H
Hong Sain Ooi
Researcher at Agency for Science, Technology and Research
Publications - 13
Citations - 7920
Hong Sain Ooi is an academic researcher from Agency for Science, Technology and Research. The author has contributed to research in topics: Chromatin immunoprecipitation & Genome. The author has an hindex of 11, co-authored 12 publications receiving 7480 citations. Previous affiliations of Hong Sain Ooi include Research Institute of Molecular Pathology & Genome Institute of Singapore.
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Journal ArticleDOI
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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 Frum,Elizabeth Rosenzweig,Neerja Karnani,Kirsten Lee,Gregory 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 R. Sunyaev,William Stafford Noble,Ian Dunham,Alexandre Reymond,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,Josep F. Abril,Atif Shahab,Christoph Flamm,Christoph Flamm,Claudia Fried,Jörg Hackermüller,Jana Hertel,Manja Lindemeyer,Kristin Missal,Andrea Tanzer,Andrea Tanzer,Stefan Washietl,Jan O. Korbel,Olof Emanuelsson,Jakob Skou Pedersen,Nancy Holroyd,Ruth Taylor,David Swarbreck,Nicholas Matthews,Mark Dickson,Daryl J. Thomas,Matthew T. Weirauch,James G. R. Gilbert,Jorg Drenkow,Ian Bell,Xiaodong Zhao,Kandhadayar G. Srinivasan,Wing-Kin Sung,Hong Sain Ooi,Kuo Ping Chiu,Sylvain Foissac,Tyler Alioto,Michael R. 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,Jia Qian Wu,Zheng Lian,Jin Lian,Peter E. Newburger,Xueqing Zhang,Peter J. Bickel,John S. Mattick,Piero Carninci,Yoshihide Hayashizaki,Sherman M. Weissman,Tim Hubbard,Richard M. Myers,Jane Rogers,Peter F. Stadler,Peter F. Stadler,Peter F. Stadler,Todd M. Lowe,Chia-Lin Wei,Yijun Ruan,Kevin Struhl,Mark Gerstein,Stylianos E. Antonarakis,Yutao Fu,Eric D. Green,Ulas Karaoz,Adam Siepel,Adam Siepel,James Taylor,Laura A. Liefer,Kris A. Wetterstrand,Peter J. Good,Elise A. Feingold,Mark S. Guyer,Gregory M. Cooper,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,Nan Zhang,Nan Zhang,Ian Holmes,James C. Mullikin,Abel Ureta-Vidal,Benedict Paten,Michael Seringhaus,Deanna M. Church,Kate R. 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 O. Barrera,Rhona K. Stuart,David C. King,Adam Ameur,Stefan Enroth,Mark Bieda,Jonghwan Kim,Akshay Bhinge,Nan Jiang,Jun Liu,Fei Yao,Vinsensius B. Vega,Charlie W.H. Lee,Patrick Ng,Annie Yang,Zarmik Moqtaderi,Zhou Zhu,Xiaoqin Xu,Sharon L. Squazzo,Matthew J. Oberley,David R. Inman,Michael A. Singer,Todd Richmond,Kyle J. Munn,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 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 C. Hon,Rosa Luna,Christopher K. Glass,M. Geoff Rosenfeld,Shelley Force Aldred,Sara J. Cooper,Anason S. Halees,Jane M. Lin,Hennady P. Shulha,Xiaoling Zhang,Mousheng Xu,Jaafar N. Haidar,Yong Yu,Vishwanath R. Iyer,Roland 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 E. Smith,Archana Thakkapallayil,Galt P. Barber,Robert M. Kuhn,Donna Karolchik,Lluís 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 S. Dimas,Eduardo Eyras,Ingileif B. Hallgrímsdóttir,Julian L. Huppert,Michael C. Zody,Gonçalo R. Abecasis,Xavier Estivill,Gerard G. Bouffard,Xiaobin Guan,Nancy F. Hansen,Jacquelyn R. Idol,Valerie 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 S. 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,Eric S. Lander,Maxim Koriabine,Mikhail Nefedov,Kazutoyo Osoegawa,Yuko Yoshinaga,Baoli Zhu,Pieter J. de Jong +320 more
TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Journal ArticleDOI
An oestrogen-receptor-α-bound human chromatin interactome
Melissa J. Fullwood,Mei Hui Liu,You Fu Pan,Jun Liu,Han Xu,Yusoff Bin Mohamed,Yuriy L. Orlov,Stoyan Velkov,Andrea Ho,Poh Huay Mei,Elaine G.Y. Chew,Phillips Yao Hui Huang,Willem Welboren,Yuyuan Han,Hong Sain Ooi,Pramila N. Ariyaratne,Vinsensius B. Vega,Yanquan Luo,Peck Yean Tan,Pei Ye Choy,K. D. Senali Abayratna Wansa,Bing Zhao,Kar Sian Lim,Shi Chi Leow,Jit Sin Yow,Roy Joseph,Haixia Li,Kartiki V. Desai,Jane S. Thomsen,Yew Kok Lee,R. Krishna Murthy Karuturi,Thoreau Herve,Guillaume Bourque,Hendrik G. Stunnenberg,Xiaoan Ruan,Valere Cacheux-Rataboul,Wing-Kin Sung,Wing-Kin Sung,Edison T. Liu,Chia-Lin Wei,Edwin Cheung,Edwin Cheung,Edwin Cheung,Yijun Ruan,Yijun Ruan +44 more
TL;DR: It is proposed that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes and is described as a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global Chromatin interactions.
Journal ArticleDOI
Global mapping of c-Myc binding sites and target gene networks in human B cells
Karen I. Zeller,Xiaodong Zhao,Charlie W.H. Lee,Kuo Ping Chiu,Fei Yao,Jason T. Yustein,Hong Sain Ooi,Yuriy L. Orlov,Atif Shahab,How Choong Yong,Yutao Fu,Zhiping Weng,Vladimir A. Kuznetsov,Wing-Kin Sung,Yijun Ruan,Chi V. Dang,Chia-Lin Wei +16 more
TL;DR: A snapshot of genome-wide, unbiased characterization of direct Myc binding targets in a model of human B lymphoid tumor using ChIP coupled with pair-end ditag sequencing analysis (ChIP-PET) provides a substantial framework for the understanding of mechanisms of Myc-induced tumorigenesis.
Journal ArticleDOI
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Guoliang Li,Melissa J. Fullwood,Han Xu,Fabianus Hendriyan Mulawadi,Stoyan Velkov,Vinsensius B. Vega,Pramila N. Ariyaratne,Yusoff Bin Mohamed,Hong Sain Ooi,Chandana Tennakoon,Chia-Lin Wei,Yijun Ruan,Yijun Ruan,Wing-Kin Sung,Wing-Kin Sung +14 more
TL;DR: Chia-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser is presented.
Journal ArticleDOI
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.
Patrick Ng,Jack J. S. Tan,Hong Sain Ooi,Yen Ling Lee,Kuo Ping Chiu,Melissa J. Fullwood,Kandhadayar G. Srinivasan,Clotilde Perbost,Lei Du,Wing-Kin Sung,Chia-Lin Wei,Yijun Ruan +11 more
TL;DR: This combined sequencing strategy achieved an approximate 100-fold efficiency increase over the current standard for PET analysis, and furthermore enables the short-read-length multiplex sequencing procedure to acquire paired-end information from large DNA fragments.