Anton Nekrutenko

Professor of Biochemistry and Molecular Biology

Anton Nekrutenko

Research Summary

Evolution of overlapping reading frames in eukaryotic genomes.

Huck Affiliations

Links

Publication Tags

Galaxies Genome Software Datasets Mutation Phylogeny Education Data Analysis Cluster Analysis Students Genes Sars Virus Workflow Libraries Biological Science Disciplines Technology Teaching Analysis Nucleotides Genomics Genetic Recombination Electronic Learning High Throughput Nucleotide Sequencing Learning Research Personnel

Most Recent Publications

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 Silver, Peter K. Quashie, Jennifer L. Rakeman, Victoria Ruiz, Lucia V. Torian, Tetyana I. Vasylyeva, Sergei L. Kosakovsky Pond, Scott Hughes, 2022, Nature Communications

RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis

Alexander G. Lucaci, Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P. Martin, Sergei L. Kosakovsky Pond, 2022, PLoS One

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

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, Anton Nekrutenko, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Björn A. Grüning, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel James Blankenberg, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. De Lima Morais, D. L. Tabernero, Delphine Lariviere, Engy Nasr, Enis Afgan, Federico Zambelli, Florian Heyl, Fotis Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Greg Von Kuster, Gulsum Gudukbay Akbulut, Helena Rasche, Hotz Hans-Rudolf, Ignacio Eguinoa, Igor Makunin, Isuru J. Ranawaka, James P. Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, Jeremy Goecks, John M. Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Le Bras Yvan, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius Van Den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie C. Föll, Michael C. Schatz, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan A. 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 Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Vandenbrouck Yves, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem De Koning, Wolfgang Maier, Peter J. Briggs, 2022, Nucleic Acids Research on p. W345-W351

RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.

A Lucaci, J Zehr, S Shank, D Bouvier, H Mei, Anton Nekrutenko, D Martin, S Kosakovsky Pond, 2022, bioRxiv : the preprint server for biology

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, MacIej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei Yuan Hsiao, Anne Von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio De Oliveira, Sergei L.Kosakovsky Pond, 2022, Molecular Biology and Evolution

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

Han Mei, Sergei Kosakovsky Pond, Anton Nekrutenko, 2021, Molecular Biology and Evolution on p. 5678-5684

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier, Nathan Coraor, Milad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P. Martin, Andrew Lonie, Björn Grüning, Sergei L. Kosakovsky Pond, Anton Nekrutenko, 2021, Nature Biotechnology on p. 1178-1179

Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses

D Larivière, L Wickham, Kenneth Keiler, Anton Nekrutenko, 2021, BMC Microbiology on p. 168

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, Bjorn Gruning, Nate Coraor, Nathan Roach, Enis Afgan, 2021, on p. 194-203

Fostering accessible online education using Galaxy as an e-learning platform

B Serrano-Solano, M Föll, C Gallardo-Alba, A Erxleben, H Rasche, S Hiltemann, M Fahrner, M Dunning, M Schulz, B Scholtz, D Clements, Anton Nekrutenko, B Batut, B Grüning, 2021, PLoS Computational Biology on p. e1008923

Most-Cited Papers

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 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 Nekrutenko, Daniel Blankenberg, 2018, Nucleic Acids Research on p. W537-W544

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

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 Nekrutenko, Jeremy Goecks, 2016, Nucleic Acids Research on p. W3-W10

Ten Simple Rules for Reproducible Computational Research

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig, 2013, PLoS Computational Biology

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko, 2020, Nucleic Acids Research on p. W395-W402

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

Boris Rebolledo-Jaramillo, Marcia Su, Nicholas Stoler, Jennifer A. McElhoe, N Stoler, Ben Dickins, D Blankenberg, Thorfinn S. Korneliussen, Francesca Chiaromonte, Rasmus Nielsen, M Holland, Ian M. Paul, Anton Nekrutenko, Kateryna D. Makova, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 15474-15479

Dissemination of scientific software with Galaxy ToolShed

Daniel Blankenberg, Gregory Von Kuster, Emil Bouvier, Dannon Baker, Enis Afgan, Nicholas Stoler, James Taylor, Anton Nekrutenko, Dave Clements, Nate Coraor, Carl Eberhard, Dorine Francheteau, Jeremy Goecks, Sam Guerler, Jennifer Jackson, Ira Cooke, Jim Johnson, Ed Kirton, Peter Cock, Brad Chapman, Bjürn Grüning, Ross Lazarus, 2014, Genome Biology

HyPhy 2.5 - A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Sergei L. Kosakovsky Pond, Art F.Y. Poon, Ryan Velazquez, Steven Weaver, N. Lance Hepler, Ben Murrell, Stephen D. Shank, Brittany Rife Magalis, Dave Bouvier, Anton Nekrutenko, Sadie Wisotsky, Stephanie J. Spielman, Simon D.W. Frost, Spencer V. Muse, 2020, Molecular Biology and Evolution on p. 295-299

Community-Driven Data Analysis Training for Biology

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning, 2018, Cell Systems on p. 752-758.e1

Practical Computational Reproducibility in the Life Sciences

Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor, 2018, Cell Systems on p. 631-635

Sequencing error profiles of Illumina sequencing instruments

Nicholas Stoler, Anton Nekrutenko, 2021, NAR Genomics and Bioinformatics