T
Tao Liu
Researcher at Chinese Academy of Sciences
Publications - 85
Citations - 23849
Tao Liu is an academic researcher from Chinese Academy of Sciences. The author has contributed to research in topics: Gene & Chromatin. The author has an hindex of 33, co-authored 73 publications receiving 19175 citations. Previous affiliations of Tao Liu include Brigham and Women's Hospital & Massachusetts Institute of Technology.
Papers
More filters
Journal ArticleDOI
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Journal ArticleDOI
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt,Georgi K. Marinov,Anshul Kundaje,Pouya Kheradpour,Florencia Pauli,Serafim Batzoglou,Bradley E. Bernstein,Peter J. Bickel,James B. Brown,Philip Cayting,Yiwen Chen,Gilberto DeSalvo,Charles B. Epstein,Katherine I. Fisher-Aylor,Ghia Euskirchen,Mark Gerstein,Jason Gertz,Alexander J. Hartemink,Michael M. Hoffman,Vishwanath R. Iyer,Youngsook L. Jung,Subhradip Karmakar,Manolis Kellis,Peter V. Kharchenko,Qiang Li,Tao Liu,X. Shirley Liu,Lijia Ma,Aleksandar Milosavljevic,Richard M. Myers,Peter J. Park,Michael J. Pazin,Marc D. Perry,Debasish Raha,Timothy E. Reddy,Joel Rozowsky,Noam Shoresh,Arend Sidow,Matthew Slattery,John A. Stamatoyannopoulos,Michael Y. Tolstorukov,Kevin P. White,Simon Xi,Peggy J. Farnham,Jason D. Lieb,Barbara J. Wold,Michael Snyder +46 more
TL;DR: This work discusses how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data and develops a set of working standards and guidelines for ChIP experiments that are updated routinely.
Journal ArticleDOI
Identifying ChIP-seq enrichment using MACS
TL;DR: This protocol provides a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and theH3K36me3 mark with broad enrichment.
Journal ArticleDOI
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
Mark Gerstein,Zhi John Lu,Eric L. Van Nostrand,Chao Cheng,Bradley I. Arshinoff,Tao Liu,Kevin Y. Yip,R. Robilotto,Andreas Rechtsteiner,Kohta Ikegami,P. Alves,A. Chateigner,Marc D. Perry,Mitzi Morris,Raymond K. Auerbach,X. Feng,Jing Leng,A. Vielle,Wei Niu,Kahn Rhrissorrakrai,Ashish Agarwal,Roger P. Alexander,Galt P. Barber,Cathleen M. Brdlik,J. Brennan,Jeremy Brouillet,Adrian Carr,Ming Sin Cheung,Hiram Clawson,Sergio Contrino,Luke Dannenberg,Abby F. Dernburg,Arshad Desai,L. Dick,Andréa C. Dosé,Jiang Du,Thea A. Egelhofer,Sevinc Ercan,Ghia Euskirchen,Brent Ewing,Elise A. Feingold,Reto Gassmann,Peter J. Good,Philip Green,Francois Gullier,M. Gutwein,Mark S. Guyer,Lukas Habegger,Ting Han,Jorja G. Henikoff,Stefan R. Henz,Angie S. Hinrichs,H. Holster,Tony Hyman,A. Leo Iniguez,J. Janette,M. Jensen,Masaomi Kato,W. James Kent,E. Kephart,Vishal Khivansara,Ekta Khurana,John Kim,P. Kolasinska-Zwierz,Eric C. Lai,Isabel J. Latorre,Amber Leahey,Suzanna E. Lewis,Paul Lloyd,Lucas Lochovsky,Rebecca F. Lowdon,Yaniv Lubling,Rachel Lyne,Michael J. MacCoss,Sebastian D. Mackowiak,Marco Mangone,Sheldon J. McKay,D. Mecenas,Gennifer E. Merrihew,David M. Miller,A. Muroyama,John I. Murray,Siew Loon Ooi,Hoang Pham,T. Phippen,Elicia Preston,Nikolaus Rajewsky,Gunnar Rätsch,Heidi Rosenbaum,Joel Rozowsky,Kim Rutherford,P. Ruzanov,Mihail Sarov,Rajkumar Sasidharan,Andrea Sboner,P. Scheid,Eran Segal,Hyunjin Shin,C. Shou,Frank J. Slack,C. Slightam,Richard J.H. Smith,William C. Spencer,Eo Stinson,S. Taing,Teruaki Takasaki,D. Vafeados,Ksenia Voronina,Guilin Wang,Nicole L. Washington,Christina M. Whittle,Beijing Wu,Koon-Kiu Yan,Georg Zeller,Z. Zha,Mei Zhong,Xingliang Zhou,Julie Ahringer,Susan Strome,Kristin C. Gunsalus,Gos Micklem,X. Shirley Liu,Valerie Reinke,Stuart K. Kim,LaDeana W. Hillier,Steven Henikoff,Fabio Piano,Michael Snyder,Lincoln Stein,Jason D. Lieb,Robert H. Waterston +130 more
TL;DR: These studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized, providing insights into the organization, structure, and function of the two genomes.
Journal ArticleDOI
EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent
Kexin Xu,Zhenhua Jeremy Wu,Anna C. Groner,Housheng Hansen He,Changmeng Cai,Rosina T. Lis,Rosina T. Lis,Xiaoqiu Wu,Edward C. Stack,Edward C. Stack,Massimo Loda,Tao Liu,Han Xu,Laura Cato,James E. Thornton,James E. Thornton,Richard I. Gregory,Richard I. Gregory,Colm Morrissey,Robert L. Vessella,Rodolfo Montironi,Cristina Magi-Galluzzi,Philip W. Kantoff,Steven P. Balk,X. Shirley Liu,Myles Brown +25 more
TL;DR: It is found that the oncogenic function of EZH2 in cells of castration-resistant prostate cancer is independent of its role as a transcriptional repressor, and involves the ability of EzH2 to act as a coactivator for critical transcription factors including the androgen receptor.