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 Datasets Quality Control Phylogeny Education Research Personnel Mutation Students Cluster Analysis High Throughput Nucleotide Sequencing Software Biological Science Disciplines Genome Analysis Technology Teaching Nucleotides Libraries Genomics Sequencing Learning Bioinformatics Workflow Electronic Learning

Most Recent Papers

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 unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.

D Martin, S Lytras, A Lucaci, W Maier, B Grüning, S Shank, S Weaver, O MacLean, R Orton, P Lemey, Maciej Boni, H Tegally, G Harkins, C Scheepers, J Bhiman, J Everatt, D Amoako, J San, J Giandhari, A Sigal, C Williamson, N Hsiao, A von Gottberg, A De Klerk, R Shafer, D Robertson, R Wilkinson, B Sewell, R Lessells, A Nekrutenko, A Greaney, T Starr, J Bloom, B Murrell, E Wilkinson, R Gupta, T de Oliveira, 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

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

Delphine Larivière, Laura Wickham, Kenneth Keiler, Anton Nekrutenko, 2021, BMC Microbiology

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

GYAN

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

Sequencing error profiles of Illumina sequencing instruments

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

Increased yields of duplex sequencing data by a series of quality control tools

Gundula Povysil, Monika Heinzl, Renato Salazar, Nicholas Stoler, Anton Nekrutenko, Irene Tiemann-Boege, 2021, NAR Genomics and Bioinformatics

Most-Cited Papers

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

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

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

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

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

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