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.
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 Plasmids Pipelines High Throughput Nucleotide Sequencing Rna Secondary Structure Horses Software Profiling Sequencing InfrastructureMost 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
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