Literature DB >> 28245214

Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation.

Elior Rahmani1,2,3, Noah Zaitlen2, Yael Baran3, Celeste Eng2, Donglei Hu2, Joshua Galanter2,4,5, Sam Oh2, Esteban G Burchard2,4, Eleazar Eskin6,7, James Zou8, Eran Halperin6,9.   

Abstract

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Year:  2017        PMID： 28245214      PMCID： PMC5548185          DOI： 10.1038/nmeth.4190

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


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  9 in total

1.  Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies.

Authors:  Andrew E Teschendorff; Joanna Zhuang; Martin Widschwendter
Journal:  Bioinformatics       Date:  2011-04-06       Impact factor: 6.937

2.  Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Authors:  Shijie C Zheng; Stephan Beck; Andrew E Jaffe; Devin C Koestler; Kasper D Hansen; Andres E Houseman; Rafael A Irizarry; Andrew E Teschendorff
Journal:  Nat Methods       Date:  2017-02-28       Impact factor: 28.547

3.  Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.

Authors:  Elior Rahmani; Noah Zaitlen; Yael Baran; Celeste Eng; Donglei Hu; Joshua Galanter; Sam Oh; Esteban G Burchard; Eleazar Eskin; James Zou; Eran Halperin
Journal:  Nat Methods       Date:  2016-03-28       Impact factor: 28.547

4.  Epigenetic signature of birth weight discordance in adult twins.

Authors:  Qihua Tan; Morten Frost; Bastiaan T Heijmans; Jacob von Bornemann Hjelmborg; Elmar W Tobi; Kaare Christensen; Lene Christiansen
Journal:  BMC Genomics       Date:  2014-12-04       Impact factor: 3.969

5.  Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.

Authors:  Yun Liu; Martin J Aryee; Leonid Padyukov; M Daniele Fallin; Espen Hesselberg; Arni Runarsson; Lovisa Reinius; Nathalie Acevedo; Margaret Taub; Marcus Ronninger; Klementy Shchetynsky; Annika Scheynius; Juha Kere; Lars Alfredsson; Lars Klareskog; Tomas J Ekström; Andrew P Feinberg
Journal:  Nat Biotechnol       Date:  2013-01-20       Impact factor: 54.908

6.  DNA methylation arrays as surrogate measures of cell mixture distribution.

Authors:  Eugene Andres Houseman; William P Accomando; Devin C Koestler; Brock C Christensen; Carmen J Marsit; Heather H Nelson; John K Wiencke; Karl T Kelsey
Journal:  BMC Bioinformatics       Date:  2012-05-08       Impact factor: 3.169

7.  Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL).

Authors:  Devin C Koestler; Meaghan J Jones; Joseph Usset; Brock C Christensen; Rondi A Butler; Michael S Kobor; John K Wiencke; Karl T Kelsey
Journal:  BMC Bioinformatics       Date:  2016-03-08       Impact factor: 3.169

8.  DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer.

Authors:  Andrew E Teschendorff; Yang Gao; Allison Jones; Matthias Ruebner; Matthias W Beckmann; David L Wachter; Peter A Fasching; Martin Widschwendter
Journal:  Nat Commun       Date:  2016-01-29       Impact factor: 14.919

9.  An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation.

Authors:  Eilis Hannon; Emma Dempster; Joana Viana; Joe Burrage; Adam R Smith; Ruby Macdonald; David St Clair; Colette Mustard; Gerome Breen; Sebastian Therman; Jaakko Kaprio; Timothea Toulopoulou; Hilleke E Hulshoff Pol; Marc M Bohlken; Rene S Kahn; Igor Nenadic; Christina M Hultman; Robin M Murray; David A Collier; Nick Bass; Hugh Gurling; Andrew McQuillin; Leonard Schalkwyk; Jonathan Mill
Journal:  Genome Biol       Date:  2016-08-30       Impact factor: 13.583
  9 in total
  17 in total

1.  Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives.

Authors:  Andy Dahl; Vincent Guillemot; Joel Mefford; Hugues Aschard; Noah Zaitlen
Journal:  Genetics       Date:  2019-01-28       Impact factor: 4.562

2.  Using R for Cell-Type Composition Imputation in Epigenome-Wide Association Studies.

Authors:  Chong Wu
Journal:  Methods Mol Biol       Date:  2022

3.  Exposure to violence, chronic stress, nasal DNA methylation, and atopic asthma in children.

Authors:  Qi Yan; Erick Forno; Andres Cardenas; Cancan Qi; Yueh-Ying Han; Edna Acosta-Pérez; Soyeon Kim; Rong Zhang; Nadia Boutaoui; Glorisa Canino; Judith M Vonk; Cheng-Jian Xu; Wei Chen; Anna Marsland; Emily Oken; Diane R Gold; Gerard H Koppelman; Juan C Celedón
Journal:  Pediatr Pulmonol       Date:  2021-03-22

4.  The nasal methylome as a biomarker of asthma and airway inflammation in children.

Authors:  Andres Cardenas; Joanne E Sordillo; Sheryl L Rifas-Shiman; Wonil Chung; Liming Liang; Brent A Coull; Marie-France Hivert; Peggy S Lai; Erick Forno; Juan C Celedón; Augusto A Litonjua; Kasey J Brennan; Dawn L DeMeo; Andrea A Baccarelli; Emily Oken; Diane R Gold
Journal:  Nat Commun       Date:  2019-07-12       Impact factor: 14.919

5.  TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis.

Authors:  Ziyi Li; Hao Wu
Journal:  Genome Biol       Date:  2019-09-04       Impact factor: 13.583

6.  Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing.

Authors:  Xiaojian Shao; Marie Hudson; Ines Colmegna; Celia M T Greenwood; Marvin J Fritzler; Philip Awadalla; Tomi Pastinen; Sasha Bernatsky
Journal:  Clin Epigenetics       Date:  2019-07-31       Impact factor: 6.551

7.  Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM.

Authors:  Jerry Fong; Jacob R Gardner; Jared M Andrews; Amanda F Cashen; Jacqueline E Payton; Kilian Q Weinberger; John R Edwards
Journal:  Nucleic Acids Res       Date:  2021-09-20       Impact factor: 16.971

8.  BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference.

Authors:  Elior Rahmani; Regev Schweiger; Liat Shenhav; Theodora Wingert; Ira Hofer; Eilon Gabel; Eleazar Eskin; Eran Halperin
Journal:  Genome Biol       Date:  2018-09-21       Impact factor: 13.583

9.  DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex.

Authors:  Gilles Gasparoni; Sebastian Bultmann; Pavlo Lutsik; Theo F J Kraus; Sabrina Sordon; Julia Vlcek; Vanessa Dietinger; Martina Steinmaurer; Melanie Haider; Christopher B Mulholland; Thomas Arzberger; Sigrun Roeber; Matthias Riemenschneider; Hans A Kretzschmar; Armin Giese; Heinrich Leonhardt; Jörn Walter
Journal:  Epigenetics Chromatin       Date:  2018-07-25       Impact factor: 4.954

10.  Detecting cord blood cell type-specific epigenetic associations with gestational diabetes mellitus and early childhood growth.

Authors:  Tianyuan Lu; Andres Cardenas; Patrice Perron; Marie-France Hivert; Luigi Bouchard; Celia M T Greenwood
Journal:  Clin Epigenetics       Date:  2021-06-26       Impact factor: 6.551
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