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 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 TechnologyMost 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
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