Beyond Invariable Sites
Sergei L. Kosakovsky Pond, Hannah Verdonk, Steven Weaver, Gallean Brown, Danielle Callan, Anton Nekrutenko, Darren P. Martin,
Aug 2026,
In: Genome biology and evolution
Date: Aug 2026
MoleRate
Avery G. Selberg, Nathan Clark, Anton Nekrutenko, Maria Chikina, Sergei L. Kosakovsky Pond,
Mar 1 2026,
In: Evolution
Date: Mar 1 2026
KegAlign
A. Burak Gulhan, Richard Burhans, Robert Harris, Mahmut Kandemir, Maximilian Haeussler, Anton Nekrutenko,
Dec 2025,
In: Genome biology
Date: Dec 2025
Evaluation of sequencing reads at scale using rdeval
Giulio Formenti, Bonhwang Koo, Marco Sollitto, Jennifer Balacco, Nadolina Brajuka, Richard Burhans, Erick Duarte, Alice M. Giani, Kirsty McCaffrey, Jack A. Medico, Eugene W. Myers, Patrik Smeds, Anton Nekrutenko, Erich D. Jarvis,
Sep 1 2025,
In: Bioinformatics
Date: Sep 1 2025
The Galaxy platform for accessible, reproducible, and collaborative data analyses
Linelle Ann L. Abueg, Enis Afgan, Olivier Allart, Ahmed H. Awan, Wendi A. Bacon, Dannon Baker, Madeline Bassetti, Bérénice Batut, Matthias Bernt, Daniel Blankenberg, Aureliano Bombarely, Anthony Bretaudeau, Catherine J. Bromhead, Melissa L. Burke, Patrick K. Capon, Martin Čech, María Chavero-Dí...,
Jul 5 2024,
In: Nucleic acids research
Date: Jul 5 2024
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D. Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R. Balacco, Mark J.P. Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra De...,
Mar 2024,
In: Nature Biotechnology
Date: Mar 2024
Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko,
Dec 2023,
In: BMC bioinformatics
Date: Dec 2023
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter J.A. Cock, Björn Grüning, Anton Nekrutenko,
2023,
In: Genome Research
Date: 2023
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Joel O. Wertheim, Jade C. Wang, Mindy Leelawong, Darren P. Martin, Jennifer L. Havens, Moinuddin A. Chowdhury, Jonathan E. Pekar, Helly Amin, Anthony Arroyo, Gordon A. Awandare, Hoi Yan Chow, Edimarlyn Gonzalez, Elizabeth Luoma, Collins M. Morang’a, Anton Nekrutenko, Stephen D. Shank, Stefan Silve...,
Dec 2022,
In: Nature communications
Date: Dec 2022
RASCL
Alexander G. Lucaci, Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P. Martin, Sergei L. Kosakovsky Pond,
Nov 2022,
In: PloS one
Date: Nov 2022
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses
Enis Afgan, Dannon Baker, Bérénice Batut, Marius Van Den Beek, Dave Bouvier, Martin Ech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekruten...,
Jul 2 2018,
In: Nucleic acids research
Citations: 2,951
Galaxy
Jeremy Goecks, Anton Nekrutenko, James Taylor, Enis Afgan, Guruprasad Ananda, Dannon Baker, Dan Blankenberg, Ramkrishna Chakrabarty, Nate Coraor, Greg Von Kuster, Ross Lazarus, Kanwei Li, James Taylor, Kelly Vincent,
Aug 25 2010,
In: Genome biology
Citations: 2,916
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Ladeana W. Hillier, Webb Miller, Ewan Birney, Wesley Warren, Ross C. Hardison, Chris P. Ponting, Peer Bork, David W. Burt, Martien A.M. Groenen, Mary E. Delany, Jerry B. Dodgson, Asif T. Chinwalla, Paul F. Cliften, Sandra W. Clifton, Kimberly D. Delehaunty, Catrina Fronick, Robert S. Fulton, Tina A....,
Dec 9 2004,
In: Nature
Citations: 2,366
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Richard A. Gibbs, George M. Weinstock, Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C. Worley, Paula E. Burch, Geoffrey Okwuonu, Sandra Hines, Lora Lewis, Christine Deramo, Oliver Delgado, Shannon Dugan-Rocha, George Miner, Margaret Morgan,...,
Apr 1 2004,
In: Nature
Citations: 1,820
Galaxy
Belinda Giardine, Cathy Riemer, Ross C. Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor, Webb Miller, W. James Kent, Anton Nekrutenko,
Oct 2005,
In: Genome Research
Citations: 1,671
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses
Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenk...,
Jul 8 2016,
In: Nucleic acids research
Citations: 1,544
Galaxy
Daniel Blankenberg, Gregory Von Kuster, Nathaniel Coraor, Guruprasad Ananda, Ross Lazarus, Mary Mangan, Anton Nekrutenko, James Taylor,
2010,
In: Current Protocols in Molecular Biology
Citations: 1,161
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses
Enis Afgan, Anton Nekrutenko, Bjórn A. Grüning, Daniel 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-Sol...,
Jul 5 2022,
In: Nucleic acids research
Citations: 881
The Galaxy platform for accessible, reproducible, and collaborative data analyses
Linelle Ann L. Abueg, Enis Afgan, Olivier Allart, Ahmed H. Awan, Wendi A. Bacon, Dannon Baker, Madeline Bassetti, Bérénice Batut, Matthias Bernt, Daniel Blankenberg, Aureliano Bombarely, Anthony Bretaudeau, Catherine J. Bromhead, Melissa L. Burke, Patrick K. Capon, Martin Čech, María Chavero-Dí...,
Jul 5 2024,
In: Nucleic acids research
Citations: 678
Ten Simple Rules for Reproducible Computational Research
Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig,
Oct 2013,
In: PLoS computational biology
Citations: 612
