Shaying Zhao

Shaying Zhao

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Shaying Zhao

Publications by authors named "Shaying Zhao"

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Proteins with Evolutionarily Hypervariable Domains are Associated with Immune Response and Better Survival of Basal-like Breast Cancer Patients.

Comput Struct Biotechnol J 2019 19;17:430-440. Epub 2019 Mar 19.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602-7229, USA.

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http://dx.doi.org/10.1016/j.csbj.2019.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451114PMC
March 2019

Proliferative and Invasive Colorectal Tumors in Pet Dogs Provide Unique Insights into Human Colorectal Cancer.

Cancers (Basel) 2018 Sep 14;10(9). Epub 2018 Sep 14.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.3390/cancers10090330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162437PMC
September 2018

SEG - A Software Program for Finding Somatic Copy Number Alterations in Whole Genome Sequencing Data of Cancer.

Comput Struct Biotechnol J 2018 7;16:335-341. Epub 2018 Sep 7.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA.

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http://dx.doi.org/10.1016/j.csbj.2018.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154469PMC
September 2018

Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis.

Oncotarget 2018 Jun 26;9(49):29162-29179. Epub 2018 Jun 26.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.18632/oncotarget.25646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044369PMC
June 2018

Nucleosome positioning changes during human embryonic stem cell differentiation.

Epigenetics 2016 06 18;11(6):426-37. Epub 2016 Apr 18.

a Department of Biochemistry and Molecular Biology , Institute of Bioinformatics, University of Georgia , Athens , GA , USA.

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http://dx.doi.org/10.1080/15592294.2016.1176649DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939925PMC
June 2016

Cell-Cycle Control of Bivalent Epigenetic Domains Regulates the Exit from Pluripotency.

Stem Cell Reports 2015 Sep 13;5(3):323-36. Epub 2015 Aug 13.

Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2015.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618451PMC
September 2015

Comprehensive characterization of the genomic alterations in human gastric cancer.

Int J Cancer 2015 Jul 3;137(1):86-95. Epub 2014 Dec 3.

Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE; Department of Biochemistry and Molecular Biology, Computational Systems Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, GA.

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http://dx.doi.org/10.1002/ijc.29352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776643PMC
July 2015

Canine spontaneous head and neck squamous cell carcinomas represent their human counterparts at the molecular level.

PLoS Genet 2015 Jun 1;11(6):e1005277. Epub 2015 Jun 1.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4452692PMC
June 2015

Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells.

Stem Cell Reports 2013 5;1(6):532-44. Epub 2013 Dec 5.

Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA.

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http://dx.doi.org/10.1016/j.stemcr.2013.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871385PMC
May 2015

Cancer driver candidate genes AVL9, DENND5A and NUPL1 contribute to MDCK cystogenesis.

Oncoscience 2014 15;1(12):854-865. Epub 2014 Dec 15.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303893PMC
http://dx.doi.org/10.18632/oncoscience.107DOI Listing
January 2015

Molecular homology and difference between spontaneous canine mammary cancer and human breast cancer.

Cancer Res 2014 Sep 31;74(18):5045-56. Epub 2014 Jul 31.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia.

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http://dx.doi.org/10.1158/0008-5472.CAN-14-0392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167563PMC
September 2014

Frequent alteration of the tumor suppressor gene APC in sporadic canine colorectal tumors.

PLoS One 2012 10;7(12):e50813. Epub 2012 Dec 10.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050813PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519478PMC
June 2013

Copy number abnormalities in sporadic canine colorectal cancers.

Genome Res 2010 Mar 19;20(3):341-50. Epub 2010 Jan 19.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1101/gr.092726.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840980PMC
March 2010

Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao.

BMC Evol Biol 2009 Jun 5;9:128. Epub 2009 Jun 5.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA.

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http://dx.doi.org/10.1186/1471-2148-9-128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700803PMC
June 2009

Comparative analysis of Alu repeats in primate genomes.

Genome Res 2009 May;19(5):876-85

USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA.

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http://dx.doi.org/10.1101/gr.083972.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675976PMC
May 2009

DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome.

Genomics 2008 Mar;91(3):249-58

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602-7229, USA.

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http://dx.doi.org/10.1016/j.ygeno.2007.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092482PMC
March 2008

Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

BMC Genomics 2007 Mar 15;8:75. Epub 2007 Mar 15.

Dairy Science and Technology Section, AgResearch Ruakura, Private Bag 3123, Hamilton, New Zealand.

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http://dx.doi.org/10.1186/1471-2164-8-75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839098PMC
March 2007

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome.

Proc Natl Acad Sci U S A 2007 Feb 16;104(8):2767-72. Epub 2007 Feb 16.

Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1073/pnas.0606204104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1815256PMC
February 2007

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

BAC resources for the rat genome project.

Genome Res 2004 Apr;14(4):780-5

Children's Hospital and Research Center at Oakland, Oakland, California 94609, USA.

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http://dx.doi.org/10.1101/gr.2033904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383325PMC
April 2004

End-sequence profiling: sequence-based analysis of aberrant genomes.

Proc Natl Acad Sci U S A 2003 Jun 4;100(13):7696-701. Epub 2003 Jun 4.

Cancer Research Institute and Department of Laboratory Medicine, University of California Comprehensive Cancer Center, 2340 Sutter Street, San Francisco, CA 94115, USA.

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http://dx.doi.org/10.1073/pnas.1232418100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC164650PMC
June 2003

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.

Genome Res 2003 Mar;13(3):358-68

Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.

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http://dx.doi.org/10.1101/gr.923303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430288PMC
March 2003

The genome sequence of the malaria mosquito Anopheles gambiae.

Authors:
Robert A Holt G Mani Subramanian Aaron Halpern Granger G Sutton Rosane Charlab Deborah R Nusskern Patrick Wincker Andrew G Clark José M C Ribeiro Ron Wides Steven L Salzberg Brendan Loftus Mark Yandell William H Majoros Douglas B Rusch Zhongwu Lai Cheryl L Kraft Josep F Abril Veronique Anthouard Peter Arensburger Peter W Atkinson Holly Baden Veronique de Berardinis Danita Baldwin Vladimir Benes Jim Biedler Claudia Blass Randall Bolanos Didier Boscus Mary Barnstead Shuang Cai Angela Center Kabir Chaturverdi George K Christophides Mathew A Chrystal Michele Clamp Anibal Cravchik Val Curwen Ali Dana Art Delcher Ian Dew Cheryl A Evans Michael Flanigan Anne Grundschober-Freimoser Lisa Friedli Zhiping Gu Ping Guan Roderic Guigo Maureen E Hillenmeyer Susanne L Hladun James R Hogan Young S Hong Jeffrey Hoover Olivier Jaillon Zhaoxi Ke Chinnappa Kodira Elena Kokoza Anastasios Koutsos Ivica Letunic Alex Levitsky Yong Liang Jhy-Jhu Lin Neil F Lobo John R Lopez Joel A Malek Tina C McIntosh Stephan Meister Jason Miller Clark Mobarry Emmanuel Mongin Sean D Murphy David A O'Brochta Cynthia Pfannkoch Rong Qi Megan A Regier Karin Remington Hongguang Shao Maria V Sharakhova Cynthia D Sitter Jyoti Shetty Thomas J Smith Renee Strong Jingtao Sun Dana Thomasova Lucas Q Ton Pantelis Topalis Zhijian Tu Maria F Unger Brian Walenz Aihui Wang Jian Wang Mei Wang Xuelan Wang Kerry J Woodford Jennifer R Wortman Martin Wu Alison Yao Evgeny M Zdobnov Hongyu Zhang Qi Zhao Shaying Zhao Shiaoping C Zhu Igor Zhimulev Mario Coluzzi Alessandra della Torre Charles W Roth Christos Louis Francis Kalush Richard J Mural Eugene W Myers Mark D Adams Hamilton O Smith Samuel Broder Malcolm J Gardner Claire M Fraser Ewan Birney Peer Bork Paul T Brey J Craig Venter Jean Weissenbach Fotis C Kafatos Frank H Collins Stephen L Hoffman

Science 2002 Oct;298(5591):129-49

Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://ccb.jhu.edu/people/salzberg/docs/Anopheles-gambiae-re
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http://www.sciencemag.org/cgi/doi/10.1126/science.1076181
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http://dx.doi.org/10.1126/science.1076181DOI Listing
October 2002

A physical map of the mouse genome.

Nature 2002 Aug 4;418(6899):743-50. Epub 2002 Aug 4.

The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature00957DOI Listing
August 2002