Literature DB >> 23629413

Exploring long-range genome interactions using the WashU Epigenome Browser.

Xin Zhou, Rebecca F Lowdon, Daofeng Li, Heather A Lawson, Pamela A F Madden, Joseph F Costello, Ting Wang.   

Abstract

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Year:  2013        PMID： 23629413      PMCID： PMC3820286          DOI： 10.1038/nmeth.2440

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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2.  My5C: web tools for chromosome conformation capture studies.

Authors:  Bryan R Lajoie; Nynke L van Berkum; Amartya Sanyal; Job Dekker
Journal:  Nat Methods       Date:  2009-10       Impact factor: 28.547

3.  Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Authors:  Guoliang Li; Xiaoan Ruan; Raymond K Auerbach; Kuljeet Singh Sandhu; Meizhen Zheng; Ping Wang; Huay Mei Poh; Yufen Goh; Joanne Lim; Jingyao Zhang; Hui Shan Sim; Su Qin Peh; Fabianus Hendriyan Mulawadi; Chin Thing Ong; Yuriy L Orlov; Shuzhen Hong; Zhizhuo Zhang; Steve Landt; Debasish Raha; Ghia Euskirchen; Chia-Lin Wei; Weihong Ge; Huaien Wang; Carrie Davis; Katherine I Fisher-Aylor; Ali Mortazavi; Mark Gerstein; Thomas Gingeras; Barbara Wold; Yi Sun; Melissa J Fullwood; Edwin Cheung; Edison Liu; Wing-Kin Sung; Michael Snyder; Yijun Ruan
Journal:  Cell       Date:  2012-01-20       Impact factor: 41.582

4.  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

5.  The NIH Roadmap Epigenomics Mapping Consortium.

Authors:  Bradley E Bernstein; John A Stamatoyannopoulos; Joseph F Costello; Bing Ren; Aleksandar Milosavljevic; Alexander Meissner; Manolis Kellis; Marco A Marra; Arthur L Beaudet; Joseph R Ecker; Peggy J Farnham; Martin Hirst; Eric S Lander; Tarjei S Mikkelsen; James A Thomson
Journal:  Nat Biotechnol       Date:  2010-10       Impact factor: 54.908

6.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

7.  CTCF-mediated functional chromatin interactome in pluripotent cells.

Authors:  Lusy Handoko; Han Xu; Guoliang Li; Chew Yee Ngan; Elaine Chew; Marie Schnapp; Charlie Wah Heng Lee; Chaopeng Ye; Joanne Lim Hui Ping; Fabianus Mulawadi; Eleanor Wong; Jianpeng Sheng; Yubo Zhang; Thompson Poh; Chee Seng Chan; Galih Kunarso; Atif Shahab; Guillaume Bourque; Valere Cacheux-Rataboul; Wing-Kin Sung; Yijun Ruan; Chia-Lin Wei
Journal:  Nat Genet       Date:  2011-06-19       Impact factor: 38.330

8.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

9.  Conserved role of intragenic DNA methylation in regulating alternative promoters.

Authors:  Alika K Maunakea; Raman P Nagarajan; Mikhail Bilenky; Tracy J Ballinger; Cletus D'Souza; Shaun D Fouse; Brett E Johnson; Chibo Hong; Cydney Nielsen; Yongjun Zhao; Gustavo Turecki; Allen Delaney; Richard Varhol; Nina Thiessen; 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; Joseph F Costello
Journal:  Nature       Date:  2010-07-08       Impact factor: 49.962

10.  The long-range interaction landscape of gene promoters.

Authors:  Amartya Sanyal; Bryan R Lajoie; Gaurav Jain; Job Dekker
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962
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  104 in total

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2.  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

3.  4DGenome: a comprehensive database of chromatin interactions.

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Journal:  Bioinformatics       Date:  2015-03-18       Impact factor: 6.937

Review 4.  Genetic Moderation of Stress Effects on Corticolimbic Circuitry.

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5.  methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser.

Authors:  Xin Zhou; Daofeng Li; Rebecca F Lowdon; Joseph F Costello; Ting Wang
Journal:  Bioinformatics       Date:  2014-04-10       Impact factor: 6.937

Review 6.  Chromosome conformation capture technologies and their impact in understanding genome function.

Authors:  Satish Sati; Giacomo Cavalli
Journal:  Chromosoma       Date:  2016-04-30       Impact factor: 4.316

Review 7.  Candidate gene-environment interaction research: reflections and recommendations.

Authors:  Danielle M Dick; Arpana Agrawal; Matthew C Keller; Amy Adkins; Fazil Aliev; Scott Monroe; John K Hewitt; Kenneth S Kendler; Kenneth J Sher
Journal:  Perspect Psychol Sci       Date:  2015-01

8.  The KASH-containing isoform of Nesprin1 giant associates with ciliary rootlets of ependymal cells.

Authors:  C Potter; D Razafsky; D Wozniak; M Casey; S Penrose; X Ge; M R Mahjoub; D Hodzic
Journal:  Neurobiol Dis       Date:  2018-04-06       Impact factor: 5.996

9.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

Authors:  Neva C Durand; James T Robinson; Muhammad S Shamim; Ido Machol; Jill P Mesirov; Eric S Lander; Erez Lieberman Aiden
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10.  Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis.

Authors:  Caitlin E Carey; Arpana Agrawal; Bo Zhang; Emily D Conley; Louisa Degenhardt; Andrew C Heath; Daofeng Li; Michael T Lynskey; Nicholas G Martin; Grant W Montgomery; Ting Wang; Laura J Bierut; Ahmad R Hariri; Elliot C Nelson; Ryan Bogdan
Journal:  J Abnorm Psychol       Date:  2015-11
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