Z
Zhengqing Ouyang
Researcher at University of Massachusetts Amherst
Publications - 56
Citations - 6778
Zhengqing Ouyang is an academic researcher from University of Massachusetts Amherst. The author has contributed to research in topics: RNA & Gene. The author has an hindex of 20, co-authored 51 publications receiving 6225 citations. Previous affiliations of Zhengqing Ouyang include University of Connecticut Health Center & Stanford University.
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An integrated encyclopedia of DNA elements in the human genome
Ian Dunham,Anshul Kundaje,Shelley Force Aldred,Patrick J. Collins,Carrie A. Davis,Francis Doyle,Charles B. Epstein,Seth Frietze,Jennifer Harrow,Rajinder Kaul,Jainab Khatun,Bryan R. Lajoie,Stephen G. Landt,Bum Kyu Lee,Florencia Pauli,Kate R. Rosenbloom,Peter J. Sabo,Alexias Safi,Amartya Sanyal,Noam Shoresh,Jeremy M. Simon,Lingyun Song,Nathan D. Trinklein,Robert C. Altshuler,Ewan Birney,James B. Brown,Chao Cheng,Sarah Djebali,Xianjun Dong,Jason Ernst,Terrence S. Furey,Mark Gerstein,Belinda Giardine,Melissa C. Greven,Ross C. Hardison,Robert S. Harris,Javier Herrero,Michael M. Hoffman,Sowmya Iyer,Manolis Kellis,Pouya Kheradpour,Timo Lassmann,Qiang Li,Xinying Lin,Georgi K. Marinov,Angelika Merkel,Ali Mortazavi,Stephen C. J. Parker,Timothy E. Reddy,Joel Rozowsky,Felix Schlesinger,Robert E. Thurman,Jie Wang,Lucas D. Ward,Troy W. Whitfield,Steven P. Wilder,Weisheng Wu,Hualin S. Xi,Kevin Y. Yip,Jiali Zhuang,Bradley E. Bernstein,Eric D. Green,Chris Gunter,Michael Snyder,Michael J. Pazin,Rebecca F. Lowdon,Laura A.L. Dillon,Leslie B. Adams,Caroline J. Kelly,Julia Zhang,Judith R. Wexler,Peter J. Good,Elise A. Feingold,Gregory E. Crawford,Job Dekker,Laura Elnitski,Peggy J. Farnham,Morgan C. Giddings,Thomas R. Gingeras,Roderic Guigó,Tim Hubbard,W. James Kent,Jason D. Lieb,Elliott H. Margulies,Richard M. Myers,John A. Stamatoyannopoulos,Scott A. Tenenbaum,Zhiping Weng,Kevin P. White,Barbara J. Wold,Yanbao Yu,John A. Wrobel,Brian A. Risk,Harsha P. Gunawardena,Heather C. Kuiper,Christopher W. Maier,Ling Xie,Xian Chen,Tarjei S. Mikkelsen,Shawn M. Gillespie,Alon Goren,Oren Ram,Xiaolan Zhang,Li Wang,Robbyn Issner,Michael Coyne,Timothy Durham,Manching Ku,Thanh Truong,Matthew L. Eaton,Alexander Dobin,Andrea Tanzer,Julien Lagarde,Wei Lin,Chenghai Xue,Brian A. Williams,Chris Zaleski,Marion S. Röder,Felix Kokocinski,Rehab F. Abdelhamid,Tyler Alioto,Igor Antoshechkin,Michael T. Baer,Philippe Batut,Ian Bell,Kimberly Bell,Sudipto K. Chakrabortty,Jacqueline Chrast,Joao Curado,Thomas Derrien,Jorg Drenkow,Erica Dumais,Jackie Dumais,Radha Duttagupta,Megan Fastuca,Kata Fejes-Toth,Pedro G. Ferreira,Sylvain Foissac,Melissa J. Fullwood,Hui Gao,David Gonzalez,Assaf Gordon,Cédric Howald,Sonali Jha,Rory Johnson,Philipp Kapranov,Brandon King,Colin Kingswood,Guoliang Li,Oscar Junhong Luo,Eddie Park,Jonathan B. Preall,Kimberly Presaud,Paolo Ribeca,Daniel Robyr,Xiaoan Ruan,Michael Sammeth,Kuljeet Singh Sandhu,Lorain Schaeffer,Lei-Hoon See,Atif Shahab,Jørgen Skancke,Ana Maria Suzuki,Hazuki Takahashi,Hagen Tilgner,Diane Trout,Nathalie Walters,Huaien Wang,Yoshihide Hayashizaki,Alexandre Reymond,Stylianos E. Antonarakis,Gregory J. Hannon,Yijun Ruan,Piero Carninci,Cricket A. Sloan,Katrina Learned,Venkat S. Malladi,Matthew C. Wong,Galt P. Barber,Melissa S. Cline,Timothy R. Dreszer,Steven G. Heitner,Donna Karolchik,Vanessa M. Kirkup,Laurence R. Meyer,Jeffrey C. Long,Morgan Maddren,Brian J. Raney,Linda L. Grasfeder,Paul G. Giresi,Anna Battenhouse,Nathan C. Sheffield,Kimberly A. Showers,Darin London,Akshay Bhinge,Christopher Shestak,Matthew R. Schaner,Seul K.C. Kim,Zhuzhu Zhang,Piotr A. Mieczkowski,Joanna O. Mieczkowska,Zheng Liu,Ryan M. McDaniell,Yunyun Ni,Naim U. Rashid,Min Jae Kim,Sheera Adar,Zhancheng Zhang,Tianyuan Wang,Deborah R. Winter,Damian Keefe,Vishwanath R. Iyer,Meizhen Zheng,Ping Wang,Jason Gertz,Jost Vielmetter,Partridge Ec,Katherine E. Varley,Clarke Gasper,Anita Bansal,Shirley Pepke,Preti Jain,Henry Amrhein,Kevin M. Bowling,Michael Anaya,Marie K. Cross,Michael Muratet,Kimberly M. Newberry,Kenneth McCue,Amy S. Nesmith,Katherine I. Fisher-Aylor,Barbara N. Pusey,Gilberto DeSalvo,Stephanie L. Parker,Sreeram Balasubramanian,Nicholas S. Davis,Sarah Meadows,Tracy Eggleston,J. Scott Newberry,Shawn Levy,Devin Absher,Wing Hung Wong,Matthew J. Blow,Axel Visel,Len A. Pennachio,Hanna Petrykowska,Alexej Abyzov,Bronwen Aken,Daniel Barrell,Gemma Barson,Andrew Berry,Alexandra Bignell,Veronika Boychenko,Giovanni Bussotti,Claire Davidson,Gloria Despacio-Reyes,Mark Diekhans,Iakes Ezkurdia,Adam Frankish,James Gilbert,José M. González,Ed Griffiths,Rachel A. Harte,David A. Hendrix,Toby Hunt,Irwin Jungreis,M. Kay,Ekta Khurana,Jing Leng,Michael F. Lin,Jane E. Loveland,Zhi Lu,Deepa Manthravadi,Marco Mariotti,Jonathan M. Mudge,Gaurab Mukherjee,Cedric Notredame,Baikang Pei,Jose Manuel Rodriguez,Gary Saunders,Andrea Sboner,Stephen M. J. Searle,Cristina Sisu,Catherine E. Snow,Charles A. Steward,Electra Tapanari,Michael L. Tress,Marijke J. van Baren,Stefan Washietl,Laurens G. Wilming,Amonida Zadissa,Zhengdong D. Zhang,Michael R. Brent,David Haussler,Alfonso Valencia,Nicholas Addleman,Roger P. Alexander,Raymond K. Auerbach,Suganthi Balasubramanian,Keith Bettinger,Nitin Bhardwaj,Alan P. Boyle,Alina R. Cao,Philip Cayting,Alexandra Charos,Yong Cheng,Catharine L. Eastman,Ghia Euskirchen,Joseph D. Fleming,Fabian Grubert,Lukas Habegger,Manoj Hariharan,Arif Harmanci,Sushma Iyengar,Victor X. Jin,Konrad J. Karczewski,Maya Kasowski,Phil Lacroute,Hugo Y. K. Lam,Nathan Lamarre-Vincent,Jin Lian,Marianne Lindahl-Allen,Renqiang Min,Benoit Miotto,Hannah Monahan,Zarmik Moqtaderi,Xinmeng J. Mu,Henriette O'Geen,Zhengqing Ouyang,Dorrelyn Patacsil,Debasish Raha,Lucía Ramírez,Brian Reed,Minyi Shi,Teri Slifer,Heather Witt,Linfeng Wu,Xiaoqin Xu,Koon-Kiu Yan,Xinqiong Yang,Kevin Struhl,Sherman M. Weissman,Luiz O. F. Penalva,Subhradip Karmakar,Raj R. Bhanvadia,Alina Choudhury,Marc Domanus,Lijia Ma,Jennifer L. Moran,Alec Victorsen,Thomas O. Auer,Lazaro Centanin,Michael P. Eichenlaub,Franziska Gruhl,Stephan Heermann,Burkhard Hoeckendorf,Daigo Inoue,Tanja Kellner,Stephan Kirchmaier,Claudia Mueller,Robert Reinhardt,Lea Schertel,Stephanie Schneider,Rebecca Sinn,Beate Wittbrodt,Jochen Wittbrodt,E. Christopher Partridge,Gaurav Jain,Gayathri Balasundaram,Daniel Bates,Rachel Byron,Theresa K. Canfield,Morgan Diegel,Douglas Dunn,Abigail K. Ebersol,Tristan Frum,Kavita Garg,Erica Gist,R. Scott Hansen,Lisa Boatman,Eric Haugen,Richard Humbert,Audra K. Johnson,Ericka M. Johnson,Tattyana V. Kutyavin,Kristen Lee,Dimitra Lotakis,Matthew T. Maurano,Shane Neph,Fiedencio V. Neri,Eric D. Nguyen,Hongzhu Qu,Alex Reynolds,Vaughn Roach,Eric Rynes,Minerva E. Sanchez,Richard Sandstrom,Anthony Shafer,Andrew B. Stergachis,Sean Thomas,Benjamin Vernot,Jeff Vierstra,Shinny Vong,Hao Wang,Molly Weaver,Yongqi Yan,Miaohua Zhang,Joshua M. Akey,M. A. Bender,Michael O. Dorschner,Mark Groudine,Michael J. MacCoss,Patrick A. Navas,George Stamatoyannopoulos,Kathryn Beal,Alvis Brazma,Paul Flicek,Nathan R. Johnson,Margus Lukk,Nicholas M. Luscombe,Daniel Sobral,Juan M. Vaquerizas,Serafim Batzoglou,Arend Sidow,Nadine Hussami,Sofia Kyriazopoulou-Panagiotopoulou,Max Libbrecht,Marc A. Schaub,Webb Miller,Peter J. Bickel,Balazs Banfai,Nathan Boley,Haiyan Huang,Jingyi Jessica Li,William Stafford Noble,Jeff A. Bilmes,Orion J. Buske,Avinash Das Sahu,Peter V. Kharchenko,Peter J. Park,Dannon Baker,James Taylor,Lucas Lochovsky +442 more
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Architecture of the human regulatory network derived from ENCODE data
Mark Gerstein,Anshul Kundaje,Manoj Hariharan,Stephen G. Landt,Koon-Kiu Yan,Chao Cheng,Xinmeng Jasmine Mu,Ekta Khurana,Joel Rozowsky,Roger P. Alexander,Renqiang Min,Renqiang Min,P. Alves,Alexej Abyzov,Nicholas Addleman,Nitin Bhardwaj,Alan P. Boyle,Philip Cayting,Alexandra Charos,David Z. Chen,Yong Cheng,Declan Clarke,Catharine L. Eastman,Ghia Euskirchen,Seth Frietze,Yao Fu,Jason Gertz,Fabian Grubert,Arif Harmanci,Preti Jain,Maya Kasowski,Phil Lacroute,Jing Jane Leng,Jin Lian,Hannah Monahan,Henriette O'Geen,Zhengqing Ouyang,E. Christopher Partridge,Dorrelyn Patacsil,Florencia Pauli,Debasish Raha,Lucía Ramírez,Timothy E. Reddy,Brian Reed,Minyi Shi,Teri Slifer,Jing Wang,Linfeng Wu,Xinqiong Yang,Kevin Y. Yip,Kevin Y. Yip,Gili Zilberman-Schapira,Serafim Batzoglou,Arend Sidow,Peggy J. Farnham,Richard M. Myers,Sherman M. Weissman,Michael Snyder +57 more
TL;DR: The combinatorial, co-association of transcription factors is found to be highly context specific: distinct combinations of factors bind at specific genomic locations.
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Landscape and variation of RNA secondary structure across the human transcriptome
Yue Wan,Kun Qu,Qiangfeng Cliff Zhang,Ryan A. Flynn,Ohad Manor,Zhengqing Ouyang,Jiajing Zhang,Robert C. Spitale,Michael Snyder,Eran Segal,Howard Y. Chang +10 more
TL;DR: The initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child) is reported, which provides a comprehensive RSS map of human coding and non-coding RNAs.
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ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
TL;DR: In mouse embryonic stem cells (ESCs), a remarkably high proportion of variation in gene expression can be explained by the binding signals of 12 transcription factors (TFs), and this approach offers higher power in predicting gene expression from ChIP-Seq data and provides a way to capture cooperation among regulators.
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Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
Eleni P. Mimitou,Anthony Cheng,Antonino Montalbano,Stephanie Hao,Marlon Stoeckius,Mateusz Legut,Timothy Roush,Alberto Herrera,Efthymia Papalexi,Zhengqing Ouyang,Zhengqing Ouyang,Rahul Satija,Neville E. Sanjana,Sergei B. Koralov,Peter Smibert +14 more
TL;DR: Expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq) is described for the high-throughput characterization of at least five modalities of information from each single cell.