Literature DB >> 22690667

The NIH Roadmap Epigenomics Program data resource.

Lisa Helbling Chadwick1.   

Abstract

The NIH Roadmap Reference Epigenome Mapping Consortium is developing a community resource of genome-wide epigenetic maps in a broad range of human primary cells and tissues. There are large amounts of data already available, and a number of different options for viewing and analyzing the data. This report will describe key features of the websites where users will find data, protocols and analysis tools developed by the consortium, and provide a perspective on how this unique resource will facilitate and inform human disease research, both immediately and in the future.

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Year:  2012        PMID： 22690667      PMCID： PMC3381455          DOI： 10.2217/epi.12.18

Source DB:  PubMed          Journal:  Epigenomics        ISSN： 1750-192X            Impact factor:   4.778


  17 in total

1.  Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development.

Authors:  Dana C Dolinoy; Dale Huang; Randy L Jirtle
Journal:  Proc Natl Acad Sci U S A       Date:  2007-08-01       Impact factor: 11.205

2.  Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice.

Authors:  G L Wolff; R L Kodell; S R Moore; C A Cooney
Journal:  FASEB J       Date:  1998-08       Impact factor: 5.191

3.  The Human Epigenome Browser at Washington University.

Authors:  Xin Zhou; Brett Maricque; Mingchao Xie; Daofeng Li; Vasavi Sundaram; Eric A Martin; Brian C Koebbe; Cydney Nielsen; Martin Hirst; Peggy Farnham; Robert M Kuhn; Jingchun Zhu; Ivan Smirnov; W James Kent; David Haussler; Pamela A F Madden; Joseph F Costello; Ting Wang
Journal:  Nat Methods       Date:  2011-11-29       Impact factor: 28.547

4.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  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 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 D 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; Jörg Hackermüller; 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 M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; 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; 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; Todd A Richmond; 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; Gonçalo R 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 M 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
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

5.  Human DNA methylomes at base resolution show widespread epigenomic differences.

Authors:  Ryan Lister; Mattia Pelizzola; Robert H Dowen; R David Hawkins; Gary Hon; Julian Tonti-Filippini; Joseph R Nery; Leonard Lee; Zhen Ye; Que-Minh Ngo; Lee Edsall; Jessica Antosiewicz-Bourget; Ron Stewart; Victor Ruotti; A Harvey Millar; James A Thomson; Bing Ren; Joseph R Ecker
Journal:  Nature       Date:  2009-10-14       Impact factor: 49.962

Review 6.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

7.  Mapping and analysis of chromatin state dynamics in nine human cell types.

Authors:  Jason Ernst; Pouya Kheradpour; Tarjei S Mikkelsen; Noam Shoresh; Lucas D Ward; Charles B Epstein; Xiaolan Zhang; Li Wang; Robbyn Issner; Michael Coyne; Manching Ku; Timothy Durham; Manolis Kellis; Bradley E Bernstein
Journal:  Nature       Date:  2011-03-23       Impact factor: 49.962

8.  Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.

Authors:  Alexander Meissner; Andreas Gnirke; George W Bell; Bernard Ramsahoye; Eric S Lander; Rudolf Jaenisch
Journal:  Nucleic Acids Res       Date:  2005-10-13       Impact factor: 16.971

9.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.

Authors:  Jay R Hesselberth; Xiaoyu Chen; Zhihong Zhang; Peter J Sabo; Richard Sandstrom; Alex P Reynolds; Robert E Thurman; Shane Neph; Michael S Kuehn; William S Noble; Stanley Fields; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2009-03-22       Impact factor: 28.547

10.  Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome.

Authors:  Dana C Dolinoy; Jennifer R Weidman; Robert A Waterland; Randy L Jirtle
Journal:  Environ Health Perspect       Date:  2006-04       Impact factor: 9.031
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  109 in total

1.  Neuroepigenomics: Resources, Obstacles, and Opportunities.

Authors:  John S Satterlee; Andrea Beckel-Mitchener; Roger Little; Dena Procaccini; Joni L Rutter; Amy C Lossie
Journal:  Neuroepigenetics       Date:  2015-01-01

2.  Omicseq: a web-based search engine for exploring omics datasets.

Authors:  Xiaobo Sun; William S Pittard; Tianlei Xu; Li Chen; Michael E Zwick; Xiaoqian Jiang; Fusheng Wang; Zhaohui S Qin
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

3.  EPITRANS: a database that integrates epigenome and transcriptome data.

Authors:  Soo Young Cho; Jin Choul Chai; Soo Jun Park; Hyemyung Seo; Chae-Bong Sohn; Young Seek Lee
Journal:  Mol Cells       Date:  2013-11-08       Impact factor: 5.034

4.  A genome-wide association study yields five novel thyroid cancer risk loci.

Authors:  Julius Gudmundsson; Gudmar Thorleifsson; Jon K Sigurdsson; Lilja Stefansdottir; Jon G Jonasson; Sigurjon A Gudjonsson; Daniel F Gudbjartsson; Gisli Masson; Hrefna Johannsdottir; Gisli H Halldorsson; Simon N Stacey; Hannes Helgason; Patrick Sulem; Leigha Senter; Huiling He; Sandya Liyanarachchi; Matthew D Ringel; Esperanza Aguillo; Angeles Panadero; Enrique Prats; Almudena Garcia-Castaño; Ana De Juan; Fernando Rivera; Li Xu; Lambertus A Kiemeney; Gudmundur I Eyjolfsson; Olof Sigurdardottir; Isleifur Olafsson; Hoskuldur Kristvinsson; Romana T Netea-Maier; Thorvaldur Jonsson; Jose I Mayordomo; Theo S Plantinga; Hannes Hjartarson; Jon Hrafnkelsson; Erich M Sturgis; Unnur Thorsteinsdottir; Thorunn Rafnar; Albert de la Chapelle; Kari Stefansson
Journal:  Nat Commun       Date:  2017-02-14       Impact factor: 14.919

Review 5.  Genetics of Common Endocrine Disease: The Present and the Future.

Authors:  Mark O Goodarzi
Journal:  J Clin Endocrinol Metab       Date:  2016-02-23       Impact factor: 5.958

6.  Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.

Authors:  Taejeong Bae; Livia Tomasini; Jessica Mariani; Bo Zhou; Tanmoy Roychowdhury; Daniel Franjic; Mihovil Pletikos; Reenal Pattni; Bo-Juen Chen; Elisa Venturini; Bridget Riley-Gillis; Nenad Sestan; Alexander E Urban; Alexej Abyzov; Flora M Vaccarino
Journal:  Science       Date:  2017-12-07       Impact factor: 47.728

Review 7.  Unraveling tumor grading and genomic landscape in lung neuroendocrine tumors.

Authors:  Giuseppe Pelosi; Mauro Papotti; Guido Rindi; Aldo Scarpa
Journal:  Endocr Pathol       Date:  2014-06       Impact factor: 3.943

8.  Identification of a Core Module for Bone Mineral Density through the Integration of a Co-expression Network and GWAS Data.

Authors:  Olivia L Sabik; Gina M Calabrese; Eric Taleghani; Cheryl L Ackert-Bicknell; Charles R Farber
Journal:  Cell Rep       Date:  2020-09-15       Impact factor: 9.423

9.  Common and Rare Coding Genetic Variation Underlying the Electrocardiographic PR Interval.

Authors:  Honghuang Lin; Jessica van Setten; Albert V Smith; Nathan A Bihlmeyer; Helen R Warren; Jennifer A Brody; Farid Radmanesh; Leanne Hall; Niels Grarup; Martina Müller-Nurasyid; Thibaud Boutin; Niek Verweij; Henry J Lin; Ruifang Li-Gao; Marten E van den Berg; Jonathan Marten; Stefan Weiss; Bram P Prins; Jeffrey Haessler; Leo-Pekka Lyytikäinen; Hao Mei; Tamara B Harris; Lenore J Launer; Man Li; Alvaro Alonso; Elsayed Z Soliman; John M Connell; Paul L Huang; Lu-Chen Weng; Heather S Jameson; William Hucker; Alan Hanley; Nathan R Tucker; Yii-Der Ida Chen; Joshua C Bis; Kenneth M Rice; Colleen M Sitlani; Jan A Kors; Zhijun Xie; Chengping Wen; Jared W Magnani; Christopher P Nelson; Jørgen K Kanters; Moritz F Sinner; Konstantin Strauch; Annette Peters; Melanie Waldenberger; Thomas Meitinger; Jette Bork-Jensen; Oluf Pedersen; Allan Linneberg; Igor Rudan; Rudolf A de Boer; Peter van der Meer; Jie Yao; Xiuqing Guo; Kent D Taylor; Nona Sotoodehnia; Jerome I Rotter; Dennis O Mook-Kanamori; Stella Trompet; Fernando Rivadeneira; André Uitterlinden; Mark Eijgelsheim; Sandosh Padmanabhan; Blair H Smith; Henry Völzke; Stephan B Felix; Georg Homuth; Uwe Völker; Massimo Mangino; Timothy D Spector; Michiel L Bots; Marco Perez; Mika Kähönen; Olli T Raitakari; Vilmundur Gudnason; Dan E Arking; Patricia B Munroe; Bruce M Psaty; Cornelia M van Duijn; Emelia J Benjamin; Jonathan Rosand; Nilesh J Samani; Torben Hansen; Stefan Kääb; Ozren Polasek; Pim van der Harst; Susan R Heckbert; J Wouter Jukema; Bruno H Stricker; Caroline Hayward; Marcus Dörr; Yalda Jamshidi; Folkert W Asselbergs; Charles Kooperberg; Terho Lehtimäki; James G Wilson; Patrick T Ellinor; Steven A Lubitz; Aaron Isaacs
Journal:  Circ Genom Precis Med       Date:  2018-05

10.  SEA: a super-enhancer archive.

Authors:  Yanjun Wei; Shumei Zhang; Shipeng Shang; Bin Zhang; Song Li; Xinyu Wang; Fang Wang; Jianzhong Su; Qiong Wu; Hongbo Liu; Yan Zhang
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971
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