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ETOPE: evolutionary test of predicted exons.
Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li: ETOPE: evolutionary test of predicted exons. Nucleic Acids Res. 31(13): 3564-3567 (2003)
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Rapid and asymmetric divergence of duplicate genes in the human gene...
Wen-Yu Chung, Réka Albert, István Albert, Anton Nekrutenko, Kateryna D. Makova: Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinform. 7: 46 (2006)
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A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes.
Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko: A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes. PLoS Comput. Biol. 3(5) (2007)
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Galaxy CloudMan: delivering cloud compute clusters.
Enis Afgan, Dannon Baker, Nathan Coraor, Brad Chapman, Anton Nekrutenko, James Taylor: Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinform. 11(S-12): S4 (2010)
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Manipulation of FASTQ data with Galaxy.
Daniel J. Blankenberg, Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko: Manipulation of FASTQ data with Galaxy. Bioinform. 26(14): 1783-1785 (2010)
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Galaxy: A Gateway to Tools in e-Science.
Enis Afgan, Jeremy Goecks, Dannon Baker, Nate Coraor, Anton Nekrutenko, James Taylor: Galaxy: A Gateway to Tools in e-Science. Guide to e-Science 2011: 145-177
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Making whole genome multiple alignments usable for biologists.
Daniel J. Blankenberg, James Taylor, Anton Nekrutenko: Making whole genome multiple alignments usable for biologists. Bioinform. 27(17): 2426-2428 (2011)
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Integrating diverse databases into an unified analysis framework: a Galaxy...
Daniel J. Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko: Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database J. Biol....
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Lessons learned from Galaxy, a Web-based platform for high-throughput genomic...
Jeremy Goecks, The Galaxy Team, Anton Nekrutenko, James Taylor: Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses. eScience 2012: 1-6
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A reference model for deploying applications in virtualized environments.
Enis Afgan, Dannon Baker, Anton Nekrutenko, James Taylor: A reference model for deploying applications in virtualized environments. Concurr. Comput. Pract. Exp. 24(12): 1349-1361 (2012)
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A sustainable national gateway for biological computation.
James Taylor, Anton Nekrutenko, Nathan Coraor, Philip D. Blood, Alex Ropelewski, Zhihui Zhang, Josephine Palencia, Sergiu Sanielevici, Jared Yanovich, Robert Budden: A sustainable national gateway for...
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Ten Simple Rules for Reproducible Computational Research.
Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig: Ten Simple Rules for Reproducible Computational Research. PLoS Comput. Biol. 9(10) (2013)
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Wrangling Galaxy's reference data.
Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko: Wrangling Galaxy's reference data. Bioinform. 30(13): 1917-1919 (2014)
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StructureFold: genome-wide RNA secondary structure mapping and reconstruction...
Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua, Sarah M. Assmann: StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo....
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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: A guide and best practices for R/Bioconductor tool integration in Galaxy. F1000Research...
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The Galaxy platform for accessible, reproducible and collaborative biomedical...
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, Jennifer...
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Jupyter and Galaxy: Easing entry barriers into complex data analyses for...
Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko: Jupyter and Galaxy: Easing entry...
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The Galaxy platform for accessible, reproducible and collaborative biomedical...
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, Saskia D....
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Predicting runtimes of bioinformatics tools based on historical data: five...
Anastasia Tyryshkina, Nate Coraor, Anton Nekrutenko: Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage. Bioinform. 35(18): 3453-3460 (2019)
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The Galaxy platform for accessible, reproducible and collaborative biomedical...
Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel J. Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko: The Galaxy platform for accessible, reproducible and collaborative biomedical...
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Family reunion via error correction: an efficient analysis of duplex...
Nicholas Stoler, Barbara Arbeithuber, Gundula Povysil, Monika Heinzl, Renato Salazar, Kateryna D. Makova, Irene Tiemann-Boege, Anton Nekrutenko: Family reunion via error correction: an efficient...
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GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation...
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: GYAN: Accelerating...
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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...
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The Galaxy platform for accessible, reproducible and collaborative biomedical...
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...
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Fast and accurate genome-wide predictions and structural modeling of...
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: Fast and accurate genome-wide...
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