bioconductor: DMRcate | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02388-x

Gene set enrichment analysis for genome-wide DNA methylation data
Cited by: 61
Author(s): Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
Software Mentions: 16
Published: over 3 years ago

Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles
Cited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: almost 4 years ago

10.3390/ijms22062790

Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy
Cited by: 4
Author(s): Steffan Noe Christiansen, Stine Jacobsen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Linea C Trudsø, Karsten Olsen, Jacob Tfelt-Hansen, Jytte Banner, Niels Morling
Software Mentions: 13
Published: over 3 years ago

10.1186/s13072-020-00380-6

Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling
Cited by: 7
Author(s): Jamie Grit, Benjamin K. Johnson, Patrick S. Dischinger, Curt J. Essenburg, Marie Adams, Stacy Campbell, Kai Pollard, Christine A. Pratilas, Tim Triche, Carrie R. Graveel, Matthew R. Steensma
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.8839.3

A cross-package Bioconductor workflow for analysing methylation array data
Cited by: 80
Author(s): Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
Software Mentions: 12
Published: over 7 years ago

10.12688/f1000research.24187.2

ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
Cited by: 0
Author(s): Charlotte Soneson, Fédérico Marini, Florian Geier, Michael I. Love, Michael Stadler
Software Mentions: 12
Published: about 4 years ago

10.1186/s13059-021-02329-8

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
Cited by: 13
Author(s): Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos
Software Mentions: 11
Published: over 3 years ago

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
Published: over 4 years ago

10.1186/s40478-018-0548-7

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential
Cited by: 35
Author(s): Samuel Rivero-Hinojosa, Ling San Lau, Mojca Stampar, Jerome A. Staal, Huizhen Zhang, Heather Gordish‐Dressman, Paul A. Northcott, Stefan M. Pfister, Michael D. Taylor, Kristy J. Brown, Brian R. Rood
Software Mentions: 10
Published: over 6 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: about 4 years ago

10.1186/s13058-018-1090-z

Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier
Cited by: 4
Author(s): Youdinghuan Chen, Yue Wang, Lucas A. Salas, Todd W. Miller, Kenneth M. K. Mark, Jonathan D. Marotti, Arminja N. Kettenbach, Chao Cheng, Brock C. Christensen
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0209656

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn’s disease patients
Cited by: 14
Author(s): Andrew Y. Li Yim, Jessica R. de Bruyn, Nicolette W. Duijvis, Catriona Sharp, Enrico Ferrero, Wouter J. de Jonge, Manon E. Wildenberg, Marcel M.A.M. Mannens, Christianne J. Buskens, Geert R. D’Haens, Peter Henneman, Anje A. te Velde
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: about 6 years ago

10.1186/s13148-020-0824-9

Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic population
Cited by: 18
Author(s): Heather E. Rizzo, Elia N. Escaname, Nicholas B. Alana, Elizabeth Lavender, Jonathan Gelfond, Roman Fernandez, Matthew A. Hibbs, Julie King, Nicholas Carr, Cynthia L. Blanco
Software Mentions: 9
Published: over 4 years ago

10.3390/ijms21134763

The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose
Cited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: over 4 years ago

10.1186/s40246-019-0242-2

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis
Cited by: 4
Author(s): Carlos Ruiz‐Arenas, Alejandro Cáceres, Vı́ctor Moreno, Juan R. González
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13148-019-0678-1

Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis
Cited by: 22
Author(s): Lara Kular, Maria Needhamsen, Milena Z. Adzemovic, Tatiana V. Kramarova, David Gomez-Cabrero, Ewoud Ewing, Eliane Piket, Jesper Tegnér, Stephan Beck, Fredrik Piehl, Lou Brundin, Maja Jagodic
Software Mentions: 9
Published: over 5 years ago

10.3389/fphys.2021.660906

Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp Trek
Cited by: 6
Author(s): Ainash Childebayeva, Taylor Harman, Julien Weinstein, Trevor A. Day, Tom D. Brutsaert, Abigail W. Bigham
Software Mentions: 8
Published: over 3 years ago

10.3389/fgene.2019.00624

Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma
Cited by: 53
Author(s): Nitish K. Mishra, Siddesh Southekal, Chittibabu Guda
Software Mentions: 8
Published: about 5 years ago

10.1186/s13148-020-00931-4

TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma
Cited by: 7
Author(s): Rachel L. Clifford, Chen Xi Yang, Nick Fishbane, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Sean May, Marcos Castellanos-Uribe, Parameswaran Nair, Ma’en Obeidat, Michæl S. Kobor, Alan J. Knox, Tillie-Louise Hackett
Software Mentions: 8
Published: about 4 years ago

10.1186/s12859-020-03734-9

MADA: a web service for analysing DNA methylation array data
Cited by: 1
Author(s): Xinyu Hu, Li Tang, Linconghua Wang, Fang‐Xiang Wu, Min Li
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13148-020-00837-1

Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients
Cited by: 21
Author(s): Rujiraporn Pitaksalee, AN Burska, Shoaib Ajaib, Joshua Hugh Rogers, Rekha Parmar, K. Mydlova, Xuanxiao Xie, Alastair Droop, Jagtar Singh Nijjar, P Chambers, Paul Emery, Richard Hodgett, Iain B. McInnes, Frédérique Ponchel
Software Mentions: 7
Published: over 4 years ago

10.1186/s12940-021-00754-7

Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes
Cited by: 11
Author(s): Anne K. Bozack, Philippe Boileau, Linqing Wei, Alan Hubbard, Fenna C.M. Sillé, Catterina Ferreccio, Johanna Acevedo, Lifang Hou, Vesna Ilievski, Craig Steinmaus, Martyn T. Smith, Ana Navas-Acién, Mary V. Gamble, Andrés Cárdenas
Software Mentions: 7
Published: about 3 years ago

10.1038/s41598-018-37746-6

The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region
Cited by: 22
Author(s): Nora Fernández-Jiménez, Koldo García-Etxebarria, Leticia Plaza-Izurieta, Irati Romero-Garmendia, Amaia Jauregi-Miguel, María Legarda, Szilvia Ecsedi, Ainara Castellanos–Rubio, Vincent Cahais, Cyrille Cuenin, Davide Degli Esposti, Iñaki Irastorza, Héctor Hernández-Vargas, Zdenko Herceg, José Ramón Bilbao
Software Mentions: 7
Published: over 5 years ago

10.1038/srep28657

Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood
Cited by: 57
Author(s): Kristian Almstrup, Marie Johansen, Alexander Busch, Casper P Hagen, John Nielsen, Jørgen Holm Petersen, Anders Juul
Software Mentions: 7
Published: over 8 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: over 6 years ago

10.1186/s13148-021-01145-y

Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile
Cited by: 17
Author(s): Andrea Ciolfi, Aidin Foroutan, Alessandro Capuano, Lucia Pedace, Lorena Travaglini, Simone Pizzi, Marco Andreani, Evelina Miele, Federica Invernizzi, Chiara Reale, Celeste Panteghini, Maria Iascone, Marcello Niceta, Ralitza H. Gavrilova, Laura Schultz‐Rogers, Emanuele Agolini, Maria Francesca Bedeschi, Paolo Prontera, Matteo Garibaldi, Serena Galosi, Vincenzo Leuzzi, Paola Soliveri, Rory J. Olson, Giovanna Zorzi, Barbara Garavaglia, Marco Tartaglia, Bekim Sadiković
Software Mentions: 7
Published: about 3 years ago

10.1186/s13148-019-0658-5

Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome
Cited by: 65
Author(s): Eric G. Bend, Erfan Aref‐Eshghi, David B. Everman, R. Curtis Rogers, Sara Cathey, Eloise J. Prijoles, Michael J. Lyons, Heather L. Davis, Katie Clarkson, Karen W. Gripp, Dong Liu, Elizabeth Bhoj, Elaine H. Zackai, Paul R. Mark, Hákon Hákonarson, Laurie A. Demmer, Michael A. Levy, Jennifer Kerkhof, Alan Stuart, David I. Rodenhiser, Michael J. Friez, Roger E. Stevenson, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: over 5 years ago

10.1186/1756-8935-8-6

De novo identification of differentially methylated regions in the human genome
Cited by: 639
Author(s): Timothy J. Peters, Michael Buckley, Aaron L. Statham, Ruth Pidsley, Katherine Samaras, Reginald V. Lord, Susan J. Clark, Peter L. Molloy
Software Mentions: 7
Published: over 9 years ago

10.3390/ijms20092075

Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy
Cited by: 31
Author(s): Ray O. Bahado‐Singh, Sangeetha Vishweswaraiah, Buket Aydas, Nitish K. Mishra, Chittibabu Guda, Uppala Radhakrishna
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-019-3224-4

Vertical and horizontal integration of multi-omics data with miodin
Cited by: 35
Author(s): Benjamin Ulfenborg
Software Mentions: 6
Published: almost 5 years ago

10.3389/fgene.2019.00325

The Cord Blood Insulin and Mitochondrial DNA Content Related Methylome
Cited by: 5
Author(s): Brigitte Reimann, Bram G. Janssen, Rossella Alfano, Akram Ghantous, Almudena Espín-Pérez, Theo M. de Kok, Nelly D. Saenen, Bianca Cox, Oliver Robinson, Marc Chadeau‐Hyam, Joris Penders, Zdenko Herceg, Paolo Víneis, Tim S. Nawrot, Michelle Plusquin
Software Mentions: 6
Published: over 5 years ago

10.3390/cells8080921

Genes Controlled by DNA Methylation Are Involved in Wilms Tumor Progression
Cited by: 12
Author(s): João Victor da Silva Guerra, Bruna Maria de Sá Pereira, Jéssica Gonçalves Vieira da Cruz, Nicole de Miranda Scherer, Carolina Furtado, Rafaela Montalvão de Azevedo, Paulo Sérgio Lopes de Oliveira, Paulo Faria, Mariana Boroni, Beatriz de Camargo, Mariana Maschietto
Software Mentions: 6
Published: about 5 years ago

10.1186/s13148-018-0593-x

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1009506

Comparative analysis reveals distinctive epigenetic features of the human cerebellum
Cited by: 11
Author(s): Elaine E. Guevara, William D. Hopkins, Patrick R. Hof, John J. Ely, Brenda J. Bradley, Chet C. Sherwood
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-019-5553-0

Comparing DNA methylation profiles in saliva and intestinal mucosa
Cited by: 13
Author(s): Nerissa L. Hearn, Aaron S. Coleman, Vincent Ho, Christine L Chiu, Joanne M. Lind
Software Mentions: 6
Published: over 5 years ago

10.3390/cancers12113088

DNA Methylation and Breast Cancer Risk: An Epigenome-Wide Study of Normal Breast Tissue and Blood
Cited by: 15
Author(s): Kaoutar Ennour‐Idrissi, Dzevka Dragic, Elissar Issa, Annick Michaud, Sue-Ling Chang, Louise Provencher, Francine Durocher, Caroline Diorio
Software Mentions: 6
Published: almost 4 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: over 3 years ago

10.1186/s13148-019-0637-x

Association of leukocyte DNA methylation changes with dietary folate and alcohol intake in the EPIC study
Cited by: 20
Author(s): Flavie Perrier, Vivian Viallon, Srikant Ambatipudi, Akram Ghantous, Cyrille Cuenin, Héctor Hernández-Vargas, Véronique Chajès, Laura Baglietto, Marco Matejcic, Hortensia Moreno-Macías, Tilman Kühn, Heiner Boeing, Anna Karakatsani, Αναστασία Κοτανίδου, Antonia Trichopoulou, Sabina Sieri, Salvatore Panico, Francesca Fasanelli, Martijn E.T. Dollé, N. Charlotte Onland‐Moret, Ivonne Sluijs, Elisabete Weiderpass, J. Ramón Quiŕos, Antonio Agudo, José María Huerta, Eva Ardanaz, Miren Dorronsoro, Tammy Y.N. Tong, Konstantinos K. Tsilidis, Elio Riboli, Marc J. Gunter, Zdenko Herceg, Pietro Ferrari, Isabelle Romieu
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pmed.1003229

Maternal dysglycaemia, changes in the infant’s epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial
Cited by: 52
Author(s): Elie Antoun, Negusse Tadesse Kitaba, Philip Titcombe, Kathryn V. Dalrymple, Emma Garratt, Sheila J. Barton, Robert Murray, Paul Seed, Joanna D. Holbrook, Michael S. Kobor, David T.S. Lin, Julia L. MacIsaac, Graham C. Burdge, Sara L. White, Lucilla Poston, Keith M. Godfrey, Karen A. Lillycrop
Software Mentions: 5
Published: almost 4 years ago

10.1093/gigascience/giaa049

Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy
Cited by: 11
Author(s): Katarzyna Murat, Björn Grüning, Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J. Tobin, Krzysztof Poterlowicz
Software Mentions: 5
Published: over 4 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

10.1007/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

10.1186/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: over 5 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

10.1186/s12920-020-0670-9

Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals
Cited by: 9
Author(s): Nerissa L. Hearn, Christine L Chiu, Joanne M. Lind
Software Mentions: 5
Published: over 4 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: about 3 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

10.1038/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

10.1186/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

10.18632/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: almost 5 years ago

10.1111/acel.13178

The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0214282

DNA methylation among firefighters
Cited by: 13
Author(s): Jin Zhou, Timothy G. Jenkins, Alesia M. Jung, Kyoung Sook Jeong, Jing Zhai, Elizabeth T. Jacobs, Stephanie Griffin, Devi Dearmon-Moore, Sally R. Littau, Wayne F. Peate, Nathan A. Ellis, Peter Lance, Yin Chen, Jefferey L. Burgess
Software Mentions: 4
Published: over 5 years ago

10.1186/s13148-021-01102-9

Blood DNA methylation and COVID-19 outcomes
Cited by: 61
Author(s): Joseph Balnis, Andy Madrid, Kirk Hogan, Lisa A. Drake, Hau Chieng, Anupama Tiwari, Vincent Colot, Amit Chopra, Peter Vincent, Michael D. Robek, Harold A. Singer, Reid S. Alisch, Ariel Jaitovich
Software Mentions: 4
Published: over 3 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

10.1186/s13148-016-0281-7

Effect of prenatal DHA supplementation on the infant epigenome: results from a randomized controlled trial
Cited by: 62
Author(s): Susan J. van Dijk, Jing Zhou, Timothy J. Peters, Michael Buckley, Brodie Sutcliffe, Yalchin Oytam, Robert Gibson, Andrew J McPhee, Lisa N Yelland, Maria Makrides, Peter L. Molloy, Beverly S. Mühlhäusler
Software Mentions: 4
Published: almost 8 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

10.1186/s13148-017-0408-5

Newborn genome-wide DNA methylation in association with pregnancy anxiety reveals a potential role for GABBR1
Cited by: 29
Author(s): Elise Vangeel, Ehsan Pishva, Titia Hompes, Daniël L.A. van den Hove, Diether Lambrechts, Karel Allegaert, Kathleen Freson, Benedetta Izzi, Stephan Claes
Software Mentions: 4
Published: about 7 years ago

10.1186/s13148-018-0581-1

Methylome profiling of healthy and central precocious puberty girls
Cited by: 28
Author(s): Danielle Bessa, Mariana Maschietto, Carlos F. Aylwin, Ana Pinheiro Machado Canton, Vinícius Nahime Brito, Delanie B Macedo, Marina Cunha-Silva, Heloísa Marcelina Cunha Palhares, Elisabete Aparecida Mantovani Rodrigues de Resende, Maria de Fátima Borges, Berenice B. Mendonca, Irène Netchine, Ana Cristina Victorino Krepischi, Alejandro Lomniczi, Sergio R. Ojeda, Ana Cláudia Latronico
Software Mentions: 4
Published: almost 6 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

10.1080/15592294.2020.1748916

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

10.1186/s12979-021-00223-2

Age-related differences in monocyte DNA methylation and immune function in healthy Kenyan adults and children
Cited by: 8
Author(s): Katherine R. Dobbs, Paula Embury, Emmily Koech, Sidney Ogolla, Stephen Munga, James W. Kazura, Arlene E. Dent
Software Mentions: 4
Published: over 3 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: almost 4 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: almost 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

10.1038/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

10.1186/s13072-016-0074-4

DNA methylation signature of human fetal alcohol spectrum disorder
Cited by: 115
Author(s): Élodie Portales-Casamar, Alexandre A. Lussier, Meaghan J. Jones, Julia L. MacIsaac, Rachel D. Edgar, Sarah M Mah, Amina Barhdadi, Sylvie Provost, Louis-Philippe Lemieux-Perreault, Max S. Cynader, Albert E. Chudley, Marie‐Pierre Dubé, James N. Reynolds, Paul Pavlidis, Michæl S. Kobor
Software Mentions: 3
Published: over 8 years ago

10.1186/s13148-019-0707-0

Impact of a diet and activity health promotion intervention on regional patterns of DNA methylation
Cited by: 30
Author(s): Elizabeth A. Hibler, Lei Huang, Jorge Andrade, Bonnie Spring
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-016-0238-x

Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction
Cited by: 49
Author(s): Maian Roifman, Sanaa Choufani, Andrei L. Turinsky, Sascha Drewlo, Sarah Keating, Michael Brudno, John Kingdom, Rosanna Weksberg
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1008778

Profiling of immune related genes silenced in EBV-positive gastric carcinoma identified novel restriction factors of human gammaherpesviruses
Cited by: 11
Author(s): Guillaume Fiches, Dawei Zhou, Weili Kong, Ayan Biswas, Elshafa H. Ahmed, Robert A. Baiocchi, Jian Zhu, Netty Santoso
Software Mentions: 3
Published: about 4 years ago

10.1186/s12863-018-0647-2

Application of novel and existing methods to identify genes with evidence of epigenetic association: results from GAW20
Cited by: 1
Author(s): Angga M Fuady, Samantha Lent, Chloé Sarnowski, Nathan L. Tintle
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0227728

Associations between high blood pressure and DNA methylation
Cited by: 34
Author(s): Nabila Kazmi, Hannah R Elliott, Kimberley Burrows, Therese Tillin, Alun D. Hughes, Nishi Chaturvedi, Tom R. Gaunt, Caroline L Relton
Software Mentions: 3
Published: over 4 years ago

10.1155/2018/4390789

A DNA-Methylated Sight on Autoimmune Inflammation Network across RA, pSS, and SLE
Cited by: 9
Author(s): Xingqiang Wang, Dongyun Lei, Jie Ding, Shuang Liu, Tao Li, Fan Zhang, Jiangyun Peng, Jian Xu
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-80857-2

Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment
Cited by: 18
Author(s): Oladele A. Oluwayiose, Haotian Wu, Hachem Saddiki, Brian W. Whitcomb, Laura B. Balzer, Nicole Brandon, Alexander Suvorov, Tayyab Rahil, Cynthia K. Sites, Lisa Hill, Chelsea Marcho, J. Richard Pilsner
Software Mentions: 3
Published: over 3 years ago

10.1093/bioinformatics/btx513

ChAMP: updated methylation analysis pipeline for Illumina BeadChips
Cited by: 496
Author(s): Yuan Tian, Tiffany Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E. Teschendorff
Software Mentions: 3
Published: about 7 years ago

10.1038/s12276-020-00493-8

Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer
Cited by: 78
Author(s): Jae Won Cho, Min Hee Hong, Sang Jun Ha, Young-Joon Kim, Byoung Chul Cho, Insuk Lee, Hye Ryun Kim
Software Mentions: 3
Published: about 4 years ago

10.1186/s12916-021-01917-6

Serum transferrin as a biomarker of hepatocyte nuclear factor 4 alpha activity and hepatocyte function in liver diseases
Cited by: 6
Author(s): Nurdan Güldiken, Josepmaría Argemi, Berivan Gurbuz, Stephen R. Atkinson, Martin Oliverius, Petr Fila, Karim Hamesch, Tony Bruns, Joaquín Cabezas, Juan José Lozano, Jelena Mann, Sheng Cao, Philippe Maury, Vijay H. Shah, Christian Trautwein, Mark Thursz, R. Bataller, Pavel Strnad
Software Mentions: 3
Published: over 3 years ago

10.1186/s13148-015-0154-5

The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects
Cited by: 98
Author(s): Dieuwertje E. Kok, R.A.M. Dhonukshe-Rutten, Carolien Lute, Sandra G. Heil, André G. Uitterlinden, Nathalie van der Velde, Joyce B. J. van Meurs, Natasja M. van Schoor, Guido Hooiveld, Lisette C. P. G. M. de Groot, Ellen Kampman, Wilma T. Steegenga
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13148-019-0680-7

DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data
Cited by: 13
Author(s): Yujie He, Lot de Witte, Lotte C Houtepen, Danny M Nispeling, Zhida Xu, Qiong Yu, Yaqin Yu, Elly M. Hol, René S. Kahn, Marco P. Boks
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-019-0740-z

Detecting multiple differentially methylated CpG sites and regions related to dimensional psychopathology in youths
Cited by: 12
Author(s): Letícia Spíndola, Marcos Santoro, Pedro Mário Pan, Vanessa Kiyomi Ota, Gabriela Xavier, Carolina Muniz Carvalho, Fernanda Talarico, Patrick Sleiman, Michael March, Renata Pellegrino, Elisa Brietzke, Rodrigo Grassi‐Oliveira, Jair J. Mari, Ary Gadelha, Eurípedes Constantino Miguel, Luís Augusto Rohde, Rodrigo Bressan, Diego R. Mazzotti, João Ricardo Sato, Giovanni Abrahão Salum, Hákon Hákonarson, Síntia Belangero
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41398-021-01225-w

DNA methylation differences associated with social anxiety disorder and early life adversity
Cited by: 19
Author(s): Ariane Wiegand, Benjamin Kreifelts, Matthias H. J. Munk, Nadja Geiselhart, Katia E Ramadori, Julia L. MacIsaac, Andreas J. Fallgatter, Michæl S. Kobor, Vanessa Nieratschker
Software Mentions: 3
Published: over 3 years ago

10.1186/s13148-020-00992-5

Pre-adolescence DNA methylation is associated with lung function trajectories from pre-adolescence to adulthood
Cited by: 8
Author(s): Shadia Khan Sunny, Hongmei Zhang, Fawaz Mzayek, Caroline L Relton, Susan M. Ring, A. John Henderson, Susan Ewart, John W. Holloway, Syed Hasan Arshad
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2020.551787

Epigenetic Variation Analysis Leads to Biomarker Discovery in Gastric Adenocarcinoma
Cited by: 1
Author(s): Yan Zhang, Dianjing Guo
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2021.622599

DNA Methylation Analysis to Unravel Altered Genetic Pathways Underlying Early Onset and Late Onset Neonatal Sepsis. A Pilot Study
Cited by: 12
Author(s): Sheila Lorente-Pozo, Paula Navarrete, María José Garzón, Inmaculada Lara-Cantón, Jesús Beltrán-García, Rebeca Osca-Verdegal, Salvador Mena-Mollá, Eva García-López, Máximo Vento, Federico V. Pallardó, José Luis García‐Gimenez
Software Mentions: 3
Published: over 3 years ago

10.1186/s13072-021-00388-6

Genome-wide impact of hydrogen peroxide on maintenance DNA methylation in replicating cells
Cited by: 14
Author(s): Annika R. Seddon, Yusmiati Liau, Paul E. Pace, Allison L. Miller, Andrew B. Das, Martin A. Kennedy, Mark B. Hampton, Aaron J. Stevens
Software Mentions: 3
Published: over 3 years ago

10.1186/s13148-019-0764-4

Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome
Cited by: 15
Author(s): Cecilie Bucher-Johannessen, Christian M. Page, Trine B. Haugen, Marcin W. Wojewodzic, Sophie D. Fosså, Tom Grotmol, Hege Sagstuen Haugnes, Trine B. Rounge
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13148-017-0344-4

Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals
Cited by: 27
Author(s): Donia Macartney-Coxson, Miles C. Benton, R. A. J. Blick, Richard S. Stubbs, R. D. Hagan, Michael A. Langston
Software Mentions: 3
Published: over 7 years ago

10.1038/s41398-020-00948-6

Association between DNA methylation levels in brain tissue and late-life depression in community-based participants
Cited by: 23
Author(s): Anke Hüls, Chloe Robins, Karen N. Conneely, Philip L. De Jager, David A. Bennett, Michael P. Epstein, Thomas S. Wingo, Aliza P. Wingo
Software Mentions: 3
Published: about 4 years ago

10.1038/s41398-019-0550-2

Genome-wide profiling of DNA methylome and transcriptome in peripheral blood monocytes for major depression: A Monozygotic Discordant Twin Study
Cited by: 47
Author(s): Yun Zhu, Eric Strachan, Emily Fowler, Tamara J. Bacus, Peter Roy‐Byrne, Jinying Zhao
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.65715

Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status
Cited by: 8
Author(s): Ilhame Diboun, Sachin Wani, Stuart H. Ralston, Omar Albagha
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-017-0419-z

Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas
Cited by: 59
Author(s): Davide Degli Esposti, Athéna Sklias, Sheila Coelho Soares Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernández-Jiménez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Héctor Hernandez-Vargas, Luís Felipe Ribeiro Pinto, Ellen Van Obberghen-Schilling, Zdenko Herceg
Software Mentions: 3
Published: over 7 years ago

10.1093/ajcn/nqaa193

Effect of maternal preconceptional and pregnancy micronutrient interventions on children’s DNA methylation: Findings from the EMPHASIS study
Cited by: 17
Author(s): Ayden Saffari, Smeeta Shrestha, Prachand Issarapu, Sara Sajjadi, Modupeh Betts, Sirazul A. Sahariah, Ashutosh Singh Tomar, Philip James, Akshay Dedaniya, Dilip Kumar Yadav, Kalyanaraman Kumaran, Andrew M. Prentice, Karen A. Lillycrop, Caroline Fall, Giriraj Ratan Chandak, Matt J. Silver
Software Mentions: 3
Published: about 4 years ago

10.1186/s13148-019-0725-y

DNA methylome-wide alterations associated with estrogen receptor-dependent effects of bisphenols in breast cancer
Cited by: 20
Author(s): Zainab Awada, Rihab Nasr, Reem Akika, Vincent Cahais, Cyrille Cuenin, Maria Zhivagui, Zdenko Herceg, Akram Ghantous, Nathalie K. Zgheib
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-015-2034-y

Sex differences in DNA methylation assessed by 450 K BeadChip in newborns
Cited by: 154
Author(s): Paul Yousefi, Karen Huen, Vrushank Davé, Lisa F. Barcellos, Brenda Eskenazi, Nina Holland
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13148-021-01072-y

Disease-associated DNA methylation signatures in esophageal biopsies of children diagnosed with Eosinophilic Esophagitis
Cited by: 1
Author(s): Caterina Strisciuglio, Felicity Payne, Komal Nayak, Marta Andreozzi, Alessandra Vitale, Erasmo Miele, Matthias Zilbauer
Software Mentions: 2
Published: over 3 years ago

10.3389/fphys.2021.619447

The Comparative Methylome and Transcriptome After Change of Direction Compared to Straight Line Running Exercise in Human Skeletal Muscle
Cited by: 18
Author(s): Mohd Firdaus Maasar, Daniel C. Turner, Piotr P. Gorski, Robert A. Seaborne, Juliette A. Strauss, Sam Shepherd, Matt Cocks, Nicolas Pillon, Juleen R. Zierath, Andrew T. Hulton, Barry Drust, Adam P. Sharples
Software Mentions: 2
Published: over 3 years ago

10.1186/s13578-019-0278-y

Regional methylome profiling reveals dynamic epigenetic heterogeneity and convergent hypomethylation of stem cell quiescence-associated genes in breast cancer following neoadjuvant chemotherapy
Cited by: 13
Author(s): Yan Luo, Juan Huang, Yi Tang, Xitu Luo, Lingxia Ge, Xiujie Sheng, Xiaofang Sun, Yaoyong Chen, Detu Zhu
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13122915

DNA Methylation Markers from Negative Surgical Margins Can Predict Recurrence of Oral Squamous Cell Carcinoma
Cited by: 10
Author(s): Bruna Pereira Sorroche, Fazlur Rahman Talukdar, Sheila Coelho Soares Lima, Matias Eliseo Melendez, Ana Carolina de Carvalho, Gisele Caravina de Almeida, Pedro De Marchi, Monique de Souza Almeida Lopes, Luís Felipe Ribeiro Pinto, André Lopes Carvalho, Zdenko Herceg, Lídia Maria Rebolho Batista Arantes
Software Mentions: 2
Published: over 3 years ago

10.1186/s12863-018-0637-4

Comparison of novel and existing methods for detecting differentially methylated regions
Cited by: 10
Author(s): Samantha Lent, Hanfei Xu, Lan Wang, Zhe Wang, Chloé Sarnowski, Marie‐France Hivert, Josée Dupuis
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0226555

Association of cord blood methylation with neonatal leptin: An epigenome wide association study
Cited by: 10
Author(s): Rachel Kadakia, Yinan Zheng, Zhou Zhang, Wei Zhang, Jami L. Josefson, Lifang Hou
Software Mentions: 2
Published: almost 5 years ago

Projects: bioconductor: DMRcate

Papers Mentioning DMRcate 132