Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: wateRmelon
https://packages.ecosyste.ms/registries/bioconductor.org/packages/wateRmelon
Illumina 450 and EPIC methylation array normalization and metrics
1 version
Latest release: about 1 year ago
5 dependent packages
123,443 downloads total
Papers Mentioning wateRmelon 108
10.1186/s13059-021-02388-x
Gene set enrichment analysis for genome-wide DNA methylation dataCited by: 61
Author(s): Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
Software Mentions: 16
Published: over 3 years ago
10.1093/bioinformatics/bty713
Bigmelon: tools for analysing large DNA methylation datasetsCited 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 expressionCited 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 cancerCited 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 scoreCited 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 dataCited 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 agingCited 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 dissimilarityCited 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 CarcinomaCited by: 2
Author(s): Dan Luo, Xiang Zhang, Xiaokai Li, Gang Chen
Software Mentions: 7
Published: about 3 years ago
10.1186/s13148-021-01145-y
Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profileCited 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
10.1371/journal.pone.0229763
Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platformCited 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 regionCited 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 BeadChipCited 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 dysregulationCited 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 adenocarcinomaCited 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 mucosaCited 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 associationsCited 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 exacerbationsCited 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 analysesCited 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 BloodCited 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 schizophreniaCited 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 carcinomaCited 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 surveyCited 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 osteoarthritisCited 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: about 7 years ago
10.1186/s12864-016-2819-7
An evaluation of processing methods for HumanMethylation450 BeadChip dataCited 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 studyCited 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 dataCited 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 diseaseCited 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 individualsCited 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 developmentCited 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 severityCited 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 methylationCited 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 epidemiologyCited 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 variantsCited 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 cortexCited 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 carcinomaCited by: 7
Author(s): Hengyu Chen, Xianxiong Ma, Ming Yang, Mengyi Wang, Lei Li, Tao Huang
Software Mentions: 4
Published: about 4 years ago
10.1186/s13148-016-0281-7
Effect of prenatal DHA supplementation on the infant epigenome: results from a randomized controlled trialCited 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 smokingCited 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 managementCited 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 microdeletionCited 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 GABBR1Cited 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 brainCited 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 cellsCited 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 diseasesCited 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 statusCited 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 studyCited 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 networkCited 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 methylationCited 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 TraitsCited 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 arrayCited 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 BeadChipCited 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 placentaCited 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 twinsCited 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 exposureCited 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 diseaseCited 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 modelCited 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 carcinomasCited 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 dataCited 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 DifferentiationCited 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 TraitsCited 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 taleCited 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 progressionCited 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 CYP2E1Cited 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 adversityCited 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 diseaseCited 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 regionsCited 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 tissueCited 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 markersCited 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 CourseCited 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 MenCited 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 StudyCited 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 DisorderCited 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 cerebellumCited 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: over 8 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 regulationCited 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 neuronsCited 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 aneuploidyCited 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 driftCited 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 suicideCited 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 expressionCited 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 traitsCited 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 experiencesCited 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 AgingCited 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 carcinomaCited 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 exposuresCited 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 biomarkersCited 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: almost 6 years ago
10.1155/2018/2624981
Assessing the Role of DNA Methylation-Derived Neutrophil-to-Lymphocyte Ratio in Rheumatoid ArthritisCited 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: about 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 ChildrenCited 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 lifeCited 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 carcinomaCited 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 FailureCited 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 ratioCited 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 PathogenesisCited 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 profilingCited 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 courseCited 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 genesCited 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 twinsCited 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 completersCited 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: over 4 years ago
10.3390/ijms160511259
The Potential Role of DNA Methylation in Abdominal Aortic AneurysmsCited 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 adolescenceCited 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 problemsCited 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: about 8 years ago