Anton Nekrutenko

Anton Nekrutenko

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Anton Nekrutenko

Anton Nekrutenko

Publications by authors named "Anton Nekrutenko"

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63Publications

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

Genome Biol Evol 2019 10;11(10):3022-3034

Department of Biochemistry and Molecular Biology, The Pennsylvania State University.

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https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe
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http://dx.doi.org/10.1093/gbe/evz197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827461PMC
October 2019

Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage.

Bioinformatics 2019 Sep;35(18):3453-3460

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6931352PMC
September 2019

Biology Needs Evolutionary Software Tools: Let's Build Them Right.

Mol Biol Evol 2018 06;35(6):1372-1375

Lerner Research Institute, Cleveland Clinic, Cleveland, OH.

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http://dx.doi.org/10.1093/molbev/msy084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967460PMC
June 2018

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

PLoS Comput Biol 2017 05 25;13(5):e1005425. Epub 2017 May 25.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444614PMC
May 2017

Streamlined analysis of duplex sequencing data with Du Novo.

Genome Biol 2016 08 26;17(1):180. Epub 2016 Aug 26.

Graduate Program in Bioinformatics and Genomics, The Huck Institutes for the Life Sciences, Penn State University, 505 Wartik Lab, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1186/s13059-016-1039-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000403PMC
August 2016

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

Bioinformatics 2015 Aug 16;31(16):2668-75. Epub 2015 Apr 16.

Department of Biology, Center for RNA Molecular Biology, Bioinformatics and Genomics Graduate Program, Plant Biology Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280868PMC
August 2015

Online resources for genomic analysis using high-throughput sequencing.

Cold Spring Harb Protoc 2015 Feb 5;2015(4):324-35. Epub 2015 Feb 5.

Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802;

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http://dx.doi.org/10.1101/pdb.top083667DOI Listing
February 2015

Wrangling Galaxy's reference data.

Bioinformatics 2014 Jul 28;30(13):1917-9. Epub 2014 Feb 28.

Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USADepartment of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071198PMC
July 2014

RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.

Genome Res 2013 Nov 2;23(11):1789-96. Epub 2013 Aug 2.

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;

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http://dx.doi.org/10.1101/gr.161265.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814879PMC
November 2013

Ten simple rules for reproducible computational research.

PLoS Comput Biol 2013 Oct 24;9(10):e1003285. Epub 2013 Oct 24.

Department of Informatics, University of Oslo, Blindern, Oslo, Norway ; Centre for Cancer Biomedicine, University of Oslo, Blindern, Oslo, Norway.

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http://dx.doi.org/10.1371/journal.pcbi.1003285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812051PMC
October 2013

Web-based visual analysis for high-throughput genomics.

BMC Genomics 2013 Jun 13;14:397. Epub 2013 Jun 13.

Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1186/1471-2164-14-397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691752PMC
June 2013

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study.

Genome Biol 2011 23;12(6):R59. Epub 2011 Jun 23.

The Huck Institutes of Life Sciences and Department of Biology, Penn State University, 305 Wartik Lab, University Park, PA 16802, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-6-r59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218847PMC
December 2012

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Nat Rev Genet 2012 09;13(9):667-72

Huck Institutes of the Life Sciences and the Department of Biochemistry and Molecular Biology, Penn State University, Wartik 505, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1038/nrg3305DOI Listing
September 2012

Using Galaxy to perform large-scale interactive data analyses.

Curr Protoc Bioinformatics 2012 Jun;Chapter 10:Unit10.5

Penn State University, University Park, PA, USA.

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http://dx.doi.org/10.1002/0471250953.bi1005s38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282168PMC
June 2012

Making whole genome multiple alignments usable for biologists.

Bioinformatics 2011 Sep 19;27(17):2426-8. Epub 2011 Jul 19.

The Huck Institutes for the Life Sciences and Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157923PMC
September 2011

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Genome Biol 2010 25;11(8):R86. Epub 2010 Aug 25.

Department of Biology and Department of Mathematics and Computer Science, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1186/gb-2010-11-8-r86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945788PMC
January 2011

Galaxy CloudMan: delivering cloud compute clusters.

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S4. Epub 2010 Dec 21.

Department of Biology, Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S12-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040530PMC
December 2010

Manipulation of FASTQ data with Galaxy.

Bioinformatics 2010 Jul 18;26(14):1783-5. Epub 2010 Jun 18.

Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894519PMC
July 2010

Galaxy: a web-based genome analysis tool for experimentalists.

Curr Protoc Mol Biol 2010 Jan;Chapter 19:Unit 19.10.1-21

The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471142727.mb1910s89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264107PMC
January 2010

High-resolution mapping of evolutionary trajectories in a phage.

Genome Biol Evol 2009 Aug 11;1:294-307. Epub 2009 Aug 11.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, USA.

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http://dx.doi.org/10.1093/gbe/evp029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817424PMC
August 2009

Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing.

Proc Natl Acad Sci U S A 2009 Aug 17;106(31):12741-6. Epub 2009 Jul 17.

Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.0902417106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722358PMC
August 2009

Wheels within wheels: clues to the evolution of the Gnas and Gnal loci.

Mol Biol Evol 2008 Dec 8;25(12):2745-57. Epub 2008 Oct 8.

Center for Comparative Genomics and Bioinformatics, Huck Institutes for the Life Sciences, Penn State University, USA.

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http://dx.doi.org/10.1093/molbev/msn229DOI Listing
December 2008

Using galaxy to perform large-scale interactive data analyses.

Curr Protoc Bioinformatics 2007 Sep;Chapter 10:Unit 10.5

New York University, New York, New York, USA.

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http://dx.doi.org/10.1002/0471250953.bi1005s19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382PMC
September 2007

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function.

Proc Natl Acad Sci U S A 2007 Jul 24;104(31):12807-12. Epub 2007 Jul 24.

Centre for Integrative Bioinformatics, Vrije University, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.0703238104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1937548PMC
July 2007

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Genome Res 2007 Jun;17(6):960-4

Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5578007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891355PMC
June 2007

A first look at ARFome: dual-coding genes in mammalian genomes.

PLoS Comput Biol 2007 May;3(5):e91

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868773PMC
May 2007

Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames.

Trends Genet 2006 Dec 10;22(12):645-8. Epub 2006 Oct 10.

Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.tig.2006.09.012DOI Listing
December 2006

mNSC1 shows no evidence of protein-coding capacity.

Gene 2006 Mar 14;370:83-5. Epub 2006 Feb 14.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.gene.2005.11.016DOI Listing
March 2006

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network.

BMC Bioinformatics 2006 Jan 27;7:46. Epub 2006 Jan 27.

Department of Biology, Penn State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/1471-2105-7-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1403810PMC
January 2006

Galaxy: a platform for interactive large-scale genome analysis.

Genome Res 2005 Oct 16;15(10):1451-5. Epub 2005 Sep 16.

Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.4086505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089PMC
October 2005

Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay.

PLoS Genet 2005 Aug 12;1(2):e18. Epub 2005 Aug 12.

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1371/journal.pgen.0010018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1186735PMC
August 2005

Comparative genomics.

Annu Rev Genomics Hum Genet 2004 ;5:15-56

The Center for Comparative Genomics and Bioinformatics, The Huck Institutes of Life Sciences, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1146/annurev.genom.5.061903.180057DOI Listing
November 2004

Identification of novel exons from rat-mouse comparisons.

Authors:
Anton Nekrutenko

J Mol Evol 2004 Nov;59(5):703-8

Department of Biochemistry and Molecular Biology, The Huck Institute for Life Sciences, and Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1007/s00239-004-2653-4DOI Listing
November 2004

Reconciling the numbers: ESTs versus protein-coding genes.

Authors:
Anton Nekrutenko

Mol Biol Evol 2004 Jul 19;21(7):1278-82. Epub 2004 Mar 19.

Department of Biochemistry and Molecular Biology, The Huck Institutes for Life Sciences, Pennsylvania State University, University Park, PA, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msh125DOI Listing
July 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

ETOPE: Evolutionary test of predicted exons.

Nucleic Acids Res 2003 Jul;31(13):3564-7

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169003PMC
http://dx.doi.org/10.1093/nar/gkg597DOI Listing
July 2003

Detection of gene duplications and block duplications in eukaryotic genomes.

J Struct Funct Genomics 2003 ;3(1-4):27-34

Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

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July 2003

Evolutionary dynamics of oncogenes and tumor suppressor genes: higher intensities of purifying selection than other genes.

Mol Biol Evol 2003 Jun 25;20(6):964-8. Epub 2003 Apr 25.

Bioinformatics Research Center, Medical College of Wisconsin, Milwaukee, WI, USA.

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http://dx.doi.org/10.1093/molbev/msg110DOI Listing
June 2003

An evolutionary approach reveals a high protein-coding capacity of the human genome.

Trends Genet 2003 Jun;19(6):306-10

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/S0168-9525(03)00114-8DOI Listing
June 2003

Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids.

Gene 2003 Mar;306:99-103

Department of Biology, Texas Tech University, Lubbock, TX 79409, USA.

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http://dx.doi.org/10.1016/s0378-1119(03)00427-xDOI Listing
March 2003

Signatures of domain shuffling in the human genome.

Genome Res 2002 Nov;12(11):1642-50

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.520702
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http://dx.doi.org/10.1101/gr.520702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187552PMC
November 2002

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.

Genome Res 2002 Jan;12(1):198-202

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.200901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155263PMC
January 2002