Anton Nekrutenko
Professor of Biochemistry and Molecular Biology
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505 Wartik Laboratory
University Park, PA 16802 - aun1@psu.edu
- 814-865-4752
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 VariationMost 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
News Articles Featuring Anton Nekrutenko
Sep 21, 2018
Mouth bacteria in toddlers may predict obesity, study says
Bacteria in a toddler's mouth might help predict later obesity, new research suggests. Scientists at Penn State University found the composition of microorganisms in the mouths of 2-year-olds offers clues to the child's future weight.
Full Article
Sep 20, 2018
Swabbing a child’s mouth for bacteria could predict how likely they are to become obese
A swab of a toddler’s mouth may predict their odds of growing into obese children, a new study suggests. Scientists at Pennsylvania State University discovered that the harmless microorganisms living in a two-year-old’s mouth were less diverse if they had gained more weight more quickly than most since birth.
Full Article
Sep 19, 2018
Child Weight Gain Trajectories Linked To Oral Microbiota Composition
Gut and oral microbiota perturbations have been observed in obese adults and adolescents; less is known about their influence on weight gain in young children.
Full Article