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 Mitochondrial Dna Data Analysis Phylogeny Bioinformatics Research Personnel Datasets High Throughput Nucleotide Sequencing Genomics Maternal Age Plasmids Horses Mothers Dna Mutation Child Analysis Data Storage Equipment Data Mining Sequence Alignment Publications Computational Biology Research Growth Technology

Most Recent Papers

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

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: the birth of Galaxy

Anton Nekrutenko, Michael Schatz, 2020, Genome Biol. on p. 105

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

Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees.

A Zaidi, P Wilton, Meng Su, Ian Paul, B Arbeithuber, K Anthony, Anton Nekrutenko, R Nielsen, Kateryna Makova, 2019, Proceedings of the National Academy of Sciences of the United States of America on p. 25172-25178

A High-Resolution View of Adaptive Event Dynamics in a Plasmid

Han Mei, Barbara Arbeithuber, Marzia A. Cremona, Michael Degiorgio, Anton Nekrutenko, Wen Hsiung Li, 2019, Genome Biology and Evolution on p. 3022-3034

Predicting runtimes of bioinformatics tools based on historical data: Five years of Galaxy usage

Anastasia Tyryshkina, Nate Coraor, Anton Nekrutenko, Jonathan Wren, 2019, Bioinformatics on p. 3453-3460

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Sarah Craig, Daniel Blankenberg, Alice Carla Luisa Parodi, Ian Paul, Leann L. Birch, Jennifer Savage Williams, Michele E. Marini, Jennifer L. Stokes, Anton Nekrutenko, Matthew Logan Reimherr, Francesca Chiaromonte, Kateryna Dmytrivna Makova, 2018, Scientific Reports

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

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

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

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

Web-based visual analysis for high-throughput genomics

Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko, James Taylor, 2013, BMC Genomics

RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

Dan Bar-Yaacov, Gal Avital, Liron Levin, Allison L. Richards, Naomi Hachen, Boris Rebolledo Jaramillo, Anton Nekrutenko, Raz Zarivach, Dan Mishmar, 2013, Genome Research on p. 1789-1796

Integrating diverse databases into an unified analysis framework

Daniel Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko, 2011, Database : the journal of biological databases and curation

Jupyter and Galaxy

Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John M. Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko, 2017, PLoS Computational Biology