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2020 – today
- 2023
[j20]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 predictions and structural modeling of protein-protein interactions using Galaxy. BMC Bioinform. 24(1): 263 (2023)- 2022
- [j19]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, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50(W1): 345-351 (2022) - 2021
- [j18]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, Bérénice Batut, Björn A. Grüning:
Fostering accessible online education using Galaxy as an e-learning platform. PLoS Comput. Biol. 17(5) (2021) - [c3]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 Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. IPDPS Workshops 2021: 194-203 - 2020
- [j17]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 analysis of duplex sequencing data. BMC Bioinform. 21(1): 96 (2020) - [j16]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 analyses: 2020 update. Nucleic Acids Res. 48(Webserver-Issue): W395-W402 (2020)
2010 – 2019
- 2019
- [j15]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) - 2018
- [j14]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. Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel J. Blankenberg:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(Webserver-Issue): W537-W544 (2018) - 2017
- [j13]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 barriers into complex data analyses for biomedical researchers. PLoS Comput. Biol. 13(5) (2017) - 2016
- [j12]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 Hillman-Jackson, Gregory Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44(Webserver-Issue): W3-W10 (2016) - [i1]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 5: 2757 (2016) - 2015
- [j11]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. Bioinform. 31(16): 2668-2675 (2015) - 2014
- [j10]Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko:
Wrangling Galaxy's reference data. Bioinform. 30(13): 1917-1919 (2014) - 2013
- [j9]Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig:
Ten Simple Rules for Reproducible Computational Research. PLoS Comput. Biol. 9(10) (2013) - [c2]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 biological computation. XSEDE 2013: 32:1-32:3 - 2012
- [j8]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) - [c1]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 - 2011
- [j7]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. Databases Curation 2011 (2011) - [j6]Daniel J. Blankenberg, James Taylor, Anton Nekrutenko:
Making whole genome multiple alignments usable for biologists. Bioinform. 27(17): 2426-2428 (2011) - [p1]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 - 2010
- [j5]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) - [j4]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)
2000 – 2009
- 2007
- [j3]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) - 2006
- [j2]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) - 2003
- [j1]Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li:
ETOPE: evolutionary test of predicted exons. Nucleic Acids Res. 31(13): 3564-3567 (2003)
Coauthor Index
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