Publications by authors named "Alexander Poliakov"

18Publications

Functionally conserved enhancers with divergent sequences in distant vertebrates.

BMC Genomics 2015 Oct 30;16:882. Epub 2015 Oct 30.

Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.

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http://dx.doi.org/10.1186/s12864-015-2070-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628251PMC
October 2015

An integrative computational approach for prioritization of genomic variants.

PLoS One 2014 15;9(12):e114903. Epub 2014 Dec 15.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America; Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114903PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266634PMC
November 2015

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.

Nucleic Acids Res 2014 Jan 12;42(Database issue):D26-31. Epub 2013 Nov 12.

Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1093/nar/gkt1069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965075PMC
January 2014

Tandem termination signal in plant mRNAs.

Gene 2011 Jul 22;481(1):1-6. Epub 2011 Apr 22.

Institute of Cytology and Genetics, Lavrentieva ave. 10, Novosibirsk, 630090, Russia.

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https://linkinghub.elsevier.com/retrieve/pii/S03781119110015
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http://dx.doi.org/10.1016/j.gene.2011.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105159PMC
July 2011

Multiple whole-genome alignments without a reference organism.

Genome Res 2009 Apr 28;19(4):682-9. Epub 2009 Jan 28.

Genome Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.081778.108
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http://dx.doi.org/10.1101/gr.081778.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665786PMC
April 2009

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Authors:
Sabeeha S Merchant Simon E Prochnik Olivier Vallon Elizabeth H Harris Steven J Karpowicz George B Witman Astrid Terry Asaf Salamov Lillian K Fritz-Laylin Laurence Maréchal-Drouard Wallace F Marshall Liang-Hu Qu David R Nelson Anton A Sanderfoot Martin H Spalding Vladimir V Kapitonov Qinghu Ren Patrick Ferris Erika Lindquist Harris Shapiro Susan M Lucas Jane Grimwood Jeremy Schmutz Pierre Cardol Heriberto Cerutti Guillaume Chanfreau Chun-Long Chen Valérie Cognat Martin T Croft Rachel Dent Susan Dutcher Emilio Fernández Hideya Fukuzawa David González-Ballester Diego González-Halphen Armin Hallmann Marc Hanikenne Michael Hippler William Inwood Kamel Jabbari Ming Kalanon Richard Kuras Paul A Lefebvre Stéphane D Lemaire Alexey V Lobanov Martin Lohr Andrea Manuell Iris Meier Laurens Mets Maria Mittag Telsa Mittelmeier James V Moroney Jeffrey Moseley Carolyn Napoli Aurora M Nedelcu Krishna Niyogi Sergey V Novoselov Ian T Paulsen Greg Pazour Saul Purton Jean-Philippe Ral Diego Mauricio Riaño-Pachón Wayne Riekhof Linda Rymarquis Michael Schroda David Stern James Umen Robert Willows Nedra Wilson Sara Lana Zimmer Jens Allmer Janneke Balk Katerina Bisova Chong-Jian Chen Marek Elias Karla Gendler Charles Hauser Mary Rose Lamb Heidi Ledford Joanne C Long Jun Minagawa M Dudley Page Junmin Pan Wirulda Pootakham Sanja Roje Annkatrin Rose Eric Stahlberg Aimee M Terauchi Pinfen Yang Steven Ball Chris Bowler Carol L Dieckmann Vadim N Gladyshev Pamela Green Richard Jorgensen Stephen Mayfield Bernd Mueller-Roeber Sathish Rajamani Richard T Sayre Peter Brokstein Inna Dubchak David Goodstein Leila Hornick Y Wayne Huang Jinal Jhaveri Yigong Luo Diego Martínez Wing Chi Abby Ngau Bobby Otillar Alexander Poliakov Aaron Porter Lukasz Szajkowski Gregory Werner Kemin Zhou Igor V Grigoriev Daniel S Rokhsar Arthur R Grossman

Science 2007 Oct;318(5848):245-50

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1126/science.1143609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087PMC
October 2007

Extensive parallelism in protein evolution.

Biol Direct 2007 Aug 16;2:20. Epub 2007 Aug 16.

Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA.

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http://dx.doi.org/10.1186/1745-6150-2-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2020468PMC
August 2007

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Nucleic Acids Res 2007 Jul 8;35(Web Server issue):W669-74. Epub 2007 May 8.

Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, 6 King's College Road, Toronto, ON, Canada M5S 3G4.

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http://dx.doi.org/10.1093/nar/gkm279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933192PMC
July 2007

VISTA: computational tools for comparative genomics.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W273-9

Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1093/nar/gkh458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441596PMC
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

Glocal alignment: finding rearrangements during alignment.

Bioinformatics 2003 ;19 Suppl 1:i54-62

Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1005DOI Listing
October 2004

Strategies and tools for whole-genome alignments.

Genome Res 2003 Jan;13(1):73-80

Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.762503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430965PMC
January 2003