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Deyou Zheng

Research Profile

Genes & Molecular Sequences

Living Beings

Mouse

Physiology

Phenomena

Evolution, Molecular

Chemicals & Drugs

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Oligonucleotide Array Sequence Analysis

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Anatomy

Neurons

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Computational Biology

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Publications

TOP 3
Qing Xie; Ying Yang; Jiri Zavadil; Deyou Zheng; Magdalena Götz; Jie Huang; Jovica Ninkovic; Ariel Vitenzon; Tessa Walcher; Louise Wolf; David C Beebe; Ales Cvekl
Pax6 interactions with chromatin and identification of its novel direct target genes in lens and forebrain.
Sandeep N Wontakal; Deyou Zheng; Cameron Smith; Michael P Snyder; Sherman M Weissman; Aviv Bergman; Emery H Bresnick; Xingyi Guo; Thomas MacCarthy; Arthur I Skoultchi
A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation.
Mingyan Lin; Erika Pedrosa; Tao Wang; Deyou Zheng; Anastasia Hrabovsky; Herbert M Lachman
Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders.

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All Publications

2013: Qing Xie; Ying Yang; Jiri Zavadil; Deyou Zheng; Magdalena Götz; Jie Huang; Jovica Ninkovic; Ariel Vitenzon; Tessa Walcher; Louise Wolf; David C Beebe; Ales Cvekl
Pax6 interactions with chromatin and identification of its novel direct target genes in lens and forebrain.
PloS one 2013;8(1):e54507.
2012: Sandeep N Wontakal; Deyou Zheng; Cameron Smith; Michael P Snyder; Sherman M Weissman; Aviv Bergman; Emery H Bresnick; Xingyi Guo; Thomas MacCarthy; Arthur I Skoultchi
A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(10):3832-7.
2012: Mingyan Lin; Erika Pedrosa; Tao Wang; Deyou Zheng; Anastasia Hrabovsky; Herbert M Lachman
Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders.
PloS one 2012;7(8):e44017.
2011: Erika Pedrosa; Shira Rockowitz; Vladislav Sandler; Abhishek Shah; Deyou Zheng; Reed Carroll; Chanjung Chang; Xingyi Guo; Herbert M Lachman
Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells.
Journal of neurogenetics 2011;25(3):88-103.
2011: Wen-Hui Lien; Lisa Polak; Richard A Young; Deyou Zheng; Xingyi Guo; Lee N Lawton; Elaine Fuchs
Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage.
Cell stem cell 2011;9(3):219-32.
2011: Sandeep N Wontakal; Deyou Zheng; Xingyi Guo; Milind C Mahajan; Debasish Raha; Minyi Shi; Michael Snyder; Ulrich Steidl; Sherman Weissman; Britta Will; Arthur I Skoultchi
A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1.
PLoS genetics 2011;7(6):e1001392.
2011: Mingyan Lin; Shahina Maqbool; Erika Pedrosa; Abhishek Shah; Deyou Zheng; Anastasia Hrabovsky; Herbert M Lachman
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.
PloS one 2011;6(9):e23356.
2011: Xingyi Guo; Laina Freyer; Bernice E Morrow; Deyou Zheng
Characterization of the past and current duplication activities in the human 22q11.2 region.
BMC genomics 2011;12():71.
2010: Erika Pedrosa; Abhishek Shah; Christopher Tenore; Michael Capogna; Catalina Villa; Xingyi Guo; Deyou Zheng; Herbert M Lachman
β-catenin promoter ChIP-chip reveals potential schizophrenia and bipolar disorder gene network.
Journal of neurogenetics 2010;24(4):182-93.
2010: Ping Chi; Yu Chen; Lei Zhang; Xingyi Guo; John Wongvipat; Tambudzai Shamu; Jonathan A Fletcher; Scott Dewell; ROBERT G MAKI; Deyou Zheng; Cristina R Antonescu; C David Allis; Charles L Sawyers
ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours.
Nature 2010;467(7317):849-53.
2010: Joseph J Abrajano; Irfan Qureshi; Solen Gokhan; Aldrin E Molero; Deyou Zheng; Aviv Bergman; Mark F Mehler
Corepressor for element-1-silencing transcription factor preferentially mediates gene networks underlying neural stem cell fate decisions.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(38):16685-90.
2010: Aaron D Goldberg; Laura A Banaszynski; Kyung-Min Noh; Peter Lewis; Simon J Elsaesser; Sonja Stadler; Scott Dewell; Martin Law; Xingyi Guo; Xuan Li; Duancheng Wen; Ariane Chapgier; Russell C DeKelver; Jeffrey C Miller; Ya-Li Lee; Elizabeth A Boydston; Michael C Holmes; Philip D Gregory; John M Greally; Shahin Rafii; Chingwen Yang; Peter J Scambler; David Garrick; Richard J Gibbons; Douglas R Higgs; Ileana M Cristea; Fyodor D Urnov; Deyou Zheng; C David Allis
Distinct factors control histone variant H3.3 localization at specific genomic regions.
Cell 2010;140(5):678-91.
2009: Andrew S. McLellan; Raul Olea; Masako Suzuki; Gael Westby; Deyou Zheng; Pilib Ó Broin; Robert Dubin; Melissa Fazzari; Qiang Jing; Shahina Maqbool; John M Greally
The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease.
Epigenomics 2009;1(1):33-8.
2009: Xingyi Guo; Zhaolei Zhang; Mark B Gerstein; Deyou Zheng
Small RNAs originated from pseudogenes: cis- or trans-acting?
PLoS computational biology 2009;5(7):e1000449.
2009: Joseph J Abrajano; Irfan Qureshi; Solen Gokhan; Deyou Zheng; Aviv Bergman; Mark F Mehler
REST and CoREST modulate neuronal subtype specification, maturation and maintenance.
PloS one 2009;4(12):e7936.
2009: Joseph J Abrajano; Irfan Qureshi; Solen Gokhan; Deyou Zheng; Aviv Bergman; Mark F Mehler
Differential deployment of REST and CoREST promotes glial subtype specification and oligodendrocyte lineage maturation.
PloS one 2009;4(11):e7665.
2009: Yuen-Jong Liu; Deyou Zheng; Suganthi Balasubramanian; Nicholas Carriero; Ekta Khurana; Rebecca Robilotto; Mark B Gerstein
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.
BMC genomics 2009;10():480.
2009: Deyou Zheng; Keji Zhao; Mark F Mehler
Profiling RE1/REST-mediated histone modifications in the human genome.
Genome biology 2009;10(1):R9.
2009: Suganthi Balasubramanian; Deyou Zheng; Yuen-Jong Liu; Gang Fang; Adam Frankish; Nicholas Carriero; Rebecca Robilotto; Philip Cayting; Mark Gerstein
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
Genome biology 2009;10(1):R2.
2008: Deyou Zheng
Gene duplication in the epigenomic era.
Epigenetics : official journal of the DNA Methylation Society 2008;3(5):250-3.
2008: Deyou Zheng
Asymmetric histone modifications between the original and derived loci of human segmental duplications.
Genome biology 2008;9(7):R105.
2007: Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas 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 Dillon 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; Jorg Hackermuller; 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 Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos Antonarakis; Yutao Fu; Eric Green; Ulaş Karaöz; Adam Siepel; James TAYLOR; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory 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; Richmond Todd; 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; Goncalo 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 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
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature 2007;447(7146):799-816.
2007: Deyou Zheng; Adam Frankish; Robert Baertsch; Philipp Kapranov; Alexandre Reymond; Siew Woh Choo; Yontao Lu; France Denoeud; Stylianos E Antonarakis; Michael Snyder; Yijun Ruan; Chia-Lin Wei; Thomas Gingeras; Roderic Guigó; Jennifer Harrow; Mark Gerstein
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Genome research 2007;17(6):839-51.
2007: Joel S Rozowsky; Daniel Newburger; Fred Sayward; Jiaqian Wu; Greg Jordan; Jan O Korbel; Ugrappa Nagalakshmi; Jin Yang; Deyou Zheng; Roderic Guigó; Thomas Gingeras; Sherman Weissman; Perry Miller; Michael Snyder; Mark Gerstein
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
Genome research 2007;17(6):732-45.
2007: Nathan D Trinklein; Ulaş Karaöz; Jiaqian Wu; Anason S Halees; Shelley Force Aldred; Patrick J Collins; Deyou Zheng; Zhengdong D Zhang; Mark B Gerstein; Michael Snyder; Richard Myers; Zhiping Weng
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.
Genome research 2007;17(6):720-31.
2007: Mark Gerstein; Can Bruce; Joel S Rozowsky; Deyou Zheng; Du Jiang; Jan O Korbel; Olof Emanuelsson; Zhengdong D Zhang; Sherman Weissman; Michael Snyder
What is a gene, post-ENCODE? History and updated definition.
Genome research 2007;17(6):669-81.
2007: Olof Emanuelsson; Ugrappa Nagalakshmi; Deyou Zheng; Joel S Rozowsky; Alexander Eckehart Urban; Du Jiang; Zheng Lian; Viktor Stolc; Sherman Weissman; Michael Snyder; Mark Gerstein
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
Genome research 2007;17(6):886-97.
2007: Deyou Zheng; Mark Gerstein
The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
Trends in genetics : TIG 2007;23(5):219-24.
2007: John Karro; Yangpan Yan; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Philip Cayting; Paul Harrrison; Mark Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
Nucleic acids research 2007;35(Database issue):D55-60.
2006: Mark Gerstein; Deyou Zheng
The real life of pseudogenes.
Scientific American 2006;295(2):48-55.
2006: Zhaolei Zhang; Nicholas Carriero; Deyou Zheng; John Karro; Paul M Harrison; Mark Gerstein
PseudoPipe: an automated pseudogene identification pipeline.
Bioinformatics (Oxford, England) 2006;22(12):1437-9.
2006: Joel S Rozowsky; J Wu; Zheng Lian; Ugrappa Nagalakshmi; Jan O Korbel; Philipp Kapranov; Deyou Zheng; S Dyke; Peter E Newburger; Perry Miller; Thomas Gingeras; Sherman Weissman; Mark Gerstein; Michael Snyder
Novel transcribed regions in the human genome.
Cold Spring Harbor symposia on quantitative biology 2006;71():111-6.
2006: Deyou Zheng; Mark Gerstein
A computational approach for identifying pseudogenes in the ENCODE regions.
Genome biology 2006;7 Suppl 1():S13.1-10.
2005: Tatjana Coric; Deyou Zheng; Mark Gerstein; Cecilia M Canessa
Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.
The Journal of physiology 2005;568(Pt 3):725-35.
2005: Deyou Zheng; Zhaolei Zhang; Paul M Harrison; John Karro; Nicholas Carriero; Mark Gerstein
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
Journal of molecular biology 2005;349(1):27-45.
2005: Paul M Harrison; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Mark Gerstein
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
Nucleic acids research 2005;33(8):2374-83.
2004: Deyou Zheng; James M Aramini; Gaetano T Montelione
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
Protein science : a publication of the Protein Society 2004;13(2):549-54.
2003: Wei Li; Yang Zhang; Daisuke Kihara; Yuanpeng J Huang; Deyou Zheng; Gaetano T Montelione; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONEX: protein structure prediction with sparse NMR data.
Proteins 2003;53(2):290-306.
2003: Deyou Zheng; John R Cort; Yiwen Chiang; Thomas B Acton; Michael A Kennedy; Gaetano T Montelione
1H, 13C and 15N resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis.
Journal of biomolecular NMR 2003;27(2):183-4.
2003: Chern-Sing Goh; Ning Lan; Nathaniel Echols; Shawn Douglas; Duncan Milburn; Paul Bertone; Rong Xiao; Li-Chung Ma; Deyou Zheng; Zeba Wunderlich; Thomas B Acton; Gaetano T Montelione; Mark Gerstein
SPINE 2: a system for collaborative structural proteomics within a federated database framework.
Nucleic acids research 2003;31(11):2833-8.
2003: Deyou Zheng; Yuanpeng J Huang; Hunter N B Moseley; Rong Xiao; James M Aramini; G V T Swapna; Gaetano T Montelione
Automated protein fold determination using a minimal NMR constraint strategy.
Protein science : a publication of the Protein Society 2003;12(6):1232-46.
2002: John R Cort; Yiwen Chiang; Deyou Zheng; Gaetano T Montelione; Michael A Kennedy
NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold.
Proteins 2002;48(4):733-6.
2001: Paul Bertone; Y Kluger; Ning Lan; Deyou Zheng; Dinesh Christendat; Adelinda Yee; A M Edwards; C H Arrowsmith; Gaetano T Montelione; Mark Gerstein
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
Nucleic acids research 2001;29(13):2884-98.
2000: Gaetano T Montelione; Deyou Zheng; Y J Huang; Kristin C Gunsalus; Thomas Szyperski
Protein NMR spectroscopy in structural genomics.
Nature structural biology 2000;7 Suppl():982-5.