C
Chibo Hong
Researcher at University of California, San Francisco
Publications - 48
Citations - 11828
Chibo Hong is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: DNA methylation & Epigenetics. The author has an hindex of 27, co-authored 38 publications receiving 10112 citations.
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Journal ArticleDOI
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Wouter Meuleman,Jason Ernst,Misha Bilenky,Angela Yen,Angela Yen,Alireza Heravi-Moussavi,Pouya Kheradpour,Pouya Kheradpour,Zhizhuo Zhang,Zhizhuo Zhang,Jianrong Wang,Jianrong Wang,Michael J. Ziller,Viren Amin,John W. Whitaker,Matthew D. Schultz,Lucas D. Ward,Lucas D. Ward,Abhishek Sarkar,Abhishek Sarkar,Gerald Quon,Gerald Quon,Richard Sandstrom,Matthew L. Eaton,Matthew L. Eaton,Yi-Chieh Wu,Yi-Chieh Wu,Andreas R. Pfenning,Andreas R. Pfenning,Xinchen Wang,Xinchen Wang,Melina Claussnitzer,Melina Claussnitzer,Yaping Liu,Yaping Liu,Cristian Coarfa,R. Alan Harris,Noam Shoresh,Charles B. Epstein,Elizabeta Gjoneska,Elizabeta Gjoneska,Danny Leung,Wei Xie,R. David Hawkins,Ryan Lister,Chibo Hong,Philippe Gascard,Andrew J. Mungall,Richard A. Moore,Eric Chuah,Angela Tam,Theresa K. Canfield,R. Scott Hansen,Rajinder Kaul,Peter J. Sabo,Mukul S. Bansal,Mukul S. Bansal,Mukul S. Bansal,Annaick Carles,Jesse R. Dixon,Kai How Farh,Soheil Feizi,Soheil Feizi,Rosa Karlic,Ah Ram Kim,Ah Ram Kim,Ashwinikumar Kulkarni,Daofeng Li,Rebecca F. Lowdon,Ginell Elliott,Tim R. Mercer,Shane Neph,Vitor Onuchic,Paz Polak,Paz Polak,Nisha Rajagopal,Pradipta R. Ray,Richard C Sallari,Richard C Sallari,Kyle Siebenthall,Nicholas A Sinnott-Armstrong,Nicholas A Sinnott-Armstrong,Michael Stevens,Robert E. Thurman,Jie Wu,Bo Zhang,Xin Zhou,Arthur E. Beaudet,Laurie A. Boyer,Philip L. De Jager,Philip L. De Jager,Peggy J. Farnham,Susan J. Fisher,David Haussler,Steven J.M. Jones,Steven J.M. Jones,Wei Li,Marco A. Marra,Michael T. McManus,Shamil R. Sunyaev,Shamil R. Sunyaev,James A. Thomson,Thea D. Tlsty,Li-Huei Tsai,Li-Huei Tsai,Wei Wang,Robert A. Waterland,Michael Q. Zhang,Lisa Helbling Chadwick,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Joseph F. Costello,Joseph R. Ecker,Martin Hirst,Alexander Meissner,Aleksandar Milosavljevic,Bing Ren,John A. Stamatoyannopoulos,Ting Wang,Manolis Kellis,Manolis Kellis +123 more
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Journal ArticleDOI
Conserved role of intragenic DNA methylation in regulating alternative promoters
Alika K. Maunakea,Raman P. Nagarajan,Mikhail Bilenky,Tracy J. Ballinger,Cletus D'Souza,Shaun D. Fouse,Brett E. Johnson,Chibo Hong,Cydney B. Nielsen,Yongjun Zhao,Gustavo Turecki,Allen Delaney,Richard Varhol,Nina Thiessen,Ksenya Shchors,Ksenya Shchors,Vivi M. Heine,David H. Rowitch,Xiaoyun Xing,Chris Fiore,Maximiliaan Schillebeeckx,Steven J.M. Jones,David Haussler,Marco A. Marra,Martin Hirst,Ting Wang,Ting Wang,Joseph F. Costello +27 more
TL;DR: An in-depth investigation of the human SHANK3 locus and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo.
Journal ArticleDOI
Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma
Brett E. Johnson,Tali Mazor,Chibo Hong,Michael R. Barnes,Koki Aihara,Cory Y. McLean,Shaun D. Fouse,Shogo Yamamoto,Hiroki R. Ueda,Kenji Tatsuno,Saurabh Asthana,Llewellyn E. Jalbert,Sarah J. Nelson,Andrew W. Bollen,W. Clay Gustafson,Elise Charron,William A. Weiss,Ivan Smirnov,Jun S. Song,Adam B. Olshen,Soonmee Cha,Yongjun Zhao,Richard A. Moore,Andrew J. Mungall,Steven J.M. Jones,Martin Hirst,Marco A. Marra,Nobuhito Saito,Hiroyuki Aburatani,Akitake Mukasa,Mitchel S. Berger,Susan M. Chang,Barry S. Taylor,Joseph F. Costello +33 more
TL;DR: Exome sequencing of exomes of 23 initial low-grade gliomas and recurrent tumors resected from the same patients suggests that recurrent tumors are often seeded by cells derived from the initial tumor at a very early stage of their evolution.
Journal ArticleDOI
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
R. Alan Harris,Ting Wang,Cristian Coarfa,Raman P. Nagarajan,Chibo Hong,Sara L. Downey,Brett E. Johnson,Shaun D. Fouse,Allen Delaney,Yongjun Zhao,Adam B. Olshen,Tracy J. Ballinger,Xin Zhou,Kevin J. Forsberg,Junchen Gu,Lorigail Echipare,Henriette O'Geen,Ryan Lister,Mattia Pelizzola,Yuanxin Xi,Charles B. Epstein,Bradley E. Bernstein,R. David Hawkins,Bing Ren,Wen-Yu Chung,Hongcang Gu,Christoph Bock,Andreas Gnirke,Michael Q. Zhang,David Haussler,Joseph A. Ecker,Wei Li,Peggy J. Farnham,Robert A. Waterland,Alexander Meissner,Marco A. Marra,Martin Hirst,Aleksandar Milosavljevic,Joseph F. Costello +38 more
TL;DR: This work combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost and detected regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with Monoallelic epigenetic marks and monoallelic expression.
Journal ArticleDOI
Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells
Yuki Ohi,Han Qin,Chibo Hong,Laure Blouin,Jose M. Polo,Jose M. Polo,Tingxia Guo,Zhongxia Qi,Sara L. Downey,Philip D. Manos,Philip D. Manos,Derrick J. Rossi,Derrick J. Rossi,Jingwei Yu,Matthias Hebrok,Konrad Hochedlinger,Konrad Hochedlinger,Joseph F. Costello,Jun S. Song,Miguel Ramalho-Santos +19 more
TL;DR: In this article, a systematic comparison of human induced pluripotent stem (iPS) cells generated from hepatocytes (representative of endoderm), skin fibroblasts (mesoderm) and melanocytes (ectoderm).