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Jonghwan Kim

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Jonghwan Kim; Stuart H Orkin
Embryonic stem cell-specific signatures in cancer: insights into genomic regulatory networks and implications for medicine.
Jonghwan Kim; Andrew J Woo; Jianlin Chu; Jonathan W Snow; Yuko Fujiwara; Chul Geun Kim; Alan B Cantor; Stuart H Orkin
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs.
K Kim; A Doi; Bo Wen; K Ng; R Zhao; Patrick Cahan; Jonghwan Kim; Martin Aryee; Hongxiu Ji; L I R Ehrlich; A Yabuuchi; A Takeuchi; K C Cunniff; H Hongguang; S McKinney-Freeman; O Naveiras; T J Yoon; Rafael A Irizarry; N Jung; J Seita; J Hanna; P Murakami; Rudolf Jaenisch; R Weissleder; S H Orkin; I L Weissman; Andrew P Feinberg; George Q Daley
Epigenetic memory in induced pluripotent stem cells.

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All Publications

2011: Jonghwan Kim; Stuart H Orkin
Embryonic stem cell-specific signatures in cancer: insights into genomic regulatory networks and implications for medicine.
Genome medicine 2011;3(11):75.
2010: Jonghwan Kim; Andrew J Woo; Jianlin Chu; Jonathan W Snow; Yuko Fujiwara; Chul Geun Kim; Alan B Cantor; Stuart H Orkin
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs.
Cell 2010;143(2):313-24.
2010: K Kim; A Doi; Bo Wen; K Ng; R Zhao; Patrick Cahan; Jonghwan Kim; Martin Aryee; Hongxiu Ji; L I R Ehrlich; A Yabuuchi; A Takeuchi; K C Cunniff; H Hongguang; S McKinney-Freeman; O Naveiras; T J Yoon; Rafael A Irizarry; N Jung; J Seita; J Hanna; P Murakami; Rudolf Jaenisch; R Weissleder; S H Orkin; I L Weissman; Andrew P Feinberg; George Q Daley
Epigenetic memory in induced pluripotent stem cells.
Nature 2010;467(7313):285-90.
2010: Jonathan W Snow; Jonghwan Kim; Caroline R Currie; Jian Xu; Stuart H Orkin
Sumoylation regulates interaction of FOG1 with C-terminal-binding protein (CTBP).
The Journal of biological chemistry 2010;285(36):28064-75.
2010: Xiaoying Bai; Jonghwan Kim; Zhongan Yang; Michael J Jurynec; Thomas E Akie; Joseph Lee; Jocelyn LeBlanc; Anna Sessa; Hong Jiang; Anthony DiBiase; Yi Zhou; David Jonah Grunwald; Shuo Lin; Alan B Cantor; Stuart H Orkin; Leonard I Zon
TIF1gamma controls erythroid cell fate by regulating transcription elongation.
Cell 2010;142(1):133-43.
2010: Jonghwan Kim; Stuart H Orkin
Systematic tracking of cell fate changes.
Nature biotechnology 2010;28(2):146-7.
2009: Jennifer J Trowbridge; Jonathan W Snow; Jonghwan Kim; Stuart H Orkin
DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells.
Cell stem cell 2009;5(4):442-9.
2009: Guang Hu; Jonghwan Kim; Qikai Xu; Yumei Leng; Stuart H Orkin; Stephen J Elledge
A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal.
Genes & development 2009;23(7):837-48.
2009: Jonghwan Kim; Alan B Cantor; Stuart H Orkin; Jianlong Wang
Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells.
Nature protocols 2009;4(4):506-17.
2008: Xiaohua Shen; Yingchun Liu; Yu-Jung Hsu; Yuko Fujiwara; Jonghwan Kim; Xiaohong Mao; Guo-Cheng Yuan; Stuart H Orkin
EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency.
Molecular cell 2008;32(4):491-502.
2008: Jonghwan Kim; Jianlin Chu; Xiaohua Shen; Jianlong Wang; Stuart H Orkin
An extended transcriptional network for pluripotency of embryonic stem cells.
Cell 2008;132(6):1049-61.
2008: Stuart H Orkin; Jianlong Wang; Jonghwan Kim; J Chu; S Rao; T W Theunissen; X Shen; D N Levasseur
The transcriptional network controlling pluripotency in ES cells.
Cold Spring Harbor symposia on quantitative biology 2008;73():195-202.
2008: Jonghwan Kim; Ji-hoon Lee; Vishwanath R Iyer
Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo.
PloS one 2008;3(3):e1798.
2007: Shireen Saleque; Jonghwan Kim; Heather M Rooke; Stuart H Orkin
Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1.
Molecular cell 2007;27(4):562-72.
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: Akshay A Bhinge; Jonghwan Kim; Ghia Euskirchen; Michael Snyder; Vishwanath R Iyer
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Genome research 2007;17(6):910-6.
2007: Paul G Giresi; Jonghwan Kim; Ryan M McDaniell; Vishwanath R Iyer; Jason Dillon Lieb
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
Genome research 2007;17(6):877-85.
2005: Jonghwan Kim; Vishwanath R Iyer
Identifying chromosomal targets of DNA-binding proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 2005;Chapter 21():Unit 21.10.
2005: Jonghwan Kim; Akshay A Bhinge; Xochitl C Morgan; Vishwanath R Iyer
Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.
Nature methods 2005;2(1):47-53.
2004: Jonghwan Kim; Vishwanath R Iyer
Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles.
Molecular and cellular biology 2004;24(18):8104-12.
1999: S J Kim; June Ho Shin; Jonghwan Kim; S H Kim; Ji Hyung Chae; E J Park; R H Seong; Seok Ho Hong; S D Park; S Jeong; Chul Geun Kim
Isolation of developmentally regulated novel genes based on sequence identity and gene expression pattern.
Molecules and cells 1999;9(2):207-18.