Zhengdong D Zhang

Zhengdong D Zhang

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Zhengdong D Zhang

Zhengdong D Zhang

Publications by authors named "Zhengdong D Zhang"

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PGA: post-GWAS analysis for disease gene identification.

Bioinformatics 2018 05;34(10):1786-1788

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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https://academic.oup.com/bioinformatics/article/34/10/1786/4
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http://dx.doi.org/10.1093/bioinformatics/btx845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946835PMC
May 2018

Epigenetic alterations to Polycomb targets precede malignant transition in a mouse model of breast cancer.

Sci Rep 2018 04 3;8(1):5535. Epub 2018 Apr 3.

Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.

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http://dx.doi.org/10.1038/s41598-018-24005-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882905PMC
April 2018

HEDD: Human Enhancer Disease Database.

Nucleic Acids Res 2018 01;46(D1):D113-D120

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

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http://academic.oup.com/nar/article/46/D1/D113/4564801
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http://dx.doi.org/10.1093/nar/gkx988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753236PMC
January 2018

Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies.

PLoS Genet 2017 12 27;13(12):e1007142. Epub 2017 Dec 27.

Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760082PMC
December 2017

Translation fidelity coevolves with longevity.

Aging Cell 2017 10 13;16(5):988-993. Epub 2017 Jul 13.

Department of Biology, University of Rochester, Rochester, NY, USA.

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http://dx.doi.org/10.1111/acel.12628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595694PMC
October 2017

Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model.

BMC Genomics 2017 02 17;18(1):185. Epub 2017 Feb 17.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

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http://dx.doi.org/10.1186/s12864-017-3563-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316186PMC
February 2017

Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia.

Genetics 2016 Dec 17;204(4):1587-1600. Epub 2016 Oct 17.

Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461

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http://dx.doi.org/10.1534/genetics.116.187195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161287PMC
December 2016

MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice.

Breast Cancer Res 2016 07 22;18(1):75. Epub 2016 Jul 22.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.

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http://dx.doi.org/10.1186/s13058-016-0735-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957901PMC
July 2016

A brief introduction to tiling microarrays: principles, concepts, and applications.

Methods Mol Biol 2013 ;1067:3-19

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

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http://dx.doi.org/10.1007/978-1-62703-607-8_1DOI Listing
March 2014

SubNet: a Java application for subnetwork extraction.

Bioinformatics 2013 Oct 13;29(19):2509-11. Epub 2013 Aug 13.

Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777115PMC
October 2013

Identification of genomic indels and structural variations using split reads.

BMC Genomics 2011 Jul 25;12:375. Epub 2011 Jul 25.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1186/1471-2164-12-375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161018PMC
July 2011

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.

BMC Bioinformatics 2010 Oct 31;11:539. Epub 2010 Oct 31.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1186/1471-2105-11-539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992546PMC
October 2010

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.

Genome Biol 2010 8;11(3):R26. Epub 2010 Mar 8.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2010-11-3-r26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864566PMC
September 2010

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

PLoS Comput Biol 2009 Jul 10;5(7):e1000432. Epub 2009 Jul 10.

Department of Computer Science, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700963PMC
July 2009

Rapid in vivo exploration of a 5S rRNA neutral network.

J Microbiol Methods 2009 Feb 30;76(2):181-7. Epub 2008 Oct 30.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1016/j.mimet.2008.10.010DOI Listing
February 2009

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Nat Biotechnol 2009 Jan 4;27(1):66-75. Epub 2009 Jan 4.

Molecular Biophysics & Biochemistry Dept., Yale University, PO Box 208114, New Haven, Connecticut 06520-8114, USA.

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http://dx.doi.org/10.1038/nbt.1518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924752PMC
January 2009

Modeling ChIP sequencing in silico with applications.

PLoS Comput Biol 2008 Aug 22;4(8):e1000158. Epub 2008 Aug 22.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507756PMC
August 2008

Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.

J Mol Evol 2008 May 15;66(5):446-56. Epub 2008 Apr 15.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1007/s00239-008-9097-1DOI Listing
May 2008

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

Mol Biol Evol 2008 Jan 7;25(1):131-43. Epub 2007 Dec 7.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1093/molbev/msm251DOI Listing
January 2008

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.

Funct Integr Genomics 2007 Oct 19;7(4):335-45. Epub 2007 Jul 19.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1007/s10142-007-0054-7DOI Listing
October 2007

Tilescope: online analysis pipeline for high-density tiling microarray data.

Genome Biol 2007 ;8(5):R81

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, 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-2007-8-5-r81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929149PMC
September 2007

Divergence of transcription factor binding sites across related yeast species.

Science 2007 Aug;317(5839):815-9

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1126/science.1140748DOI Listing
August 2007

What is a gene, post-ENCODE? History and updated definition.

Genome Res 2007 Jun;17(6):669-81

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1101/gr.6339607DOI Listing
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007