Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: EpiDISH
https://packages.ecosyste.ms/registries/bioconductor.org/packages/EpiDISH
Epigenetic Dissection of Intra-Sample-Heterogeneity
1 version
Latest release: about 1 year ago
2 dependent packages
18,670 downloads total
Papers Mentioning EpiDISH 29
10.1186/s13059-021-02335-w
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traitsCited 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 sitesCited 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 NAFLDCited 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: over 3 years ago
10.1186/s13072-018-0225-x
Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLsCited 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: about 6 years ago
10.1038/s41598-020-69725-1
Altered mechanisms of genital development identified through integration of DNA methylation and genomic measures in hypospadiasCited 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: over 4 years ago
10.1186/s13073-018-0575-9
Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twinsCited 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 analysisCited 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 analysisCited 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 psoriasisCited 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: over 4 years ago
10.1186/s13148-020-00966-7
DNA methylation signatures to predict the cervicovaginal microbiome statusCited 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 ExpressionCited by: 4
Author(s): Xia Li, Yunpeng Cai
Software Mentions: 3
Published: about 6 years ago
10.18632/aging.202353
Cell lineage-specific methylome and genome alterations in goutCited 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: almost 4 years ago
10.1186/s12859-017-1511-5
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association StudiesCited by: 261
Author(s): Andrew E. Teschendorff, Charles E. Breeze, Shiqing Zheng, Stephan Beck
Software Mentions: 3
Published: almost 8 years ago
10.1186/s12864-020-07186-6
Cell-specific characterization of the placental methylomeCited by: 52
Author(s): Victor Yuan, Diane Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain, Wendy P. Robinson
Software Mentions: 3
Published: almost 4 years ago
10.3390/cancers13112589
DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal CancerCited 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 smokersCited 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: over 5 years ago
10.1186/s13148-019-0801-3
Dysfunctional epigenetic aging of the normal colon and colorectal cancer riskCited 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: almost 5 years ago
10.1186/s13059-018-1448-7
An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArrayCited 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 SubtypesCited by: 2
Author(s): Paweł Karpiński, Łukasz Łaczmański, Maria M. Sąsiadek
Software Mentions: 3
Published: about 4 years ago
10.18632/aging.101666
Cell and tissue type independent age-associated DNA methylation changes are not rare but commonCited 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 cancerCited 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: almost 4 years ago
10.1186/s13059-020-02126-9
EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq dataCited 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 disordersCited 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 softwareCited 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: almost 5 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 StudyCited 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: almost 4 years ago
10.1186/s13073-021-00837-7
Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translationCited by: 37
Author(s): Daniela Mancarella, Christoph Plass
Software Mentions: 1
Published: almost 4 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: almost 5 years ago
10.1186/s13148-017-0313-y
The epigenomic basis of common diseasesCited by: 3
Author(s): Euan J. Rodger, Aniruddha Chatterjee
Software Mentions: 1
Published: almost 8 years ago
10.1093/bioinformatics/btz833
EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUICited 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: about 5 years ago