Anton Nekrutenko

Professor of Biochemistry and Molecular Biology

Anton Nekrutenko

Research Summary

Evolution of overlapping reading frames in eukaryotic genomes.

Graduate Students

Huck Affiliations

Links

Publication Tags

Galaxies Genome Genes Rna Research Personnel Bioinformatics Datasets Cloud Computing Genomics Research Biomedical Research Technology Computational Biology Informatics Linux Availability Pipelines Plasmids High Throughput Nucleotide Sequencing Rna Secondary Structure Horses Software Profiling Sequencing Infrastructure

Most Recent Papers

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

Han Mei, Barbara Arbeithuber, Marzia A. Cremona, Michael DeGiorgio, Anton Nekrutenko, 2019, Genome biology and evolution on p. 3022-3034

Predicting runtimes of bioinformatics tools based on historical data

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

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

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Kun Qu, Sara Garamszegi, Felix Wu, Helga Thorvaldsdottir, Ted Liefeld, Marco Ocana, Diego Borges-Rivera, Nathalie Pochet, James T. Robinson, Barry Demchak, Tim Hull, Gil Ben-Artzi, Daniel Blankenberg, Galt P. Barber, Brian T. Lee, Robert M. Kuhn, Anton Nekrutenko, Eran Segal, Trey Ideker, Michael Reich, Aviv Regev, Howard Y Chang, Jill P. Mesirov, 2016, Nature methods on p. 245-247

StructureFold

Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua, Sarah M. Assmann, 2015, Bioinformatics on p. 2668-2675

Online resources for genomic analysis using high-throughput sequencing

Daniel James Blankenberg, James Taylor, Anton Nekrutenko, 2015, Cold Spring Harbor Protocols on p. 324-335

Wrangling Galaxy's reference data

Daniel Blankenberg, James E. Johnson, James Taylor, Anton Nekrutenko, 2014, Bioinformatics on p. 1917-1919

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu Wei Su, Ian M. Paul, Daniel Blankenberg, Nicholas Stoler, Kateryna D. Makova, Anton Nekrutenko, 2014, BioTechniques on p. 134-141

Web-based visual analysis for high-throughput genomics

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

A reference model for deploying applications in virtualized environments

Enis Afgan, Dannon Baker, Anton Nekrutenko, James Taylor, 2012, Concurrency Computation Practice and Experience on p. 1349-1361

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

Manipulation of FASTQ data with galaxy

Daniel Blankenberg, Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko, Galaxy Team, 2010, Bioinformatics on p. 1783-1785

Complete Khoisan and Bantu genomes from southern Africa

Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert S. Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi, Can Alkan, Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wang, Richard Burhans, Cathy Riemer, Nicola E. Wittekindt, Priya Moorjani, Elizabeth A. Tindall, Charles G. Danko, Wee Siang Teo, Anne M. Buboltz, Zhenhai Zhang, Qianyi Ma, Arno Oosthuysen, Abraham W. Steenkamp, Hermann Oostuisen, Philippus Venter, John Gajewski, Yu Zhang, B. Franklin Pugh, Kateryna D. Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross C. Hardison, Richard A. Gibbs, Timothy T. Harkins, Vanessa M. Hayes, 2010, Nature on p. 943-947

Galaxy CloudMan

Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor, 2010, BMC bioinformatics

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

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

Making whole genome multiple alignments usable for biologists

Daniel Blankenberg, James Taylor, Anton Nekrutenko, 2011, Bioinformatics on p. 2426-2428

Integrating diverse databases into an unified analysis framework

Daniel Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko, 2011, Database

StructureFold

Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua, Sarah M. Assmann, 2015, Bioinformatics on p. 2668-2675