CyVerse: Cyberinfrastructure for open science - 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; et al. (PLoS Comput. Biol., 2024)

Prediction of whole-cell transcriptional response with machine learning - 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; et al. (Bioinform., 2022)

Large Scale Science on NSF's Frontera System - John West; Paul A. Navrátil; Maytal Dahan; Matthew Vaughn (Comput. Sci. Eng., 2021)

The relationships between misinformation and outrage trolling tactics on two Yahoo! Answers categories - Pnina Fichman; Matthew Vaughn (J. Assoc. Inf. Sci. Technol., 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 (High Performance Computing - 36th International Conference, ISC High Performance 2021, Virtual Event, June 24 - July 2, 2021, Proceedings, 2021)

Jetstream2: Accelerating cloud computing via Jetstream - David Y. Hancock; Jeremy Fischer; John Michael Lowe; Winona Snapp-Childs; Marlon E. Pierce; Suresh Marru; J. Eric Coulter; Matthew Vaughn; Brian W. Beck; Nirav C. Merchant; Edwin Skidmore; Gwen A. Jacobs (PEARC '21: Practice and Experience in Advanced Research Computing, Boston, MA, USA, July 18-22, 2021, 2021)

How to undertake ideologically contentious research: Leaning on reflexivity and positionality to address uncomfortable disjuncture's in information research - Shannon M. Oltmann; Sarah Barriage; Devon L. Greyson; Matthew Vaughn (Information for a Sustainable World: Addressing Society's Grand Challenges - Proceedings of the 83rd ASIS&T Annual Meeting, ASIST 2020, Virtual Conference, October 22 - November 1, 2020, 2020)

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 '20: Practice and Experience in Advanced Research Computing, Portland, OR, USA, July 27-31, 2020, 2020)

Jetstream - Early operations performance, adoption, and impacts - David Y. Hancock; Craig A. Stewart; Matthew Vaughn; Jeremy Fischer; John Michael Lowe; George W. Turner; Tyson Lee Swetnam; Tyler K. Chafin; Enis Afgan; Marlon E. Pierce; Winona Snapp-Childs (Concurr. Comput. Pract. Exp., 2019)

Hyperparameter Optimization of Topological Features for Machine Learning Applications - Francis C. Motta; John Harer; Nick Leiby; Franco Marinozzi; Scott Novotney; Gabe Rocklin; Jed Singer; Devin Strickland; Matt Vaughn; Christopher J. Tralie; Rossella Bedini; Fabiano Bini; et al. (18th IEEE International Conference On Machine Learning And Applications, ICMLA 2019, Boca Raton, FL, USA, December 16-19, 2019, 2019)

Platform for Automated Real-Time High Performance Analytics on Medical Image Data - William J. Allen; Refaat E. Gabr; Getaneh B. Tefera; Amol S. Pednekar; Matthew W. Vaughn; Ponnada A. Narayana (IEEE J. Biomed. Health Informatics, 2018)

Rapid Development of Scalable, Distributed Computation with Abaco - Joe Stubbs; Matthew Vaughn; Julia Looney (Proceedings of the 10th International Workshop on Science Gateways, Edinburgh, Scotland, UK, 13-15 June, 2018, 2018)

Repliscan: a tool for classifying replication timing regions - Gregory J. Zynda; Jawon Song; Lorenzo Concia; Emily E. Wear; Linda Hanley-Bowdoin; William F. Thompson; Matthew W. Vaughn (BMC Bioinform., 2017)

Engineering Academic Software (Dagstuhl Perspectives Workshop 16252) - Alice Allen; Cecilia R. Aragon; Christoph Becker; Jeffrey C. Carver; Andrei Chis; Benoît Combemale; Mike Croucher; Kevin Crowston; Daniel Garijo; Ashish Gehani; Carole A. Goble; Robert Haines; et al. (Dagstuhl Manifestos, 2017)

Jetstream: performance, early experiences, and early results - Craig A. Stewart; David Y. Hancock; Matthew Vaughn; Jeremy Fischer; Tim Cockerill; Liming Lee; Nirav C. Merchant; Therese Miller; John Michael Lowe; Daniel C. Stanzione Jr.; James Taylor; Edwin Skidmore (Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, Miami, USA, July 17-21, 2016, 2016)

Araport: an application platform for data discovery - Matthew R. Hanlon; Matthew Vaughn; Stephen A. Mock; Rion Dooley; Walter Moreira; Joe Stubbs; Christopher Town; Jason R. Miller; Vivek Krishnakumar; Erik S. Ferlanti; Eleanor Pence (Concurr. Comput. Pract. Exp., 2015)

Araport: the Arabidopsis Information Portal - Vivek Krishnakumar; Matthew R. Hanlon; Sergio Contrino; Erik S. Ferlanti; Svetlana Karamycheva; Maria Kim; Benjamin D. Rosen; Chia-Yi Cheng; Walter Moreira; Stephen A. Mock; Joseph Stubbs; Julie M. Sullivan; et al. (Nucleic Acids Res., 2015)

Feature frequency profiles for automatic sample identification using PySpark - Gregory J. Zynda; Niall Gaffney; Mehmet M. Dalkilic; Matthew W. Vaughn (Proceedings of the 5th Workshop on Python for High-Performance and Scientific Computing, PyHPC 2015, Austin, Texas, USA, November 15, 2015, 2015)

Jetstream: a self-provisioned, scalable science and engineering cloud environment - Craig A. Stewart; Timothy M. Cockerill; Ian T. Foster; David Y. Hancock; Nirav C. Merchant; Edwin Skidmore; Daniel Stanzione; James Taylor; Steven Tuecke; George W. Turner; Matthew Vaughn; Niall I. Gaffney (Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, St. Louis, MO, USA, July 26 - 30, 2015, 2015)

Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors - Lars Koesterke; James E. Koltes; Nathan T. Weeks; Kent F. Milfeld; Matthew W. Vaughn; James M. Reecy; Daniel Stanzione (Concurr. Comput. Pract. Exp., 2014)

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

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, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014, 2014)

The arabidopsis information portal: an application platform for data discovery - Matthew R. Hanlon; Matthew Vaughn; Stephen A. Mock; Rion Dooley; Walter Moreira; Joe Stubbs; Christopher Town; Jason R. Miller; Vivek Krishnakumar; Erik S. Ferlanti; Eleanor Pence (Proceedings of the 9th Gateway Computing Environments Workshop, GCE '14, New Orleans, Louisiana, USA, November 16-21, 2014, 2014)

National Center for Genome Analysis support leverages XSEDE to support life science research - Richard D. LeDuc; Thomas G. Doak; Le-Shin Wu; Philip D. Blood; Carrie L. Ganote; Matthew Vaughn (Extreme Science and Engineering Discovery Environment: Gateway to Discovery, XSEDE13, San Diego, CA, USA - July 22 - 25, 2013, 2013)

Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networks - Lars Koesterke; Kent F. Milfeld; Matthew W. Vaughn; Daniel Stanzione; James E. Koltes; Nathan T. Weeks; James M. Reecy (Extreme Science and Engineering Discovery Environment: Gateway to Discovery, XSEDE13, San Diego, CA, USA - July 22 - 25, 2013, 2013)

Quantitative Trait Locus Analysis Using a Partitioned Linear Model on a GPU Cluster - Peter E. Bailey; Tapasya Patki; Gregory M. Striemer; Ali Akoglu; David K. Lowenthal; Peter Bradbury; Matt Vaughn; Liya Wang; Stephen Goff (26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, IPDPS 2012, Shanghai, China, May 21-25, 2012, 2012)

An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association Studies - Lars Koesterke; Daniel Stanzione; Matthew W. Vaughn; Stephen M. Welch; Waclaw Kusnierczyk; Jinliang Yang; Cheng-Ting Yeh; Dan Nettleton; Patrick S. Schnable (25th IEEE International Symposium on Parallel and Distributed Processing, IPDPS 2011, Anchorage, Alaska, USA, 16-20 May 2011 - Workshop Proceedings, 2011)

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs - Vamsi Kundeti; Sanguthevar Rajasekaran; Hieu Dinh; Matthew Vaughn; Vishal Thapar (BMC Bioinform., 2010)