bioconductor: wateRmelon | Projects

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

Bigmelon: tools for analysing large DNA methylation datasets
Cited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: about 6 years ago

10.1038/s41598-019-44765-4

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Cited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: over 5 years ago

10.1186/s12885-017-3726-2

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer
Cited by: 26
Author(s): Melissa Quintero, Douglas Adamóski, Larissa Menezes dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Milton Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
Software Mentions: 9
Published: about 7 years ago

10.1038/tp.2016.275

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score
Cited by: 28
Author(s): Diana‐Maria Ciuculete, Adrian Boström, Sarah Voisin, H. Philipps, Olga E. Titova, Marcus Bandstein, Lamia Nikontovic, Michael J. Williams, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 8
Published: almost 8 years ago

10.1186/s13059-019-1664-9

RnBeads 2.0: comprehensive analysis of DNA methylation data
Cited by: 188
Author(s): Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock
Software Mentions: 8
Published: over 5 years ago

10.1186/s13148-020-00899-1

Highly accurate skin-specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging
Cited by: 23
Author(s): Mariana Boroni, Alessandra Zonari, Carolina Reis de Oliveira, Kallie Al-Katib, Edgar Andrés Ochoa Cruz, Lear E. Brace, Juliana Lott Carvalho
Software Mentions: 8
Published: over 4 years ago

10.1186/s13059-020-02223-9

Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity
Cited by: 17
Author(s): Benjamin Planterose Jiménez, Fan Liu, Amke Caliebe, Diego Montiel González, Jordana T. Bell, Manfred Kayser, Athina Vidaki
Software Mentions: 8
Published: almost 4 years ago

10.1155/2021/1801873

Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma
Cited by: 2
Author(s): Dan Luo, Xiang Zhang, Xiaokai Li, Gang Chen
Software Mentions: 7
Published: over 3 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: over 3 years ago

10.1371/journal.pone.0229763

Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform
Cited by: 8
Author(s): Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, Christine Nardini
Software Mentions: 7
Published: over 4 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: almost 6 years ago

10.1186/s12859-018-2096-3

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip
Cited by: 32
Author(s): Zhenxing Wang, Xiaoliang Wu, Yadong Wang
Software Mentions: 6
Published: over 6 years ago

10.1186/s13148-019-0787-x

Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer’s disease-related dysregulation
Cited by: 12
Author(s): Larissa Haertle, Tobias Müller, Roy Lardenoije, Anna Maierhofer, Marcus Dittrich, Renzo J. M. Riemens, Samantha Stora, M Roche, Markus Leber, Steffi G. Riedel‐Heller, Michael Wagner, Martin Scherer, Aimé Ravel, Clotilde Mircher, Cécile Cieuta‐Walti, Sophie Durand, Daniel L. A. van de Hove, Per Hoffmann, Alfredo Ramı́rez, Thomas Haaf, Nady El Hajj, André Mégarbané
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-021-89429-4

Identification of a methylomics-associated nomogram for predicting overall survival of stage I–II lung adenocarcinoma
Cited by: 1
Author(s): Heng Wang, Chuangye Wei, Peng Pan, Fengfeng Yuan, Jiancheng Cheng
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

10.1371/journal.pgen.1009035

The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations
Cited by: 12
Author(s): Fredrika Åsenius, T.J. Gorrie-Stone, Ama Brew, Yasmin Panchbhaya, Elizabeth Williamson, Leonard C Schalkwyk, Vardhman K. Rakyan, Michelle L. Holland, Sarah Marzi, David Williams
Software Mentions: 6
Published: about 4 years ago

10.1186/s12931-016-0459-8

Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations
Cited by: 47
Author(s): Robert S. Busch, Weiliang Qiu, Jessica Lasky‐Su, Jarrett Morrow, Gerard J. Criner, Dawn L. DeMeo
Software Mentions: 6
Published: about 8 years ago

10.1186/s13148-016-0241-2

Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses
Cited by: 11
Author(s): Emma Cazaly, Russell Thomson, James R. Marthick, Adele F. Holloway, Jac Charlesworth, Joanne L. Dickinson
Software Mentions: 6
Published: over 8 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: about 4 years ago

10.1186/s13059-014-0483-2

Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia
Cited by: 140
Author(s): Ruth Pidsley, Joana Viana, Eilís Hannon, Helen Spiers, Claire Troakes, Safa Al-Saraj, Naguib Mechawar, Gustavo Turecki, Leonard C. Schalkwyk, Nicholas John Bray, Jonathan Mill
Software Mentions: 6
Published: about 10 years ago

10.1016/j.ebiom.2021.103383

Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Cited by: 4
Author(s): Kevin A. Roth, Louis Coussement, Elena V. Knatko, Maureen Higgins, Sandra Steyaert, Charlotte M. Proby, Tim De Meyer, Albena T. Dinkova‐Kostova
Software Mentions: 6
Published: over 3 years ago

10.1186/s13601-016-0105-z

Cow’s milk allergy in Dutch children: an epigenetic pilot survey
Cited by: 36
Author(s): Nicole C. M. Petrus, Peter Henneman, Andrea Venema, Adri N. Mul, Femke van Sinderen, Martin A. Haagmans, Olaf R.F. Mook, Raoul C. M. Hennekam, A. B. Sprikkelman, Marcel M.A.M. Mannens
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-09335-6

Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis
Cited by: 85
Author(s): Julia Steinberg, Graham R. S. Ritchie, Theodoros I. Roumeliotis, Raveen L Jayasuriya, Matthew Clark, Roger A. Brooks, Abbie L. A. Binch, Karan M. Shah, Rachael Coyle, Mercedes Pardo, Christine Le Maitre, Yolande F M Ramos, Rob G H H Nelissen, Ingrid Meulenbelt, Andrew W. McCaskie, Jyoti S. Choudhary, J. Mark Wilkinson, Eleftheria Zeggini
Software Mentions: 5
Published: over 7 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

10.1186/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

10.1186/1471-2164-14-293

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/s13148-021-01064-y

DNA methylation and gene expression integration in cardiovascular disease
Cited by: 21
Author(s): Guillermo Palou-Márquez, Isaac Subirana, Lara Nonell, Alba Fernández‐Sanlés, Roberto Elosúa
Software Mentions: 5
Published: over 3 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: almost 5 years ago

10.1186/s12864-017-4091-x

5-hydroxymethylcytosine is highly dynamic across human fetal brain development
Cited by: 56
Author(s): Helen Spiers, Eilís Hannon, Leonard C Schalkwyk, Nicholas John Bray, Jonathan Mill
Software Mentions: 5
Published: about 7 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

10.1186/s12864-018-4652-7

Impact on birth weight of maternal smoking throughout pregnancy mediated by DNA methylation
Cited by: 41
Author(s): Stephanie H. Witt, Josef Frank, Maria Gilles, Maren Lang, Jens Treutlein, Fabian Streit, Isabella Wolf, Verena Peus, Barbara Scharnholz, Tabea Send, Stefanie Heilmann‐Heimbach, Sugirthan Sivalingam, Helene Dukal, Jana Strohmaier, Marc Sütterlin, Janine Arloth, Manfred Laucht, Markus M. Nöthen, Michael Deuschle, Marcella Rietschel
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1009443

Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology
Cited by: 27
Author(s): Eilís Hannon, Georgina Mansell, Emma Walker, Marta F. Nabais, Joe Burrage, Agnieszka Kepa, Janis Best-Lane, Anna Rose, Suzanne Heck, Terrie E. Moffitt, Avshalom Caspi, Louise Arseneault, Jonathan Mill
Software Mentions: 5
Published: over 3 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

10.1093/brain/awaa334

Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex
Cited by: 86
Author(s): Gemma Shireby, Jonathan Davies, Paul T. Francis, Joe Burrage, Emma Walker, Grant W. A. Neilson, Aisha Dahir, Alan Thomas, Seth Love, Rebecca Smith, Katie Lunnon, Meena Kumari, Leonard C Schalkwyk, Kevin Morgan, Keeley Brookes, Eilís Hannon, Jonathan Mill
Software Mentions: 4
Published: about 4 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/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: about 8 years ago

10.1016/j.ebiom.2018.10.051

Epigenetic signatures of starting and stopping smoking
Cited by: 62
Author(s): Daniel L. McCartney, Anna J. Stevenson, Robert F. Hillary, Richard M Martin, Mairead Lesley Bermingham, Stewart W. Morris, Toni‐Kim Clarke, Archie Campbell, Alison Murray, Heather C. Whalley, David J. Porteous, Peter M. Visscher, Andrew M. McIntosh, Kathryn Evans, Ian J. Deary, Riccardo E. Marioni
Software Mentions: 4
Published: about 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

10.1186/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

10.1186/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

10.4161/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

10.1080/15592294.2020.1748916

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/s13148-021-01041-5

Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases
Cited by: 11
Author(s): Chen Yao, Roby Joehanes, Rory Wilson, Toshiko Tanaka, Luigi Ferrucci, Anja Kretschmer, Holger Prokisch, Katharina Schramm, Christian Gieger, Annette Peters, Mélanie Waldenberger, Carola Marzi, Christian Herder, Daniel Levy
Software Mentions: 4
Published: over 3 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

10.1186/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

10.1042/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

10.18632/aging.202775

Male-specific age estimation based on Y-chromosomal DNA methylation
Cited by: 11
Author(s): Athina Vidaki, Diego Montiel González, Benjamin Planterose Jiménez, Manfred Kayser
Software Mentions: 3
Published: over 3 years ago

10.1016/j.ajhg.2018.09.007

Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits
Cited by: 118
Author(s): Eilís Hannon, T.J. Gorrie-Stone, Melissa Smart, Joe Burrage, Amanda Hughes, Yanchun Bao, Meena Kumari, Leonard C Schalkwyk, Jonathan Mill
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-019-5761-7

Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array
Cited by: 175
Author(s): Georgina Mansell, T.J. Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard Schalkwyk, Jonathan Mill, Eilís Hannon
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3426-3

RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip
Cited by: 89
Author(s): Zongli Xu, Sabine A. S. Langie, Patrick De Boever, Jack A. Taylor, Liang Niu
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13293-021-00381-4

A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta
Cited by: 20
Author(s): Amy M. Inkster, Victor Yuan, Chaini Konwar, Allison Matthews, Carolyn J. Brown, Wendy P. Robinson
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1007544

Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins
Cited by: 143
Author(s): Eilís Hannon, Olivia Knox, Karen Sugden, Joe Burrage, Chloe Wong, Daniel W. Belsky, David L. Corcoran, Louise Arseneault, Terrie E. Moffitt, Avshalom Caspi, Jonathan Mill
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-019-0705-2

DNA methylation modules associate with incident cardiovascular disease and cumulative risk factor exposure
Cited by: 42
Author(s): Kenneth Westerman, Paola Sebastiani, Paul F. Jacques, Simin Liu, Dawn L. DeMeo, José M. Ordovás
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-020-00864-y

Harnessing peripheral DNA methylation differences in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease
Cited by: 48
Author(s): Aparna Vasanthakumar, J. Wade Davis, Kenneth B. Idler, Jeffrey F. Waring, Elizabeth Asque, Bridget Riley-Gillis, Shaun Grosskurth, Gyan Srivastava, Sungeun Kim, Kwangsik Nho, Kelly Nudelman, Kelley Faber, Yu Sun, Tatiana Foroud, Karol Estrada, Liana G. Apostolova, Qingqin Li, Andrew J. Saykin
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-016-0279-1

Discovery and replication of a peripheral tissue DNA methylation biosignature to augment a suicide prediction model
Cited by: 46
Author(s): Makena Clive, Marco P. Boks, Christiaan H. Vinkers, Lauren M. Osborne, Jennifer L. Payne, Kerry J. Ressler, Alicia K. Smith, Holly C. Wilcox, Zachary Kaminsky
Software Mentions: 3
Published: about 8 years ago

10.1186/s13148-016-0235-0

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas
Cited by: 7
Author(s): Annette Lim, Nicholas C. Wong, Ruth Pidsley, Elena Zotenko, June Corry, Alexander Dobrovic, Susan J. Clark, Danny Rischin, Benjamin Solomon
Software Mentions: 3
Published: over 8 years ago

10.1186/s13072-019-0296-3

Accurate ethnicity prediction from placental DNA methylation data
Cited by: 39
Author(s): Victor Yuan, Emily Price, Giulia Gobbo, Sara Mostafavi, Brian Cox, Alexandra M. Binder, Karin B. Michels, Carmen J. Marsit, Wendy P. Robinson
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.647981

Characterization of DNA Methylomic Signatures in Induced Pluripotent Stem Cells During Neuronal Differentiation
Cited by: 5
Author(s): Jennifer Imm, Ehsan Pishva, Muhammadd Ali, Talitha L Kerrigan, Aaron R. Jeffries, Joe Burrage, Enrico Glaab, Emma L Cope, Kimberley M Jones, Nicholas Denby Allen, Katie Lunnon
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00016

Genome-Wide DNA Methylation Patterns in Persistent Attention-Deficit/Hyperactivity Disorder and in Association With Impulsive and Callous Traits
Cited by: 25
Author(s): Michiel Meijer, Marieke Klein, Eilís Hannon, Dennis van der Meer, Catharina A. Hartman, Jaap Oosterlaan, Dirk J. Heslenfeld, Pieter J. Hoekstra, Jan K. Buitelaar, Jonathan Mill, Barbara Franke
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2014.00354

Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale
Cited by: 40
Author(s): Olive D. Buhule, Ryan L. Minster, Nicola L. Hawley, Mario Medvedovic, Guoqiang Sun, Satupaitea Viali, Ranjan Deka, Stephen T. McGarvey, Daniel E. Weeks
Software Mentions: 3
Published: about 10 years ago

10.7150/jca.52378

Promoter hypermethylation of early B cell factor 1 (EBF1) is associated with cholangiocarcinoma progression
Cited by: 4
Author(s): Napat Armartmuntree, Apinya Jusakul, Chadamas Sakonsinsiri, Watcharin Loilome, Somchai Pinlaor, Piti Ungarreevittaya, Chern Han Yong, Anchalee Techasen, Kanokwan Imtawil, Ratthaphol Kraiklang, Nattawan Suwannakul, Waleeporn Kaewlert, Timpika Chaiprasert, Raynoo Thanan, Mariko Murata
Software Mentions: 3
Published: almost 4 years ago

10.1038/tp.2016.95

Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1
Cited by: 59
Author(s): Robert Kumsta, Sarah Marzi, Joana Viana, Emma Dempster, Bethany Crawford, Michael Rutter, Jonathan Mill, Edmund Sonuga‐Barke
Software Mentions: 3
Published: over 8 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: almost 4 years ago

10.1093/hmg/ddy210

Systematic Mendelian randomization framework elucidates hundreds of CpG sites which may mediate the influence of genetic variants on disease
Cited by: 53
Author(s): Tom G Richardson, Philip Haycock, Jie Zheng, Nicholas J. Timpson, Tom R. Gaunt, George Davey Smith, Caroline L Relton, Gibran Hemani
Software Mentions: 3
Published: over 6 years ago

10.1093/hmg/ddw373

Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions
Cited by: 48
Author(s): Joana Viana, Eilís Hannon, Emma Dempster, Ruth Pidsley, Robert C. MacDonald, Olivia Knox, Helen Spiers, Claire Troakes, Safa Al-Saraj, Gustavo Turecki, Leonard C Schalkwyk, Jonathan Mill
Software Mentions: 3
Published: almost 8 years ago

10.1093/hmg/ddz052

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue
Cited by: 62
Author(s): Chloe Wong, Rebecca G. Smith, Eilís Hannon, Gokul Ramaswami, Neelroop N. Parikshak, Elham Assary, Claire Troakes, Jérémie Poschmann, Leonard C Schalkwyk, Wenjie Sun, Shyam Prabhakar, Daniel H. Geschwind, Jonathan Mill
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.12276

Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers
Cited by: 15
Author(s): Sameer Chopra, Jie Liu, Mehrdad Alemozaffar, Peter W. Nichols, Manju Aron, Daniel J. Weisenberger, Clayton K. Collings, Sumeet Syan, Brian Hu, Mihir Desai, Monish Aron, Vinay Duddalwar, Inderbir S. Gill, Gangning Liang, Kimberly D. Siegmund
Software Mentions: 3
Published: about 8 years ago

10.1093/aje/kwy155

Socioeconomic Position and DNA Methylation Age Acceleration Across the Life Course
Cited by: 72
Author(s): Amanda Hughes, Melissa Smart, T.J. Gorrie-Stone, Eilís Hannon, Jonathan Mill, Yanchun Bao, Joe Burrage, Leo Schalkwyk, Meena Kumari
Software Mentions: 2
Published: over 6 years ago

10.3389/fnins.2020.555307

Characteristics of Epigenetic Clocks Across Blood and Brain Tissue in Older Women and Men
Cited by: 29
Author(s): Francine Grodstein, Bernardo Lemos, Lei Yu, Artemis Iatrou, Philip L. De Jager, David A. Bennett
Software Mentions: 2
Published: almost 4 years ago

10.3389/fphar.2018.00207

Epigenome-Wide Association Study of Soluble Tumor Necrosis Factor Receptor 2 Levels in the Framingham Heart Study
Cited by: 9
Author(s): Michael Mendelson, Roby Johannes, Chunyu Liu, Tianxiao Huan, Chen Yao, Xiao Miao, Joanne M. Murabito, Josée Dupuis, Daniel Levy, Emelia J. Benjamin, Honghuang Lin
Software Mentions: 2
Published: over 6 years ago

10.1111/cdev.12957

A Methylome-Wide Association Study of Trajectories of Oppositional Defiant Behaviors and Biological Overlap With Attention Deficit Hyperactivity Disorder
Cited by: 17
Author(s): Edward D. Barker, Esther Walton, Charlotte A.M. Cecil, Richard Rowe, Sara R. Jaffee, Barbara Maughan, Thomas G. O’Connor, Argyris Stringaris, Alan J. Meehan, Wendy L. McArdle, Caroline L Relton, Tom R. Gaunt
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-016-0871-x

Variation in 5-hydroxymethylcytosine across human cortex and cerebellum
Cited by: 76
Author(s): Katie Lunnon, Eilís Hannon, Rebecca Smith, Emma Dempster, Chloe Wong, Joe Burrage, Claire Troakes, Safa Al‐Sarraj, Agnieszka Kepa, Leonard C. Schalkwyk, Jonathan Mill
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41380-020-0734-4

Epigenome-wide association study and multi-tissue replication of individuals with alcohol use disorder: evidence for abnormal glucocorticoid signaling pathway gene regulation
Cited by: 23
Author(s): Falk W. Lohoff, Arunima Roy, Jeesun Jung, Martha Longley, Daniel Rosoff, Audrey Luo, Emma M. O’Connell, Jill L. Sorcher, Hui Sun, Melanie L. Schwandt, Colin A. Hodgkinson, David Goldman, Reza Momenan, Andrew M. McIntosh, Mark Adams, Rosie M. Walker, Kathryn Evans, David J. Porteous, Alicia K. Smith, Sang Hoon Lee, Christine Muench, Katrin Charlet, Toni Clarke, Zachary Kaminsky
Software Mentions: 2
Published: over 4 years ago

10.1186/s13041-021-00810-w

Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons
Cited by: 14
Author(s): Leonard C. Steg, Gemma Shireby, Jennifer Imm, Jonathan Davies, Alison S. Franklin, Robert J. Flynn, Seema C. Namboori, Akshay Bhinge, Aaron R. Jeffries, Joe Burrage, Grant W. A. Neilson, Emma Walker, Leo Perfect, John Price, Gráinne McAlonan, Deepak P. Srivastava, Nicholas John Bray, Emma L Cope, Kimberley M Jones, Nicholas Denby Allen, Ehsan Pishva, Emma Dempster, Katie Lunnon, Jonathan Mill, Eilís Hannon
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07675-2

DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy
Cited by: 8
Author(s): Yucheng Wang, Eilís Hannon, Olivia A Grant, T.J. Gorrie-Stone, Meena Kumari, Jonathan Mill, Xiaojun Zhai, Klaus D. McDonald-Maier, Leonard C Schalkwyk
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.8278

Methylomic predictors demonstrate the role of NF-κB in old-age mortality and are unrelated to the aging-associated epigenetic drift
Cited by: 8
Author(s): Juulia Jylhävä, Laura Kananen, Jani Raitanen, Saara Marttila, Tapio Nevalainen, Antti Hervonen, Marja Jylhä, Mikko Hurme
Software Mentions: 2
Published: over 8 years ago

10.1038/tp.2016.249

Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide
Cited by: 61
Author(s): Therese M. Murphy, Bethany Crawford, Emma Dempster, Eilís Hannon, Joe Burrage, Gustavo Turecki, Zachary Kaminsky, Jonathan Mill
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-015-1381-z

Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression
Cited by: 105
Author(s): Saara Marttila, Laura Kananen, Sergei Häyrynen, Juulia Jylhävä, Tapio Nevalainen, Antti Hervonen, Marja Jylhä, Matti Nykter, Mikko Hurme
Software Mentions: 2
Published: over 9 years ago

10.1038/s41398-017-0070-x

Genetic estimators of DNA methylation provide insights into the molecular basis of polygenic traits
Cited by: 12
Author(s): Virginie Freytag, Vanja Vukojević, Holger Wagner-Thelen, Annette Milnik, Christian Vogler, Markus Leber, Leonie Weinhold, Anne C. Böhmer, Steffi G. Riedel‐Heller, Wolfgang Maier, Dominique J.‐F. de Quervain, Alfredo Ramı́rez, Andreas Papassotiropoulos
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41398-019-0407-8

Longitudinal investigation of DNA methylation changes preceding adolescent psychotic experiences
Cited by: 14
Author(s): Stephen K. Roberts, Matthew Suderman, Stanley Zammit, Sarah Watkins, Eilís Hannon, Jonathan Mill, Caroline L Relton, Louise Arseneault, Chloe Wong, Helen L. Fisher
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13148-021-01150-1

Epigenetic age is associated with baseline and 3-year change in frailty in the Canadian Longitudinal Study on Aging
Cited by: 21
Author(s): Chris P. Verschoor, David T.S. Lin, Michæl S. Kobor, Oxana Mian, Jinhui Ma, Guillaume Paré, Gustavo Ybazeta
Software Mentions: 2
Published: about 3 years ago

10.1186/s13148-015-0128-7

Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma
Cited by: 19
Author(s): Pablo Conesa‐Zamora, José García‐Solano, María del Carmen Turpin, Patricia Sebastián-León, Daniel Torres-Moreno, Eduardo Estrada, Anne Tuomisto, Jamie Wilce, Markus J. Mäkinen, Miguel Pérez‐Guillermo, Ana Conesa
Software Mentions: 2
Published: about 9 years ago

10.1186/s13148-019-0780-4

Changes in DNA methylation from pre- to post-adolescence are associated with pubertal exposures
Cited by: 30
Author(s): Luhang Han, Hongmei Zhang, Akhilesh Kaushal, Faisal I. Rezwan, Latha Kadalayil, Wilfried Karmaus, A. John Henderson, Caroline L Relton, Susan M. Ring, Syed Hasan Arshad, Susan Ewart, John W. Holloway
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13148-018-0571-3

Two histologically colorectal carcinomas subsets from the serrated pathway show different methylome signatures and diagnostic biomarkers
Cited by: 12
Author(s): José García‐Solano, María C. Turpín, Daniel Torres-Moreno, Francisco Huertas-López, Anne Tuomisto, Markus J. Mäkinen, Ana Conesa, Pablo Conesa‐Zamora
Software Mentions: 2
Published: about 6 years ago

10.1155/2018/2624981

Assessing the Role of DNA Methylation-Derived Neutrophil-to-Lymphocyte Ratio in Rheumatoid Arthritis
Cited by: 12
Author(s): Srikant Ambatipudi, Gemma C Sharp, Sarah L N Clarke, Darren Plant, Jonathan H Tobias, David M. Evans, Anne Barton, Caroline L Relton
Software Mentions: 2
Published: over 6 years ago

10.3389/fnbeh.2018.00125

Prenatal Alcohol Exposure Is Associated With Adverse Cognitive Effects and Distinct Whole-Genome DNA Methylation Patterns in Primary School Children
Cited by: 18
Author(s): Stefan Frey, Anna Eichler, Valeska Stonawski, Jennifer Kriebel, Simone Wahl, Sabina Gallati, Tamme W. Goecke, Peter A. Fasching, Matthias W. Beckmann, Oliver Kratz, Gunther H. Moll, Hartmut Heinrich, Johannes Kornhuber, Yulia Golub
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0193271

Placental CpG methylation of infants born extremely preterm predicts cognitive impairment later in life
Cited by: 26
Author(s): Sloane K. Tilley, Elizabeth M. Martin, Lisa Smeester, Robert M. Joseph, Karl Kuban, Timothy Heeren, Olaf Dammann, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0174265

Targeted deep sequencing of plasma circulating cell-free DNA reveals Vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma
Cited by: 44
Author(s): Reetta Holmila, Athéna Sklias, David C. Muller, Davide Degli Esposti, Paule Guilloreau, James McKay, Suleeporn Sangrajrang, Petcharin Srivatanakul, Pierre Hainaut, Philippe Merle, Zdenko Herceg, André Nogueira da Costa
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1006034

Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure
Cited by: 27
Author(s): J. G. Smith, Janine F. Felix, Alanna C. Morrison, Ανδρέας Καλογερόπουλος, Stella Trompet, Jemma B. Wilk, Olof Gidlöf, Xinchen Wang, Michael Morley, Michael Mendelson, Roby Joehanes, Symen Ligthart, Xiaoyin Shan, Joshua C. Bis, Ying A. Wang, Marketa Sjögren, Julius S. Ngwa, Jeffrey Brandimarto, David J. Stott, David Aguilar, Kenneth Rice, Howard D. Sesso, Serkalem Demissie, Brendan M. Buckley, Kent D. Taylor, Ian Ford, Chen Yao, Chunyu Liu, Nona Sotoodehnia, Pim van der Harst, Bruno H. Ch. Stricker, Stephen B. Kritchevsky, Yongmei Liu, J. Michael Gaziano, Albert Hofman, Christine S. Moravec, André G. Uitterlinden, M Kellis, Joyce B. J. van Meurs, Kenneth B. Margulies, Abbas Dehghan, Daniel Levy, Björn Olde, Bruce M. Psaty, L. Adrienne Cupples, J. Wouter Jukema, Luc Djoussé, Oscar H. Franco, Eric Boerwinkle, Laurie A. Boyer, Christopher Newton‐Cheh, Javed Butler, Ramachandran S. Vasan, Thomas P. Cappola, Nicholas L. Smith
Software Mentions: 2
Published: over 8 years ago

10.1111/jcpp.12740

Longitudinal epigenetic predictors of amygdala:hippocampus volume ratio
Cited by: 26
Author(s): Esther Walton, Charlotte A.M. Cecil, Matthew Suderman, Jingyu Liu, Jessica A. Turner, Vince D. Calhoun, Stefan Ehrlich, Caroline L Relton, Edward D. Barker
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005553

Metabolomic Quantitative Trait Loci (mQTL) Mapping Implicates the Ubiquitin Proteasome System in Cardiovascular Disease Pathogenesis
Cited by: 75
Author(s): William E. Kraus, Deborah M. Muoio, Robert C. Stevens, Damian M. Craig, James R. Bain, Elizabeth Grass, Carol Haynes, Lydia Coulter Kwee, Xuejun Qin, Dorothy H. Slentz, Deidre R. Krupp, Michael J. Muehlbauer, Elizabeth R. Hauser, Simon G. Gregory, Christopher B. Newgard, Svati H. Shah
Software Mentions: 2
Published: about 9 years ago

10.12688/wellcomeopenres.15136.1

Assessment of dried blood spots for DNA methylation profiling
Cited by: 18
Author(s): Richard M Martin, Louise MacGillivray, Sarah McCafferty, Nicola Wrobel, Lee Murphy, Shona M. Kerr, Stewart W. Morris, Archie Campbell, Andrew M. McIntosh, David J. Porteous, Kathryn Evans
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-016-0926-z

Systematic identification of genetic influences on methylation across the human life course
Cited by: 459
Author(s): Tom R. Gaunt, Hashem A. Shihab, Gibran Hemani, Josine L. Min, Geoff Woodward, Oliver Lyttleton, Jie Zheng, Aparna Duggirala, Wendy L. McArdle, Karen Ho, Susan M. Ring, David M. Evans, George Davey Smith, Caroline L Relton
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0188664

Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation-related genes
Cited by: 17
Author(s): Martha Scott Tomlinson, Paige A. Bommarito, Elizabeth M. Martin, Lisa Smeester, Raina N. Fichorova, Andrew B. Onderdonk, Karl Kuban, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13148-015-0163-4

Methylomic markers of persistent childhood asthma: a longitudinal study of asthma-discordant monozygotic twins
Cited by: 35
Author(s): Therese M. Murphy, Chloe Wong, Louise Arseneault, Joe Burrage, Robert C. MacDonald, Eilís Hannon, Helen L. Fisher, Antony Ambler, Terrie E. Moffitt, Avshalom Caspi, Jonathan Mill
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41398-020-0752-7

Genome-wide DNA methylation meta-analysis in the brains of suicide completers
Cited by: 28
Author(s): Stefania Policicchio, Sam Washer, Joana Viana, Artemis Iatrou, Joe Burrage, Eilís Hannon, Gustavo Turecki, Zachary Kaminsky, Jonathan Mill, Emma Dempster, Therese M. Murphy
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms160511259

The Potential Role of DNA Methylation in Abdominal Aortic Aneurysms
Cited by: 26
Author(s): Evan J. Ryer, Kaitryn E. Ronning, Robert Erdman, Charles M. Schworer, James R. Elmore, Thomas C. Peeler, Christopher D. Nevius, John H. Lillvis, Robert P. Garvin, David P. Franklin, Helena Kuivaniemi, Gerard Tromp
Software Mentions: 1
Published: over 9 years ago

10.1038/tp.2016.247

DNA methylation and substance-use risk: a prospective, genome-wide study spanning gestation to adolescence
Cited by: 86
Author(s): Charlotte A.M. Cecil, Esther Walton, Rebecca Smith, Essi Viding, Eamon McCrory, Caroline L Relton, Matthew Suderman, Jean‐Baptiste Pingault, Wendy L. McArdle, Tom R. Gaunt, Jonathan Mill, Edward D. Barker
Software Mentions: 1
Published: almost 8 years ago

10.1111/jcpp.12589

Prenatal unhealthy diet, insulin-like growth factor 2 gene (<i>IGF2</i>) methylation, and attention deficit hyperactivity disorder symptoms in youth with early-onset conduct problems
Cited by: 66
Author(s): Jolien Rijlaarsdam, Charlotte A.M. Cecil, Esther Walton, Maurissa Sydney Chapman Mesirow, Caroline L Relton, Tom R. Gaunt, Wendy L. McArdle, Edward D. Barker
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: wateRmelon

Papers Mentioning wateRmelon 108