Literature DB >> 27347755

Saturation analysis for whole-genome bisulfite sequencing data.

Emanuele Libertini1, Simon C Heath2, Rifat A Hamoudi3, Marta Gut2, Michael J Ziller4,5,6, Javier Herrero7, Agata Czyz8, Victor Ruotti8, Hendrik G Stunnenberg9, Mattia Frontini10,11,12, Willem H Ouwehand10,11,12,13, Alexander Meissner4,5,6, Ivo G Gut2, Stephan Beck1.   

Abstract

Entities:  

Year:  2016        PMID: 27347755     DOI: 10.1038/nbt.3524

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  13 in total

1.  Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.

Authors:  Hongcang Gu; Zachary D Smith; Christoph Bock; Patrick Boyle; Andreas Gnirke; Alexander Meissner
Journal:  Nat Protoc       Date:  2011-03-18       Impact factor: 13.491

2.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Authors:  Thomas A Down; Vardhman K Rakyan; Daniel J Turner; Paul Flicek; Heng Li; Eugene Kulesha; Stefan Gräf; Nathan Johnson; Javier Herrero; Eleni M Tomazou; Natalie P Thorne; Liselotte Bäckdahl; Marlis Herberth; Kevin L Howe; David K Jackson; Marcos M Miretti; John C Marioni; Ewan Birney; Tim J P Hubbard; Richard Durbin; Simon Tavaré; Stephan Beck
Journal:  Nat Biotechnol       Date:  2008-07       Impact factor: 54.908

3.  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

4.  BLUEPRINT to decode the epigenetic signature written in blood.

Authors:  David Adams; Lucia Altucci; Stylianos E Antonarakis; Juan Ballesteros; Stephan Beck; Adrian Bird; Christoph Bock; Bernhard Boehm; Elias Campo; Andrea Caricasole; Fredrik Dahl; Emmanouil T Dermitzakis; Tariq Enver; Manel Esteller; Xavier Estivill; Anne Ferguson-Smith; Jude Fitzgibbon; Paul Flicek; Claudia Giehl; Thomas Graf; Frank Grosveld; Roderic Guigo; Ivo Gut; Kristian Helin; Jonas Jarvius; Ralf Küppers; Hans Lehrach; Thomas Lengauer; Åke Lernmark; David Leslie; Markus Loeffler; Elizabeth Macintyre; Antonello Mai; Joost H A Martens; Saverio Minucci; Willem H Ouwehand; Pier Giuseppe Pelicci; Hèléne Pendeville; Bo Porse; Vardhman Rakyan; Wolf Reik; Martin Schrappe; Dirk Schübeler; Martin Seifert; Reiner Siebert; David Simmons; Nicole Soranzo; Salvatore Spicuglia; Michael Stratton; Hendrik G Stunnenberg; Amos Tanay; David Torrents; Alfonso Valencia; Edo Vellenga; Martin Vingron; Jörn Walter; Spike Willcocks
Journal:  Nat Biotechnol       Date:  2012-03-07       Impact factor: 54.908

5.  Quantitative comparison of genome-wide DNA methylation mapping technologies.

Authors:  Christoph Bock; Eleni M Tomazou; Arie B Brinkman; Fabian Müller; Femke Simmer; Hongcang Gu; Natalie Jäger; Andreas Gnirke; Hendrik G Stunnenberg; Alexander Meissner
Journal:  Nat Biotechnol       Date:  2010-09-19       Impact factor: 54.908

6.  The DNA methylome of human peripheral blood mononuclear cells.

Authors:  Yingrui Li; Jingde Zhu; Geng Tian; Ning Li; Qibin Li; Mingzhi Ye; Hancheng Zheng; Jian Yu; Honglong Wu; Jihua Sun; Hongyu Zhang; Quan Chen; Ruibang Luo; Minfeng Chen; Yinghua He; Xin Jin; Qinghui Zhang; Chang Yu; Guangyu Zhou; Jinfeng Sun; Yebo Huang; Huisong Zheng; Hongzhi Cao; Xiaoyu Zhou; Shicheng Guo; Xueda Hu; Xin Li; Karsten Kristiansen; Lars Bolund; Jiujin Xu; Wen Wang; Huanming Yang; Jian Wang; Ruiqiang Li; Stephan Beck; Jun Wang; Xiuqing Zhang
Journal:  PLoS Biol       Date:  2010-11-09       Impact factor: 8.029

7.  Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Authors:  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 Olshen; Tracy 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 R Ecker; Wei Li; Peggy J Farnham; Robert A Waterland; Alexander Meissner; Marco A Marra; Martin Hirst; Aleksandar Milosavljevic; Joseph F Costello
Journal:  Nat Biotechnol       Date:  2010-09-19       Impact factor: 54.908

8.  Charting a dynamic DNA methylation landscape of the human genome.

Authors:  Michael J Ziller; Hongcang Gu; Fabian Müller; Julie Donaghey; Linus T-Y Tsai; Oliver Kohlbacher; Philip L De Jager; Evan D Rosen; David A Bennett; Bradley E Bernstein; Andreas Gnirke; Alexander Meissner
Journal:  Nature       Date:  2013-08-07       Impact factor: 49.962

9.  Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments.

Authors:  Egor Dolzhenko; Andrew D Smith
Journal:  BMC Bioinformatics       Date:  2014-06-24       Impact factor: 3.169

10.  Information recovery from low coverage whole-genome bisulfite sequencing.

Authors:  Emanuele Libertini; Simon C Heath; Rifat A Hamoudi; Marta Gut; Michael J Ziller; Agata Czyz; Victor Ruotti; Hendrik G Stunnenberg; Mattia Frontini; Willem H Ouwehand; Alexander Meissner; Ivo G Gut; Stephan Beck
Journal:  Nat Commun       Date:  2016-06-27       Impact factor: 14.919

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  10 in total

Review 1.  Epigenetics and precision medicine in cardiovascular patients: from basic concepts to the clinical arena.

Authors:  Sarah Costantino; Peter Libby; Raj Kishore; Jean-Claude Tardif; Assam El-Osta; Francesco Paneni
Journal:  Eur Heart J       Date:  2018-12-14       Impact factor: 29.983

2.  Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling.

Authors:  Zdislav Staševskij; Povilas Gibas; Juozas Gordevičius; Edita Kriukienė; Saulius Klimašauskas
Journal:  Mol Cell       Date:  2017-01-19       Impact factor: 17.970

3.  DNA methylation study of Huntington's disease and motor progression in patients and in animal models.

Authors:  Ake T Lu; Pritika Narayan; Matthew J Grant; Peter Langfelder; Nan Wang; Seung Kwak; Hilary Wilkinson; Richard Z Chen; Jian Chen; C Simon Bawden; Skye R Rudiger; Marc Ciosi; Afroditi Chatzi; Alastair Maxwell; Timothy A Hore; Jeff Aaronson; Jim Rosinski; Alicia Preiss; Thomas F Vogt; Giovanni Coppola; Darren Monckton; Russell G Snell; X William Yang; Steve Horvath
Journal:  Nat Commun       Date:  2020-09-10       Impact factor: 14.919

Review 4.  Stress and the Emerging Roles of Chromatin Remodeling in Signal Integration and Stable Transmission of Reversible Phenotypes.

Authors:  Ian C G Weaver; Austin C Korgan; Kristen Lee; Ryan V Wheeler; Amos S Hundert; Donna Goguen
Journal:  Front Behav Neurosci       Date:  2017-03-15       Impact factor: 3.558

Review 5.  Clinical implications of genome-wide DNA methylation studies in acute myeloid leukemia.

Authors:  Yan Li; Qingyu Xu; Na Lv; Lili Wang; Hongmei Zhao; Xiuli Wang; Jing Guo; Chongjian Chen; Yonghui Li; Li Yu
Journal:  J Hematol Oncol       Date:  2017-02-02       Impact factor: 17.388

6.  METHimpute: imputation-guided construction of complete methylomes from WGBS data.

Authors:  Aaron Taudt; David Roquis; Amaryllis Vidalis; René Wardenaar; Frank Johannes; Maria Colomé-Tatché
Journal:  BMC Genomics       Date:  2018-06-07       Impact factor: 3.969

7.  Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing.

Authors:  Li Zhou; Hong Kiat Ng; Daniela I Drautz-Moses; Stephan C Schuster; Stephan Beck; Changhoon Kim; John Campbell Chambers; Marie Loh
Journal:  Sci Rep       Date:  2019-07-17       Impact factor: 4.379

Review 8.  DNA methylation aging clocks: challenges and recommendations.

Authors:  Christopher G Bell; Robert Lowe; Peter D Adams; Andrea A Baccarelli; Stephan Beck; Jordana T Bell; Brock C Christensen; Vadim N Gladyshev; Bastiaan T Heijmans; Steve Horvath; Trey Ideker; Jean-Pierre J Issa; Karl T Kelsey; Riccardo E Marioni; Wolf Reik; Caroline L Relton; Leonard C Schalkwyk; Andrew E Teschendorff; Wolfgang Wagner; Kang Zhang; Vardhman K Rakyan
Journal:  Genome Biol       Date:  2019-11-25       Impact factor: 13.583

Review 9.  Genetic impacts on DNA methylation: research findings and future perspectives.

Authors:  Sergio Villicaña; Jordana T Bell
Journal:  Genome Biol       Date:  2021-04-30       Impact factor: 13.583

10.  Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle.

Authors:  Lingzhao Fang; Yang Zhou; Shuli Liu; Jicai Jiang; Derek M Bickhart; Daniel J Null; Bingjie Li; Steven G Schroeder; Benjamin D Rosen; John B Cole; Curtis P Van Tassell; Li Ma; George E Liu
Journal:  Epigenomes       Date:  2019-05-16
  10 in total

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