bioconductor: EpiDISH | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 3 years ago

10.1186/s12915-020-00910-4

Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites
Cited by: 24
Author(s): Marco F. Schmidt, Tiago Maié, Edgar Dahl, Ivan G. Costa, Wolfgang Wagner
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13148-021-01129-y

Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD
Cited by: 22
Author(s): Nicholas Johnson, Xiumei Wu, Christopher D. Still, Xin Chu, Anthony Petrick, Glenn S. Gerhard, Karen N. Conneely, Johanna K. DiStefano
Software Mentions: 7
Published: about 3 years ago

10.1186/s13072-018-0225-x

Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs
Cited by: 31
Author(s): Jenny van Dongen, Erik A. Ehli, Ritsert C. Jansen, Catharina E. M. van Beijsterveldt, Gonneke Willemsen, Jouke Jan Hottenga, Noah A. Kallsen, Stephen Peyton, Charles E. Breeze, C. Kluft, Bastiaan T. Heijmans, Meike Bartels, Gareth E. Davies, Dorret I. Boomsma
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-69725-1

Altered mechanisms of genital development identified through integration of DNA methylation and genomic measures in hypospadias
Cited by: 10
Author(s): Melissa A. Richard, Pagna Sok, Stephen Canon, Wendy N. Nembhard, Austin L. Brown, Erin C. Peckham‐Gregory, Minh Ton, Erik A. Ehli, Noah A. Kallsen, Stephen Peyton, Gareth E. Davies, Ashay Patel, Ismael Zamilpa, Charlotte A. Hobbs, Michael E. Scheurer, Philip J. Lupo
Software Mentions: 4
Published: about 4 years ago

10.1186/s13073-018-0575-9

Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins
Cited by: 60
Author(s): Amy P Webster, Darren Plant, Simone Ecker, Flore Zufferey, Jordana T. Bell, Andrew Feber, Dirk S. Paul, Stephan Beck, Anne Barton, Frances Williams, Jane Worthington
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-020-3443-8

MethylNet: an automated and modular deep learning approach for DNA methylation analysis
Cited by: 61
Author(s): Joshua Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas, Brock C. Christensen
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-019-1778-0

TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis
Cited by: 39
Author(s): Ziyi Li, Hao Wu
Software Mentions: 4
Published: about 5 years ago

10.1186/s13148-020-00877-7

Methylome profiling of young adults with depression supports a link with immune response and psoriasis
Cited by: 10
Author(s): Coral Lapsley, Rachelle E Irwin, Margaret McLafferty, Sara Jayne Thursby, Siobhan O’Neill, Anthony J. Bjourson, Colum P. Walsh, Elaine Murray
Software Mentions: 4
Published: about 4 years ago

10.1186/s13148-020-00966-7

DNA methylation signatures to predict the cervicovaginal microbiome status
Cited by: 3
Author(s): Nuno R. Nené, James E. Barrett, Allison Jones, Iona Evans, Daniel Reisel, John F. Timms, Tobias Paprotka, Andreas Leimbach, D. Franchi, Nicoletta Colombo, Line Bjørge, Michal Zikán, David Cibula, Martin Widschwendter
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms19113607

Methylation-Based Classification of Cervical Squamous Cell Carcinoma into Two New Subclasses Differing in Immune-Related Gene Expression
Cited by: 4
Author(s): Xia Li, Yunpeng Cai
Software Mentions: 3
Published: almost 6 years ago

10.18632/aging.202353

Cell lineage-specific methylome and genome alterations in gout
Cited by: 6
Author(s): Chia‐Chun Tseng, Wei‐Ting Liao, Man-Chun Wong, Chung‐Jen Chen, Su-Chen Lee, Jeng-Hsien Yen, Shun‐Jen Chang
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-017-1511-5

A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies
Cited by: 261
Author(s): Andrew E. Teschendorff, Charles E. Breeze, Shiqing Zheng, Stephan Beck
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-07186-6

Cell-specific characterization of the placental methylome
Cited by: 52
Author(s): Victor Yuan, Diane Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain, Wendy P. Robinson
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13112589

DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal Cancer
Cited by: 14
Author(s): Jihoon E. Joo, Mark Clendenning, Ee Ming Wong, Christophe Rosty, Khalid Mahmood, Peter Georgeson, Ingrid Winship, Susan Preston, Aung Ko Win, Pierre Antoine Dugué, Harindra Jayasekara, Dallas R. English, Finlay Macrae, John L. Hopper, Mark A. Jenkins, Roger L. Milne, Graham G. Giles, Melissa C. Southey, Daniel D. Buchanan
Software Mentions: 3
Published: over 3 years ago

10.1186/s13148-019-0697-y

A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers
Cited by: 18
Author(s): Gregor Richter, Jochen Kruppa, Matthias Munz, Ricarda Wiehe, Robert Häsler, André Franke, Orlando Martins, Yvonne Jockel‐Schneider, Corinna Bruckmann, Henrik Dommisch, Arne S. Schäefer
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-019-0801-3

Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk
Cited by: 42
Author(s): Ting Wang, Sean K. Maden, E. Georg Luebeck, Christopher I. Li, Polly A. Newcomb, Cornelia M. Ulrich, Ji Hoon Eric Joo, Daniel D. Buchanan, Roger L. Milne, Melissa C. Southey, Kelly Carter, Amber Willbanks, Yanxin Luo, Ming Yu, William M. Grady
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-018-1448-7

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray
Cited by: 217
Author(s): Lucas A. Salas, Devin C. Koestler, Rondi A. Butler, Helen M. Hansen, John K. Wiencke, Karl T. Kelsey, Brock C. Christensen
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/8758090

Major Histocompatibility Complex Genes as Therapeutic Opportunity for Immune Cold Molecular Cancer Subtypes
Cited by: 2
Author(s): Paweł Karpiński, Łukasz Łaczmański, Maria M. Sąsiadek
Software Mentions: 3
Published: almost 4 years ago

10.18632/aging.101666

Cell and tissue type independent age-associated DNA methylation changes are not rare but common
Cited by: 35
Author(s): Tianyu Zhu, Shiqing Zheng, Dirk S. Paul, Steve Horvath, Andrew E. Teschendorff
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.202403

Tsukushi is a novel prognostic biomarker and correlates with tumor-infiltrating B cells in non-small cell lung cancer
Cited by: 8
Author(s): Hao Huang, Zhijie Ding, Jinming Fu, Linjing Zhao, Dapeng Li, Hongru Sun, Xinyan Li, Jing Xu, Tian Tian, Lei Zhang, Ying Liu, Yuanyuan Zhang, Yong Zhao
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-020-02126-9

EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data
Cited by: 49
Author(s): Andrew E. Teschendorff, Tianyu Zhu, Charles E. Breeze, Stephan Beck
Software Mentions: 1
Published: about 4 years ago

10.1186/s13059-021-02275-5

Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders
Cited by: 39
Author(s): Marta F. Nabais, Simon M. Laws, Lin Tian, Costanza L. Vallerga, Nicola J. Armstrong, Ian P. Blair, John B. Kwok, Karen A. Mather, George D. Mellick, Perminder S. Sachdev, Leanne Wallace, Anjali K. Henders, Ramona A J Zwamborn, Paul J. Hop, Katie Lunnon, Ehsan Pishva, Janou A. Y. Roubroeks, Hilkka Soininen, Magda Tsolaki, Patrizia Mecocci, Simon Lovestone, Iwona Kłoszewska, Bruno Vellas, Sarah Furlong, Fleur Garton, Robert D. Henderson, Susan Mathers, Pamela A. McCombe, Merrilee Needham, Shyuan T. Ngo, Garth A. Nicholson, Roger Pamphlett, Dominic B. Rowe, Frederik J. Steyn, Kelly L. Williams, Tim Anderson, Steven Bentley, John C. Dalrymple‐Alford, Javed Fowder, Jacob Gratten, Glenda M. Halliday, Ian B. Hickie, Martin A. Kennedy, Simon J.G. Lewis, Grant W. Montgomery, John Pearson, Toni L. Pitcher, Peter A. Silburn, Futao Zhang, Peter M. Visscher, Jian Yang, Anna J. Stevenson, Robert F. Hillary, Riccardo E. Marioni, Sarah E. Harris, Ian J. Deary, Ashley Jones, Aleksey Shatunov, Alfredo Iacoangeli, Wouter van Rheenen, Leonard H van den Berg, Pamela J. Shaw, C. M. Shaw, Karen E. Morrison, Ammar Al‐Chalabi, Jan H. Veldink, Eilís Hannon, Jonathan Mill, Naomi R. Wray, Allan F. McRae
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-019-3307-2

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software
Cited by: 28
Author(s): Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, E. Andrés Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Yuna Blum, Magali Richard
Software Mentions: 1
Published: over 4 years ago

10.3390/antiox10020219

Polymorphisms in Glyoxalase I Gene Are Not Associated with Glyoxalase I Expression in Whole Blood or Markers of Methylglyoxal Stress: The CODAM Study
Cited by: 1
Author(s): Kim Maasen, Nordin M.J. Hanssen, Carla Kallen, Coen D. A. Stehouwer, Marleen M.J. van Greevenbroek, Casper G. Schalkwijk
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-021-00837-7

Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation
Cited by: 37
Author(s): Daniela Mancarella, Christoph Plass
Software Mentions: 1
Published: over 3 years ago

10.17179/excli2020-1224

Tumor mutation burden associated with miRNA-gene interaction outcome mediates the survival of patients with liver hepatocellular carcinoma.
Cited by: 0
Author(s): Qing-Jiang Yu, Yufeng Liang, Xiaoping Mei, Taiyong Fang
Software Mentions: 1
Published: over 4 years ago

10.1186/s13148-017-0313-y

The epigenomic basis of common diseases
Cited by: 3
Author(s): Euan J. Rodger, Aniruddha Chatterjee
Software Mentions: 1
Published: over 7 years ago

10.1093/bioinformatics/btz833

EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI
Cited by: 28
Author(s): Shiqing Zheng, Charles E. Breeze, Stephan Beck, Danyue Dong, Tianyu Zhu, Liangxiao Ma, Wei Ye, Guoqing Zhang, Andrew E. Teschendorff
Software Mentions: 1
Published: almost 5 years ago

Ecosyste.ms: Papers

Projects: bioconductor: EpiDISH

Papers Mentioning EpiDISH 29