bioconductor: minfi | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-14-293

A data-driven approach to preprocessing Illumina 450K methylation array data
Cited by: 805
Author(s): Ruth Pidsley, Chloe Wong, Manuela Volta, Katie Lunnon, Jonathan Mill, Leonard C. Schalkwyk
Software Mentions: 5
Published: over 11 years ago

10.1186/s12864-016-2819-7

An evaluation of processing methods for HumanMethylation450 BeadChip data
Cited by: 52
Author(s): Jie Liu, Kimberly D. Siegmund
Software Mentions: 5
Published: over 8 years ago

10.18632/oncotarget.17462

Epigenome-wide association study in hepatocellular carcinoma: Identification of stochastic epigenetic mutations through an innovative statistical approach
Cited by: 43
Author(s): Davide Gentilini, Stefania Scala, Germano Gaudenzi, Paolo Garagnani, Miriam Capri, Matteo Cescon, Gian Luca Grazi, Maria Giulia Bacalini, Serena Pisoni, Alessandra Dicitore, Luisa Circelli, Sara Santagata, Francesco Izzo, Anna Maria Di Blasio, Luca Persani, Claudio Franceschi, Giovanna Mantovani
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2019.01863

Molecular Characterization of Human Lymph Node Stromal Cells During the Earliest Phases of Rheumatoid Arthritis
Cited by: 13
Author(s): Emmanuel Karouzakis, J Hähnlein, Cristoforo Grasso, Johanna F. Semmelink, Paul P. Tak, Daniëlle M. Gerlag, Caroline Ospelt, Lisa G. M. van Baarsen
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.00770

Maternal Smoking During Pregnancy Induces Persistent Epigenetic Changes Into Adolescence, Independent of Postnatal Smoke Exposure and Is Associated With Cardiometabolic Risk
Cited by: 65
Author(s): Sebastian Rauschert, Phillip E. Melton, Graham C. Burdge, Jeffrey M. Craig, Keith M. Godfrey, Joanna D. Holbrook, Karen A. Lillycrop, Trevor A. Mori, Lawrence J. Beilin, Wendy H. Oddy, Craig E. Pennell, Rae‐Chi Huang
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms22168611

Identification of a DNA Methylation Episignature in the 22q11.2 Deletion Syndrome
Cited by: 10
Author(s): Kathleen Rooney, Michael A. Levy, Sadegheh Haghshenas, Jennifer Kerkhof, Daniela Rogaia, Maria Giovanna Tedesco, Valentina Imperatore, Amedea Mencarelli, Gabriella Maria Squeo, Eleonora Di Venere, Giuseppe Di Cara, Alberto Verrotti, Giuseppe Merla, Matthew L. Tedder, Barbara R. DuPont, Bekim Sadiković, Paolo Prontera
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22031111

Detection of a DNA Methylation Signature for the Intellectual Developmental Disorder, X-Linked, Syndromic, Armfield Type
Cited by: 9
Author(s): Sadegheh Haghshenas, Michael A. Levy, Jennifer Kerkhof, Erfan Aref‐Eshghi, Haley McConkey, Tugce B. Balci, Victoria Mok Siu, Cindy Skinner, Roger E. Stevenson, Bekim Sadiković, Charles E. Schwartz
Software Mentions: 5
Published: almost 4 years ago

10.3390/ijerph16040524

Age-Related Differences in miRNA Expression in Mexican-American Newborns and Children
Cited by: 6
Author(s): Karen Huen, Daneida Lizárraga, Katherine Kogut, Brenda Eskenazi, Nina Holland
Software Mentions: 5
Published: almost 6 years ago

10.1093/hmg/ddw283

Collapsed methylation quantitative trait loci analysis for low frequency and rare variants
Cited by: 11
Author(s): Tom G Richardson, Hashem A. Shihab, Gibran Hemani, Jie Zheng, Eilís Hannon, Jonathan Mill, Elena Carnero‐Montoro, Jordana T. Bell, Oliver Lyttleton, Wendy L. McArdle, Susan M. Ring, Santiago Rodriguez, Colin Campbell, George Davey Smith, Caroline L Relton, Nicholas J. Timpson, Tom R. Gaunt
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-020-64700-2

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor
Cited by: 16
Author(s): Jesús Rafael Rodríguez‐Aguilera, Szilvia Ecsedi, Chloe D. Goldsmith, Marie-Pierre Cros, Mariana Domínguez‐López, Nuria Guerrero‐Celis, Rebeca Pérez‐Cabeza de Vaca, Isabelle Chemin, Félix Recillas‐Targa, Victoria Chagoya de Sánchez, Héctor Hernández-Vargas
Software Mentions: 5
Published: over 4 years ago

10.1007/s10522-019-09818-1

Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength
Cited by: 7
Author(s): Mette Soerensen, Weilong Li, Birgit Debrabant, Marianne Nygaard, Jonas Mengel‐From, Morten Frost, Kaare Christensen, Lene Christiansen, Qihua Tan
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-61649-0

Epigenome-wide association study for perceived discrimination among sub-Saharan African migrants in Europe - the RODAM study
Cited by: 6
Author(s): Loes C. van der Laan, Karlijn Meeks, Felix P Chilunga, Charles Agyemang, Andrea Venema, Marcel M.A.M. Mannens, Mohammad Hadi Zafarmand, Kerstin Klipstein‐Grobusch, Liam Smeeth, Adebowale Adeyemo, Peter Henneman
Software Mentions: 5
Published: over 4 years ago

10.1186/s13148-016-0266-6

DNA methylation and smoking in Korean adults: epigenome-wide association study
Cited by: 48
Author(s): Mi Kyeong Lee, Yoonki Hong, Sun‐Young Kim, Stephanie J. London, Woo Jin Kim
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-019-53298-9

A pilot study of peripheral blood DNA methylation models as predictors of knee osteoarthritis radiographic progression: data from the Osteoarthritis Initiative (OAI)
Cited by: 10
Author(s): Christopher M. Dunn, Michael C. Nevitt, J.A. Lynch, Matlock A. Jeffries
Software Mentions: 5
Published: about 5 years ago

10.1038/s41398-021-01481-w

Toll-like receptor 4 methylation grade is linked to depressive symptom severity
Cited by: 10
Author(s): Annica J. Rasmusson, Maike Gallwitz, Bardia Soltanabadi, Diana M. Ciuculete, Jonas Mengel‐From, Kaare Christensen, Marianne Nygaard, Mette Soerensen, Adrian Boström, Robert Fredriksson, Eva Freyhult, Jessica Mwinyi, Darina Czamara, Elisabeth B. Binder, Helgi B. Schiöth, Janet L. Cunningham
Software Mentions: 5
Published: over 3 years ago

10.1007/s00401-020-02228-5

Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay
Cited by: 27
Author(s): Katja Kobow, Samir Jabari, Tom Pieper, Manfred Kudernatsch, Tilman Polster, Friedrich G. Woermann, Thilo Kalbhenn, Hajo M. Hamer, Karl Rössler, Angelika Mühlebner, Wim G.M. Spliet, Martha Feucht, Yanghao Hou, Damian Stichel, Andrey Korshunov, Felix Sahm, Roland Coras, Ingmar Blümcke, Andreas von Deimling
Software Mentions: 5
Published: about 4 years ago

10.1186/s13072-015-0045-1

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay
Cited by: 11
Author(s): Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13148-019-0769-z

DNA methylation associated with postpartum depressive symptoms overlaps findings from a genome-wide association meta-analysis of depression
Cited by: 6
Author(s): Dana M. Lapato, Roxann Roberson‐Nay, Robert M. Kirkpatrick, Bradley T. Webb, Timothy P. York, Patricia A. Kinser
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13073-020-00779-6

Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci
Cited by: 24
Author(s): Tianlu Li, Lourdes Ortiz-Fernández, Eduardo Andrés-León, Laura Ciudad, Biola M. Javierre, Elena López‐Isac, Alfredo Guillén‐Del‐Castillo, Carmen Pilar Simeón-Aznar, Esteban Ballestar, Javier Martín
Software Mentions: 5
Published: about 4 years ago

10.1093/gigascience/giaa112

A molecular map of lung neuroendocrine neoplasms
Cited by: 15
Author(s): Aurélie Gabriel, Emilie Mathian, Lise Mangiante, Catherine Voegele, Vincent Cahais, Akram Ghantous, James McKay, Nicolas Alcala, Lynnette Fernández-Cuesta, Matthieu Foll
Software Mentions: 5
Published: about 4 years ago

10.1080/15592294.2019.1656157

Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes
Cited by: 16
Author(s): Adrian Boström, Andreas Chatzittofis, Diana‐Maria Ciuculete, John N. Flanagan, Regina Krattinger, Marcus Bandstein, Jessica Mwinyi, Gerd A. Kullak‐Ublick, Katarina Görts Öberg, Stefan Arver, Helgi B. Schiöth, Jussi Jokinen
Software Mentions: 5
Published: about 5 years ago

10.1186/gm500

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy
Cited by: 105
Author(s): Mark N Cruickshank, Alicia Oshlack, Christiane Theda, Peter G Davis, David Martino, Penelope M. Sheehan, Yun Dai, Richard Saffery, Lex W. Doyle, Jeffrey M Craig
Software Mentions: 5
Published: almost 12 years ago

10.1007/s00401-019-02074-0

White matter DNA methylation profiling reveals deregulation of HIP1, LMAN2, MOBP, and other loci in multiple system atrophy
Cited by: 42
Author(s): Conceição Bettencourt, Sandrine C. Foti, Yasuo Miki, Juan A. Botía, A. K. Chatterjee, Thomas T. Warner, Tamás Révész, Tammaryn Lashley, R. Balázs, Emmanuelle Viré, Janice L. Holton
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-019-6019-0

Identification of methylation states of DNA regions for Illumina methylation BeadChip
Cited by: 12
Author(s): Ximei Luo, Fang Wang, Guohua Wang, Yuming Zhao
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-019-1878-x

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
Cited by: 24
Author(s): Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A.C. ’t Hoen, B.T. Heijmans, Joyce B. J. van Meurs
Software Mentions: 5
Published: about 5 years ago

10.1186/s13148-019-0608-2

Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes
Cited by: 34
Author(s): Louise F. Porter, Neil Saptarshi, Yongxiang Fang, Sonika Rathi, Anneke I. den Hollander, Eiko K. de Jong, Simon J. Clark, Paul Bishop, Timothy W. Olsen, Triantafillos Liloglou, Venkata R M Chavali, Luminita Paraoan
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0207250

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes
Cited by: 12
Author(s): Maxime Caron, Pascal St-Onge, Simon Drouin, Chantal Richer, Thomas Sontag, Stephan Busche, Guillaume Bourque, Tomi Pastinen, Daniel Sinnett
Software Mentions: 5
Published: about 6 years ago

10.1186/s13148-021-01083-9

Estimands in epigenome-wide association studies
Cited by: 9
Author(s): Jochen Kruppa, Miriam Sieg, Gregor Richter, Anne Pohrt
Software Mentions: 5
Published: over 3 years ago

10.1186/s13148-021-01149-8

Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer
Cited by: 7
Author(s): Javier Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban‐Rodríguez, María Dolores Diestro, Javier Benı́tez, Fátima Sánchez-Cabo, Rafael Álvarez, Javier de Castro
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-014-0579-8

Pancancer analysis of DNA methylation-driven genes using MethylMix
Cited by: 102
Author(s): Olivier Gevaert, Robert Tibshirani, Sylvia K. Plevritis
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0215987

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data
Cited by: 18
Author(s): Yu Kong, Deepa Rastogi, Cathal Seoighe, John M. Greally, Masako Suzuki
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1007785

Genetic variants influence on the placenta regulatory landscape
Cited by: 48
Author(s): Fabien Delahaye, Catherine Do, Yu Kong, Remi Ashkar, Martha Salas, Benjamin Tycko, Ronald J. Wapner, Francine Hughes
Software Mentions: 4
Published: about 6 years ago

10.1186/s12989-018-0244-6

Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition
Cited by: 53
Author(s): Deniz Öner, Manosij Ghosh, Hannelore Bové, Matthieu Moisse, Bram Boeckx, Radu Corneliu Duca, Katrien Poels, Katrien Luyts, Eveline Putzeys, Kirsten Van Landuydt, Jeroen Vanoirbeek, Marcel Ameloot, Diether Lambrechts, Lode Godderis, Peter Hoet
Software Mentions: 4
Published: almost 7 years ago

10.1186/gb-2013-14-5-r42

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance
Cited by: 174
Author(s): David Martino, Yuk Jing Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M. Craig
Software Mentions: 4
Published: almost 12 years ago

10.3390/nu12123602

Epigenetic Patterns in Five-Year-Old Children Exposed to a Low Glycemic Index Dietary Intervention during Pregnancy: Results from the ROLO Kids Study
Cited by: 10
Author(s): Aisling A. Geraghty, A. Sexton-Oates, Eileen C. O’Brien, Richard Saffery, Fionnuala M. McAuliffe
Software Mentions: 4
Published: almost 4 years ago

10.18632/aging.102459

Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma
Cited by: 13
Author(s): Song Jing, Fangzhou Song, Kun Liu, Wanfeng Zhang, Ruihan Luo, Yongyao Tang
Software Mentions: 4
Published: about 5 years ago

10.3389/fphys.2019.00917

Integrated Analysis of DNA Methylation and Biochemical/Metabolic Parameter During the Long-Term Isolation Environment
Cited by: 2
Author(s): Quan Yuan, Feng Liang, Yuexing Zhu, Ying Chen, Xu Zi, Fang Du, Ke Lv, Hailong Chen, Lei Qu, Ruifeng Xu, Hongyu Zhang, Jianghui Xiong, Yinghui Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s13148-018-0530-z

Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion
Cited by: 18
Author(s): Rhian L Clissold, Beth Ashfield, Joe Burrage, Eilís Hannon, Coralie Bingham, Jonathan Mill, Andrew T. Hattersley, Emma Dempster
Software Mentions: 4
Published: over 6 years ago

10.1002/cam4.3388

A methylomics‐associated nomogram predicts recurrence‐free survival of thyroid papillary carcinoma
Cited by: 7
Author(s): Hengyu Chen, Xianxiong Ma, Ming Yang, Mengyi Wang, Lei Li, Tao Huang
Software Mentions: 4
Published: over 4 years ago

10.1186/s12885-020-07194-5

A panel of DNA methylation signature from peripheral blood may predict colorectal cancer susceptibility
Cited by: 12
Author(s): Justina Ucheojor Onwuka, Dapeng Li, Yupeng Liu, Hao Huang, Jing Xu, Ying Liu, Yuanyuan Zhang, Yong Zhao
Software Mentions: 4
Published: over 4 years ago

10.1016/j.ccell.2018.04.004

Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial
Cited by: 136
Author(s): Alan Mackay, Anna Burford, Valeria Molinari, David Jones, Elisa Izquierdo, Jurriaan Brouwer‐Visser, Felice Giangaspero, Christine Haberler, Torsten Pietsch, Thomas S. Jacques, Dominique Figarella‐Branger, Daniel Rodriguez, Paul S. Morgan, Pichai Raman, Angela J. Waanders, Adam Resnick, Maura Massimino, Maria Luisa Garré, Smith Hw, David Capper, Stefan M. Pfister, Thomas Würdinger, Rachel Tam, Josep Garcia, Meghna Das Thakur, Gilles Vassal, Jacques Grill, Tim Jaspan, Pascale Varlet, Chris Jones
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22157834

Individual DNA Methylation Pattern Shifts in Nanoparticles-Exposed Workers Analyzed in Four Consecutive Years
Cited by: 6
Author(s): Andrea Rössnerová, K. Hoňková, Irena Chvojková, Daniela Pelclová, Vladimı́r Ždı́mal, Jaroslav A. Hubacek, Lucie Lischková, Štěpánka Vlčková, Jakub Ondráček, Štěpánka Dvořáčková, Jan Topinka, Pavel Rössner
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.640266

DNA Methylation and Expression Profiles of Whole Blood in Parkinson’s Disease
Cited by: 28
Author(s): Adrienne Henderson, Qi Wang, Bessie Meechoovet, Ashley L. Siniard, Marcus Naymik, Matthew De Both, Matthew J. Huentelman, Richard J. Caselli, Erika Driver‐Dunckley, Travis Dunckley
Software Mentions: 4
Published: over 3 years ago

10.3389/fnmol.2021.672614

Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma
Cited by: 11
Author(s): Zac Chatterton, Natalia Mendelev, Sean Chen, Walter Carr, Gary H. Kamimori, Yongchao Ge, Andrew J. Dwork, Fatemeh Haghighi
Software Mentions: 4
Published: over 3 years ago

10.1186/s13148-018-0464-5

Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD
Cited by: 27
Author(s): Rachel L. Clifford, Nick Fishbane, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Andrew J. Fisher, Corry‐Anke Brandsma, Parameswaran Nair, Michæl S. Kobor, Tillie-Louise Hackett, Alan J. Knox
Software Mentions: 4
Published: over 6 years ago

10.1007/s00401-020-02230-x

Epigenomic, genomic, and transcriptomic landscape of schwannomatosis
Cited by: 21
Author(s): Sheila Mansouri, Suganth Suppiah, Yasin Mamatjan, Irene Paganini, Jeffrey Liu, Shirin Karimi, Vikas Patil, Farshad Nassiri, Olivia Singh, Yogi Sundaravadanam, Pramod C. Rath, Roberta Sestini, Francesca Gensini, Sameer Agnihotri, Jaishri O. Blakeley, Kimberly Laskie Ostrow, David A. Largaespada, Scott R. Plotkin, Anat Stemmer‐Rachamimov, Marcela Maria Ferrer, Trevor J. Pugh, Kenneth Aldape, Laura Papi, Gelareh Zadeh
Software Mentions: 4
Published: about 4 years ago

10.1042/BSR20211241

Multi-omic analyses of hepatocellular carcinoma to determine immunological characteristics and key nodes in gene-expression network
Cited by: 3
Author(s): Zhihui Wang, Shuijun Zhang
Software Mentions: 4
Published: over 3 years ago

10.1042/BSR20193349

Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes in head and neck squamous cell carcinoma
Cited by: 5
Author(s): Yu Jin, Xing Qin
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2019.00801

A Novel Application of Mixed Effects Models for Reconciling Base-Pair Resolution 5-Methylcytosine and 5-Hydroxymethylcytosine Data in Neuroepigenetics
Cited by: 6
Author(s): Joseph Kochmanski, Candace Savonen, Alison I. Bernstein
Software Mentions: 4
Published: about 5 years ago

10.1186/s13148-019-0804-0

Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature
Cited by: 36
Author(s): Andrea Ciolfi, Erfan Aref‐Eshghi, Simone Pizzi, Lucia Pedace, Evelina Miele, Jennifer Kerkhof, Elisabetta Flex, Simone Martinelli, Francesca Clementina Radio, Claudia Ruivenkamp, Gijs W.E. Santen, Emilia K. Bijlsma, Daniela Q.C.M. Barge-Schaapveld, Katrin Õunap, Victoria Mok Siu, R. Frank Kooy, Bruno Dallapiccola, Bekim Sadiković, Marco Tartaglia
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2020.00091

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer
Cited by: 14
Author(s): Peng Song, Lei Wu, Wenxian Guan
Software Mentions: 4
Published: over 4 years ago

10.1186/s13148-018-0504-1

Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO
Cited by: 82
Author(s): Jonathan Heiss, Allan C. Just
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00269

Does Prenatal Stress Shape Postnatal Resilience? – An Epigenome-Wide Study on Violence and Mental Health in Humans
Cited by: 50
Author(s): Fernanda Serpeloni, Karl M. Radtke, Tobias Hecker, Johanna Sill, Vanja Vukojević, Simone Gonçalves de Assis, Maggie Schauer, Thomas Elbert, Daniel Nätt
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29156

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria
Cited by: 33
Author(s): Jaclyn Quin, Ioana Bujila, Mariama Chérif, Guillaume S. Sanou, Ying Qu, Manijeh Vafa Homann, Anna Rolicka, Sodiomon B. Sirima, Mary A. O’Connell, Andreas Lennartsson, Marita Troye‐Blomberg, Issa Nébié, Ann‐Kristin Östlund Farrants
Software Mentions: 4
Published: about 7 years ago

10.18632/oncotarget.15807

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Cited by: 39
Author(s): Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Annick De Paepe, Mohsen Karimi, Kaarel Krjutškov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström‐Lindberg, Johanna Ungerstedt
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-74798-z

Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients
Cited by: 19
Author(s): Nathalie Acevedo, Rui Benfeitas, Shintaro Katayama, Sören Bruhn, Ann‐Catrin Andersson, Gustav Wikberg, Lena Lundeberg, Jessica M. Lindvall, Dario Greco, Juha Kere, Cilla Söderhäll, Annika Scheynius
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-019-2734-4

Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data
Cited by: 73
Author(s): Hao Yang, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, Guangrong Qin
Software Mentions: 4
Published: over 5 years ago

10.1186/s13287-019-1245-6

DNA methylation dynamic of bone marrow hematopoietic stem cells after allogeneic transplantation
Cited by: 13
Author(s): Stefania Trino, Pietro Zoppoli, Angelo Michele Carella, Ilaria Laurenzana, Alessandro Weisz, Domenico Memoli, Giovanni Calice, Francesco La Rocca, Vittorio Simeon, Lucia Savino, Luigi Del Vecchio, Pellegrino Musto, Antonella Caivano, Luciana De Luca
Software Mentions: 4
Published: over 5 years ago

10.1186/s13148-020-00990-7

DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome
Cited by: 25
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Kathleen Rooney, Jennifer Kerkhof, Michael A. Levy, Haley McConkey, R. Curtis Rogers, Katy Phelan, Sara M. Sarasua, Lavanya Jain, Rini Pauly, Luigi Boccuto, Barbara R. DuPont, Gerarda Cappuccio, Nicola Brunetti‐Pierri, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 4
Published: almost 4 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: over 4 years ago

10.1038/s41398-019-0548-9

Epigenome-wide association study of depression symptomatology in elderly monozygotic twins
Cited by: 44
Author(s): Anna Starnawska, Qihua Tan, Mette Soerensen, Matt McGue, Ole Mors, Anders D. Børglum, Kaare Christensen, Mette Nyegaard, Lene Christiansen
Software Mentions: 4
Published: about 5 years ago

10.1093/bioinformatics/bty476

Meffil: efficient normalization and analysis of very large DNA methylation datasets
Cited by: 173
Author(s): Josine L. Min, Gibran Hemani, George Davey Smith, Caroline L Relton, Matthew Suderman
Software Mentions: 4
Published: over 6 years ago

10.1186/s13148-021-01176-5

DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status
Cited by: 1
Author(s): Philipp Jurmeister, Karsten E. Weber, Sonia L. Villegas, Thomas Karn, Michael Untch, Anne Thieme, Volkmar Müller, Eliane Tabea Taube, Peter A. Fasching, Wolfgang Schmitt, Frederik Marmé, Elmar Stickeler, Bruno Valentin Sinn, Paul Jank, Christian Schem, Frederick Klauschen, Marion van Mackelenbergh, Carsten Denkert, Sibylle Loibl, David Capper
Software Mentions: 4
Published: about 3 years ago

10.3389/fbioe.2020.00187

The Joint Analysis of Multi-Omics Data Revealed the Methylation-Expression Regulations in Atrial Fibrillation
Cited by: 8
Author(s): Ban Liu, Xin Shi, Keke Ding, Mengwei Lv, Yongjun Qian, Shijie Zhu, Changfa Guo, Yangyang Zhang
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-48916-5

An epigenome-wide analysis of cord blood DNA methylation reveals sex-specific effect of exposure to bisphenol A
Cited by: 25
Author(s): Ryuichi Miura, Atsuko Araki, Machiko Minatoya, Kunio Miyake, Mei Lien Chen, Sumitaka Kobayashi, Chihiro Miyashita, Jun Yamamoto, Tomohiro Matsumura, Mayumi Ishizuka, Takeo Kubota, Reiko Kishi
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-50873-y

Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation
Cited by: 9
Author(s): Rachel L. Clifford, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Simon R. Johnson, Dominick Shaw, Alan J. Knox, Tillie-Louise Hackett, Michæl S. Kobor
Software Mentions: 4
Published: about 5 years ago

10.1186/s13148-019-0749-3

A genome-wide DNA methylation signature for SETD1B-related syndrome
Cited by: 41
Author(s): Izabela M. Krzyzewska, Saskia M. Maas, Peter Henneman, Karin van der Lip, Andrea Venema, Kristin W. Barañano, Anna Chassevent, Erfan Aref‐Eshghi, Anthonie J. van Essen, Tokiko Fukuda, Hiroko Ikeda, Marie Line Jacquemont, H.-G. Kim, Audrey Labalme, Lewis Sm, Gaëtan Lesca, Irene Madrigal, Sonal Mahida, Naomichi Matsumoto, Raquel Rabionet, Evica Rajcan‐Separovic, Ying Qiao, Bekim Sadiković, Hirotomo Saitsu, David A. Sweetser, Mariëlle Alders, Marcel M.A.M. Mannens
Software Mentions: 4
Published: about 5 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: about 6 years ago

10.1038/sdata.2018.245

Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features
Cited by: 18
Author(s): Matthew P. Salomon, Javier I. J. Orozco, James S. Wilmott, Parvinder Hothi, Ayla O. Manughian-Peter, Charles S. Cobbs, Richard A. Scolyer, Dave S.B. Hoon, Diego M. Marzese
Software Mentions: 4
Published: about 6 years ago

10.1038/s41597-019-0205-4

The Personal Genome Project-UK, an open access resource of human multi-omics data
Cited by: 18
Author(s): Olga Chervova, Lucía Conde, José Afonso Guerra-Assunção, Ismail Moghul, A. D. B. Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan Tian, Vitaly Voloshin, Tiago S. Jesus, Rifat Hamoudi, Javier Herrero, Stephan Beck
Software Mentions: 4
Published: about 5 years ago

10.1186/s13148-019-0791-1

DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways
Cited by: 21
Author(s): Faiza Noreen, Taya Küng, Luigi Tornillo, Helen L. Parker, Miguel G. Silva, Stefan Weis, Giancarlo Marra, Roland Rad, Kaspar Truninger, Primo Schär
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12931-020-01544-4

Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0
Cited by: 6
Author(s): Espen E. Groth, Melanie Weber, Thomas Bahmer, Frauke Pedersen, Anne Kirsten, Daniela Börnigen, Klaus F. Rabe, Henrik Watz, Ole Ammerpohl, Torsten Goldmann
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-019-46930-1

Distinct epigenetic profiles in children with perinatally-acquired HIV on antiretroviral therapy
Cited by: 17
Author(s): Stephanie Shiau, Renate Strehlau, Shuang Wang, Avy Violari, Catherine Do, Faeezah Patel, Afaaf Liberty, Izabela Krupska, Stephen M. Arpadi, Marc Foca, Ashraf Coovadia, Elaine J. Abrams, Benjamin Tycko, Mary Beth Terry, Louise Kuhn
Software Mentions: 4
Published: over 5 years ago

10.3389/fendo.2021.690648

Epigenetic Changes in Neonates Born to Mothers With Gestational Diabetes Mellitus May Be Associated With Neonatal Hypoglycaemia
Cited by: 5
Author(s): Yoshifumi Kasuga, Tomoko Kawai, Kei Miyakoshi, Yoshifumi Saisho, Masumi Tamagawa, K. Hasegawa, Satoru Ikenoue, Daigo Ochiai, Mariko Hida, Mamoru Tanaka, Kenichiro Hata
Software Mentions: 4
Published: over 3 years ago

10.1186/s12920-020-0659-4

Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer
Cited by: 16
Author(s): Chai-Jin Lee, Hongryul Ahn, Dabin Jeong, Minwoo Pak, Ji Hwan Moon, Sun Kim
Software Mentions: 4
Published: almost 5 years ago

10.1080/15592294.2020.1748916

The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells
Cited by: 14
Author(s): Iolanda Agliata, Nora Fernández-Jiménez, Chloe D. Goldsmith, Julien C. Marie, José Ramón Bilbao, Robert Dante, Héctor Hernandez-Vargas
Software Mentions: 4
Published: over 4 years ago

10.7150/jca.44436

DNA methylation profiling to predict overall survival risk in gastric cancer: development and validation of a nomogram to optimize clinical management
Cited by: 7
Author(s): Xianxiong Ma, Hengyu Chen, Guobin Wang, Lei Li, Kaixiong Tao
Software Mentions: 4
Published: almost 5 years ago

10.3390/cancers13112760

Follow-Up Study Confirms the Presence of Gastric Cancer DNA Methylation Hallmarks in High-Risk Precursor Lesions
Cited by: 3
Author(s): Antonio Gómez, Miguel L Pato, Luís Bujanda, Núria Sala, Osmel Companioni, Ángel Cosme, Martina Tufano, David Hanly, Nadia García, José Miguel Sanz‐Anquela, Javier P. Gisbert, Consuelo López, José Ignacio Elizalde, Míriam Cuatrecasas, Victòria Andreu, María José Paúles, María Dolores Martín-Arranz, Luís Ortega, Elvira Poves, Jesús Barrio, María Ángeles Torres, Guillermo Muñoz, Ángel Ferrández, María José Ramírez‐Lázaro, Sergio Lario, Carlos González, Manel Esteller, María Berdasco
Software Mentions: 4
Published: over 3 years ago

10.1186/s12940-021-00717-y

DNA methylation in the adipose tissue and whole blood of Agent Orange-exposed Operation Ranch Hand veterans: a pilot study
Cited by: 1
Author(s): Matthew Rytel, Rondi A. Butler, Melissa Eliot, Joseph M. Braun, E. Andrés Houseman, Karl T. Kelsey
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers13092143

Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid
Cited by: 5
Author(s): Maria Hernandez-Valladares, Rebecca Wangen, Elise Aasebø, Håkon Reikvam, Frode S. Berven, Frode Selheim, Øystein Bruserud
Software Mentions: 4
Published: over 3 years ago

10.1186/s12920-018-0466-3

Comparison of DNA methylation profiles associated with spontaneous preterm birth in placenta and cord blood
Cited by: 27
Author(s): Xi-Meng Wang, Fei Tian, Lijun Fan, Chuanbo Xie, Zhongzheng Niu, Weiqing Chen
Software Mentions: 4
Published: almost 6 years ago

10.1111/jcmm.15393

DNA methylation profiling to predict recurrence risk in stage Ι lung adenocarcinoma: Development and validation of a nomogram to clinical management
Cited by: 12
Author(s): Xianxiong Ma, Jiancheng Cheng, Peng Zhao, Lei Li, Kaixiong Tao, Hengyu Chen
Software Mentions: 4
Published: over 4 years ago

10.1111/acel.13293

Novel DNA methylation marker discovery by assumption‐free genome‐wide association analysis of cognitive function in twins
Cited by: 4
Author(s): Afsaneh Mohammadnejad, Mette Soerensen, Jan Baumbach, Jonas Mengel‐From, Weilong Li, Jesper Lund, Shuxia Li, Lene Christiansen, Kaare Christensen, Jacob Hjelmborg, Qihua Tan
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12916-017-0851-3

Comprehensive DNA methylation study identifies novel progression-related and prognostic markers for cutaneous melanoma
Cited by: 55
Author(s): Jasper Wouters, Miguel Vizoso, Anna Martínez-Cardús, Francesc Carmona, Olivier Govaere, Teresa Laguna, Jesuchristopher Joseph, Peter Dynoodt, Claudia Aura, Mona Foth, Roy H. E. Cloots, Karin van den Hurk, Balázs Bálint, Ian Murphy, Enda McDermott, Kieran Sheahan, Karin Jirström, Björn Nodin, Girish Mallya-Udupi, Joost J. van den Oord, William M. Gallagher, Manel Esteller
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0241367

DNA methylation in blood—Potential to provide new insights into cell biology
Cited by: 3
Author(s): Donia Macartney-Coxson, Alanna M. Cameron, Jane Clapham, Miles C. Benton
Software Mentions: 4
Published: about 4 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: over 4 years ago

10.4161/epi.27806

Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain
Cited by: 41
Author(s): Joana Viana, Ruth Pidsley, Claire Troakes, Helen Spiers, Chloe Wong, Safa Al‐Sarraj, Ian W. Craig, Leonard C. Schalkwyk, Jonathan Mill
Software Mentions: 4
Published: almost 11 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

10.1186/1471-2164-14-475

Variable promoter methylation contributes to differential expression of key genes in human placenta-derived venous and arterial endothelial cells
Cited by: 30
Author(s): Jihoon E. Joo, Ursula Hiden, Luciana Lassance, Lavinia Gordon, David Martino, Gernot Desoyé, Richard Saffery
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0254562

DNA methylation analyses identify an intronic ZDHHC6 locus associated with time to recurrent stroke in the Vitamin Intervention for Stroke Prevention (VISP) clinical trial
Cited by: 4
Author(s): Nicole M. Davis Armstrong, Weimin Chen, Fang‐Chi Hsu, Michael S. Brewer, Natàlia Cullell, Israel Fernández‐Cadenas, Stephen R. Williams, Michèle M. Sale, Bradford B. Worrall, Keith L. Keene
Software Mentions: 4
Published: over 3 years ago

10.1093/cdn/nzaa097

Nutritional Epigenomics and Age-Related Disease
Cited by: 18
Author(s): Sophia Amenyah, Mary Ward, James J. Strain, Helene McNulty, Catherine F Hughes, Caitlin Dollin, Colum P. Walsh, Diane J. Lees-Murdock
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-021-02375-2

Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation
Cited by: 8
Author(s): Nisha Padmanabhan, Kie Kyon Huang, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-O K Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Xuewen Ong, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee, Angie Lay Keng Tan, Shamaine Ho Wei Ting, Micah A. Luftig, Dennis Kappei, Warren D. Kruger, Jun Bian, Ying Swan Ho, Ming Teh, Steve Rozen, Patrick Tan
Software Mentions: 4
Published: over 3 years ago

10.3390/genes12091433

Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity
Cited by: 3
Author(s): Viviane Neri de Souza Reis, Ana Carolina Tahira, Vinícius Daguano Gastaldi, Paula Mari, Joana Portolese, Ana Cecília Feio dos Santos, Bianca Cristina Garcia Lisbôa, Jair J. Mari, Sheila C. Caetano, Décio Brunoni, Daniela Bordini, Cristinane Silvestre de Paula, Ricardo Zorzetto Nicoliello Vêncio, John Quackenbush, Helena Brentani
Software Mentions: 3
Published: about 3 years ago

10.18632/aging.102178

Prognostic value of genome-wide DNA methylation patterns in noncoding miRNAs and lncRNAs in uveal melanomas
Cited by: 1
Author(s): Zheng Zhang, Dan Xu, Ke–Qing Shi, Minfeng Chen, Fan Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/gb-2012-13-6-r44

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
Cited by: 671
Author(s): Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack
Software Mentions: 3
Published: almost 13 years ago

10.1177/1352458517721356

Hypermethylation of <i>MIR21</i> in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes
Cited by: 31
Author(s): Sabrina Ruhrmann, Ewoud Ewing, Eliane Piket, Lara Kular, Julio C. C. Lorenzi, Sunjay Jude Fernandes, Hiromasa Morikawa, Shahin Aeinehband, Sergi Sayols-Baixeras, Stella Aslibekyan, Devin Absher, Donna K. Arnett, Jesper Tegnér, David Gomez-Cabrero, Fredrik Piehl, Maja Jagodic
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-2202-0

Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies
Cited by: 57
Author(s): Patrycja Daca-Roszak, Aleksandra Pfeifer, Jadwiga Żebracka‐Gala, Dagmara Rusinek, Aleksandra Szybińska, Barbara Jarząb, Michał Witt, Ewa Ziętkiewicz
Software Mentions: 3
Published: almost 9 years ago

10.3390/genes8060152

DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age
Cited by: 62
Author(s): Alexey Kozlenkov, Andrew E. Jaffe, Alisa Timashpolsky, Pasha Apontes, Sergei Rudchenko, Mihaela Barbu, William Byne, Yasmin L. Hurd, Steve Horvath, Stella Dracheva
Software Mentions: 3
Published: over 7 years ago

10.1186/s40478-018-0602-5

Tectal glioma as a distinct diagnostic entity: a comprehensive clinical, imaging, histologic and molecular analysis
Cited by: 27
Author(s): Anthony Pak-Yin Liu, Julie H. Harreld, Lisa M. Jacola, Madelyn Gero, Sahaja Acharya, Yahya Ghazwani, Shengjie Wu, Xiaoyü Li, Paul Klimo, Amar Gajjar, Jason Chiang, Ibrahim Qaddoumi
Software Mentions: 3
Published: about 6 years ago

Projects: bioconductor: minfi

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