [c2]Matthew C. Cowperthwaite, James D. Carson, John M. Fonner, Oscar Jiao, Jawon Song, Matthew W. Vaughn:
The Texas Advanced Computing Center: A complete scientific discovery environment for biomedical informatics and health science research. AMIA 2014 - [c1]Lucas A. Wilson, John M. Fonner:
Launcher: A Shell-based Framework for Rapid Development of Parallel Parametric Studies. XSEDE 2014: 40:1-40:8
Coauthor Index
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