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 Data Analysis Mitochondrial Dna Software Phylogeny Datasets Error Correction Research Personnel Costs Molecules High Throughput Nucleotide Sequencing Dna Analysis Technology Biomedical Research Family Horses Publications Sequence Alignment Nucleotides Biological Science Disciplines Workflow Genes Amplification Genetic Variation

Most Recent Papers

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

Beatriz Serrano Solano, Melanie C. Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A. Grüning, 2021, PLoS Computational Biology

Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update

Alexander Ostrovsky, Jennifer Hillman-Jackson, Dave Bouvier, Dave Clements, Enis Afgan, Daniel Blankenberg, Michael C. Schatz, Anton Nekrutenko, James Taylor, The Galaxy Team, Delphine Lariviere, 2021, Current Protocols

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Mehmet Tekman, Berenice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez, Graham J. Etherington, Hans Rudolf Hotz, Jelle Scholtalbers, Jonathan R. Manning, Lea Bellenger, Maria A. Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Bjorn Gruning, 2021, GigaScience

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Mehmet Tekman, Batut, B\'er\'enice, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez, Graham Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan Manning, Lea Bellenger, Maria Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, D Blankenberg, Rolf Backofen, Gr\"uning, Bj\"orn, 2020, Gigascience

Erratum

Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko, 2020, Nucleic Acids Research on p. 8205-8207

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Nicholas Keener, Delphine Larivière, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver, 2020, PLoS Pathogens

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

In memory of James Taylor

Anton Nekrutenko, Michael C. Schatz, 2020, Genome Biology on p. 105

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, 2020, BMC Bioinformatics

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

Most-Cited Papers

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

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 M. Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Lynne 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

Ten Simple Rules for Reproducible Computational Research

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

Next-generation sequencing data interpretation

Anton Nekrutenko, James Taylor, 2012, Nature Reviews Genetics on p. 667-672

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

Boris Rebolledo-Jaramillo, Marcia Shu Wei Su, Nicholas Stoler, Jennifer A. McElhoe, Benjamin Dickins, Daniel Blankenberg, Thorfinn S. Korneliussen, Francesca Chiaromonte, Rasmus Nielsen, Mitchell 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

Harnessing cloud computing with Galaxy Cloud

Enis Afgan, Dannon Baker, Nate Coraor, Hiroki Goto, Ian Paul, Kateryna Dmytrivna Makova, Anton Nekrutenko, James Taylor, 2011, Nature Biotechnology on p. 972-974

Using galaxy to perform large-scale interactive data analyses

Jennifer Hillman-Jackson, Dave Clements, Daniel Blankenberg, James Taylor, Anton Nekrutenko, Galaxy Team, 2012, Current Protocols in Bioinformatics

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

Hiroki Goto, Benjamin Dickins, Enis Afgan, Ian Paul, James Taylor, Kateryna Dmytrivna Makova, Anton Nekrutenko, 2011, Genome Biology

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses

Hiroki Goto, Oliver A. Ryder, Allison R. Fisher, Bryant Schultz, Sergei L.Kosakovsky Pond, Anton Nekrutenko, Kateryna D. Makova, 2011, Genome Biology and Evolution on p. 1096-1106