ETOPE: evolutionary test of predicted exons. - Anton Nekrutenko; Wen-Yu Chung; Wen-Hsiung Li (Nucleic Acids Res., 2003)

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. - Wen-Yu Chung; Réka Albert; István Albert; Anton Nekrutenko; Kateryna D. Makova (BMC Bioinform., 2006)

A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes. - Wen-Yu Chung; Samir Wadhawan; Radek Szklarczyk; Sergei L. Kosakovsky Pond; Anton Nekrutenko (PLoS Comput. Biol., 2007)

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)

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)

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)

Wrangling Galaxy's reference data. - Daniel J. Blankenberg; James E. Johnson; The Galaxy Team; James Taylor 001; Anton Nekrutenko (Bioinform., 2014)

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo. - Yin Tang; Emil Bouvier; Chun Kit Kwok; Yiliang Ding; Anton Nekrutenko; Philip C. Bevilacqua; Sarah M. Assmann (Bioinform., 2015)

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)

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)

Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage. - Anastasia Tyryshkina; Nate Coraor; Anton Nekrutenko (Bioinform., 2019)

Family reunion via error correction: an efficient analysis of duplex sequencing data. - Nicholas Stoler; Barbara Arbeithuber; Gundula Povysil; Monika Heinzl; Renato Salazar; Kateryna D. Makova; Irene Tiemann-Boege; Anton Nekrutenko (BMC 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)

GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. - Gulsum Gudukbay; Jashwant Raj Gunasekaran; Yilin Feng; Mahmut T. Kandemir; Anton Nekrutenko; Chita R. Das; Paul Medvedev; Björn A. Grüning; Nate Coraor; Nathan Roach; Enis Afgan (IPDPS Workshops, 2021)

Fostering accessible online education using Galaxy as an e-learning platform. - Beatriz Serrano-Solano; Melanie Christine Föll; Cristóbal Gallardo-Alba; Anika Erxleben; Helena Rasche; Saskia D. Hiltemann; Matthias Fahrner; Mark J. Dunning; Marcel H. Schulz; Beáta Scholtz; Dave Clements; Anton Nekrutenko; et al. (PLoS Comput. Biol., 2021)

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)

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. - Aysam Guerler; Dannon Baker; Marius van den Beek; Björn A. Grüning; Dave Bouvier; Nate Coraor; Stephen D. Shank; Jordan D. Zehr; Michael C. Schatz; Anton Nekrutenko (BMC Bioinform., 2023)