Manipulation of FASTQ data with Galaxy. - Daniel J. Blankenberg; Assaf Gordon; Gregory Von Kuster; Nathan Coraor; James Taylor 001; Anton Nekrutenko (Bioinform., 2010)

Galaxy CloudMan: delivering cloud compute clusters. - Enis Afgan; Dannon Baker; Nathan Coraor; Brad Chapman; Anton Nekrutenko; James Taylor 001 (BMC Bioinform., 2010)

The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool. - Jeremy Goecks; Kanwei Li; Dave Clements; The Galaxy Team; James Taylor 001 (BioVis, 2011)

Integrating diverse databases into an unified analysis framework: a Galaxy approach. - Daniel J. Blankenberg; Nathan Coraor; Gregory Von Kuster; James Taylor 001; Anton Nekrutenko (Database J. Biol. Databases Curation, 2011)

Making whole genome multiple alignments usable for biologists. - Daniel J. Blankenberg; James Taylor 001; Anton Nekrutenko (Bioinform., 2011)

Galaxy: A Gateway to Tools in e-Science. - Enis Afgan; Jeremy Goecks; Dannon Baker; Nate Coraor; Anton Nekrutenko; James Taylor 001 (Guide to e-Science, 2011)

Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses. - Jeremy Goecks; The Galaxy Team; Anton Nekrutenko; James Taylor 001 (eScience, 2012)

CloudMan as a platform for tool, data, and analysis distribution. - Enis Afgan; Brad Chapman; James Taylor 001 (BMC Bioinform., 2012)

A reference model for deploying applications in virtualized environments. - Enis Afgan; Dannon Baker; Anton Nekrutenko; James Taylor 001 (Concurr. Comput. Pract. Exp., 2012)

A sustainable national gateway for biological computation. - James Taylor 001; Anton Nekrutenko; Nathan Coraor; Philip D. Blood; Alex Ropelewski; Zhihui Zhang; Josephine Palencia; Sergiu Sanielevici; Jared Yanovich; Robert Budden (XSEDE, 2013)

Ten Simple Rules for Reproducible Computational Research. - Geir Kjetil Sandve; Anton Nekrutenko; James Taylor 001; Eivind Hovig (PLoS Comput. Biol., 2013)

Galaxy cluster to cloud - genomics at scale. - Enis Afgan; Dannon Baker; John Chilton; Nathan Coraor; James Taylor 001 (GCE@SC, 2014)

Wrangling Galaxy's reference data. - Daniel J. Blankenberg; James E. Johnson; The Galaxy Team; James Taylor 001; Anton Nekrutenko (Bioinform., 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)

Topologically associating domains are stable units of replication-timing regulation Open. - Benjamin D. Pope; Tyrone Ryba; Vishnu Dileep; Feng Yue; Wei-Sheng Wu; Olgert Denas; Daniel L. Vera; Yanli Wang; R. Scott Hansen; Theresa K. Canfield; Robert E. Thurman; Yong Cheng; et al. (Nat., 2014)

Building and provisioning bioinformatics environments on public and private Clouds. - Enis Afgan; Konstantinos Krampis; Nuwan Goonasekera; Karolj Skala; James Taylor 001 (MIPRO, 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 001; Steven Tuecke; George W. Turner; Matthew Vaughn; Niall I. Gaffney (XSEDE, 2015)

Enabling cloud bursting for life sciences within Galaxy. - Enis Afgan; Nathan Coraor; John Chilton; Dannon Baker; James Taylor 001; The Galaxy Team (Concurr. Comput. Pract. Exp., 2015)

Architectural models for deploying and running virtual laboratories in the cloud. - Enis Afgan; Andrew Lonie; James Taylor 001; Karolj Skala; Nuwan Goonasekera (MIPRO, 2016)

CloudBridge: a Simple Cross-Cloud Python Library. - Nuwan Goonasekera; Andrew Lonie; James Taylor 001; Enis Afgan (XSEDE, 2016)

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 001; Edwin Skidmore (XSEDE, 2016)

A guide and best practices for R/Bioconductor tool integration in Galaxy. - Nitesh Turaga; Mallory Ann Freeberg; Dannon Baker; John Chilton; The Galaxy Team; Anton Nekrutenko; James Taylor 001 (F1000Research, 2016)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. - Enis Afgan; Dannon Baker; Marius van den Beek; Daniel J. Blankenberg; Dave Bouvier; Martin Cech; John Chilton; Dave Clements; Nate Coraor; Carl Eberhard; Björn A. Grüning; Aysam Guerler; et al. (Nucleic Acids Res., 2016)

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. - Björn A. Grüning; Eric Rasche; Boris Rebolledo-Jaramillo; Carl Eberhard; Torsten Houwaart; John Chilton; Nate Coraor; Rolf Backofen; James Taylor 001; Anton Nekrutenko (PLoS Comput. Biol., 2017)

Federated Galaxy: Biomedical Computing at the Frontier. - Enis Afgan; Vahid Jalili; Nuwan Goonasekera; James Taylor 001; Jeremy Goecks (IEEE CLOUD, 2018)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. - Enis Afgan; Dannon Baker; Bérénice Batut; Marius van den Beek; Dave Bouvier; Martin Cech; John Chilton; Dave Clements; Nate Coraor; Björn A. Grüning; Aysam Guerler; Jennifer Hillman-Jackson; et al. (Nucleic Acids Res., 2018)

CloudLaunch: Discover and deploy cloud applications. - Enis Afgan; Andrew Lonie; James Taylor 001; Nuwan Goonasekera (Future Gener. Comput. Syst., 2019)

Cloud bursting galaxy: federated identity and access management. - Vahid Jalili; Enis Afgan; James Taylor 001; Jeremy Goecks (Bioinform., 2020)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. - Vahid Jalili; Enis Afgan; Qiang Gu; Dave Clements; Daniel J. Blankenberg; Jeremy Goecks; James Taylor 001; Anton Nekrutenko (Nucleic Acids Res., 2020)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. - Enis Afgan; Anton Nekrutenko; Björn A. Grüning; Daniel J. Blankenberg; Jeremy Goecks; Michael C. Schatz; Alexander E. Ostrovsky; Alexandru Mahmoud; Andrew J. Lonie; Anna Syme; Anne Fouilloux; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2022)