bioconductor: ChAMP | 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: about 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

10.3389/fonc.2020.01317

The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study
Cited by: 17
Author(s): Hao Gu, Lu-Lu Lin, Zhang Chao, Min Yang, Hongshan Zhong, Renxiong Wei
Software Mentions: 13
Published: about 4 years ago

10.1093/bioinformatics/bty713

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: almost 6 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

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: over 6 years ago

10.1186/s13059-021-02484-y

Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications
Cited by: 5
Author(s): Benjamin Planterose Jiménez, Manfred Kayser, Athina Vidaki
Software Mentions: 10
Published: almost 3 years ago

10.3390/ijms22031190

Genome-Wide DNA Methylation Analysis of a Cohort of 41 Patients Affected by Oculo-Auriculo-Vertebral Spectrum (OAVS)
Cited by: 12
Author(s): Valentina Guida, Luciano Calzari, Maria Teresa Fadda, Francesca Piceci‐Sparascio, María Cristina Digilio, Laura Bernardini, Francesco Brancati, Teresa Mattina, Daniela Melis, Francesca Forzano, Silvana Briuglia, Tommaso Mazza, Sebastiano Bianca, Enza Maria Valente, Leila Bagherjad Salehi, Paolo Prontera, Mario Pagnoni, Romano Tenconi, Bruno Dallapiccola, Giorgio Iannetti, Luigi Corsaro, Alessandro De Luca, Davide Gentilini
Software Mentions: 10
Published: over 3 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: about 6 years ago

10.1007/s00401-020-02224-9

Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Cited by: 14
Author(s): Luke C. Dabin, Fernando Guntoro, Tracy Campbell, Tony Bélicard, Adam R. Smith, Rebecca G. Smith, Rachel Raybould, Jonathan M. Schott, Katie Lunnon, Peter Sarkies, John Collinge, Simon Mead, Emmanuelle Viré
Software Mentions: 10
Published: almost 4 years ago

10.3389/fonc.2021.624395

Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers
Cited by: 12
Author(s): Xiaonan Liu, Pei Wang, Xufei Teng, Zhang Zhang, Shuhui Song
Software Mentions: 9
Published: over 3 years ago

10.1186/s13073-015-0225-4

Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers
Cited by: 104
Author(s): Sarah Voisin, Markus Sällman Almén, Galina Yurevna Zheleznyakova, Lina Lundberg, Sanaz Zarei, Sandra Castillo, Fia Ence Eriksson, Emil Nilsson, Matthias Blüher, Yvonne Böttcher, Peter Kovacs, Jānis Kloviņš, Mathias Rask‐Andersen, Helgi B. Schiöth
Software Mentions: 9
Published: almost 9 years ago

10.3390/cancers13061189

Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers
Cited by: 10
Author(s): Siddesh Southekal, Nitish K. Mishra, Chittibabu Guda
Software Mentions: 9
Published: over 3 years ago

10.3389/fphar.2021.746910

Spermine-Related DNA Hypermethylation and Elevated Expression of Genes for Collagen Formation are Susceptible Factors for Chemotherapy-Induced Hand-Foot Syndrome in Chinese Colorectal Cancer Patients
Cited by: 3
Author(s): Mingming Li, Jiani Chen, Shaoqun Liu, Xiaomeng Sun, Huilin Xu, Qianmin Gao, Xintao Chen, Chaowen Xi, Doudou Huang, Yi Deng, Feng zhang, Shouhong Gao, Shi Qiu, Xin Tao, Jingwen Zhai, Hua Wei, Houshan Yao, Wansheng Chen
Software Mentions: 9
Published: almost 3 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: about 5 years ago

10.3390/cancers12030653

Molecular-Clinical Correlation in Pediatric Medulloblastoma: A Cohort Series Study of 52 Cases in Taiwan
Cited by: 6
Author(s): Kuo Sheng Wu, Donald Ming Tak Ho, Shiann-Tarng Jou, Alice L. Yu, Huy Tran, Muh Lii Liang, Hsin Hung Chen, Yi Yen Lee, Yi Wei Chen, Shih Chieh Lin, Feng Chi Chang, Meng‐Li Tsai, Yen‐Lin Liu, Hsin Lun Lee, Kevin Hsieh, Wen Chang Huang, Shian Ying Sung, Che-Chang Chang, Chun A. Changou, Kung‐Hao Liang, Tsung Han Hsieh, Yun Ru Liu, Meng En Chao, Chonghua Wan, Shing Shung Chu, Er Chieh Cho, Tai-Tong Wong
Software Mentions: 9
Published: over 4 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/s12964-021-00728-9

Multi-omics analysis of tumor angiogenesis characteristics and potential epigenetic regulation mechanisms in renal clear cell carcinoma
Cited by: 28
Author(s): Wenzhong Zheng, Shiqiang Zhang, Huan Guo, Xiaobao Chen, Zhangcheng Huang, Shaoqin Jiang, Mengqiang Li
Software Mentions: 8
Published: over 3 years ago

10.1080/15592294.2019.1603963

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects
Cited by: 32
Author(s): Jyotirmoy Das, Deepti Verma, Mika Gustafsson, Maria Lerm
Software Mentions: 8
Published: over 5 years ago

10.3390/cancers13143621

HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements
Cited by: 10
Author(s): Diego Camuzi, Luisa Aguirre Buexm, Simone De Queiroz Chaves Lourenço, Davide Degli Esposti, Cyrille Cuenin, Monique de Souza Almeida Lopes, Francesca Manara, Fazlur Rahman Talukdar, Zdenko Herceg, Luís Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima
Software Mentions: 8
Published: about 3 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: about 3 years ago

10.1186/s13058-018-1022-y

Clonal relatedness in tumour pairs of breast cancer patients
Cited by: 14
Author(s): Jana Biermann, Toshima Z. Parris, Szilárd Nemes, Anna Danielsson, Hanna Engqvist, Elisabeth Werner Rönnerman, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 8
Published: almost 6 years ago

10.3389/fnins.2021.682247

Decreased MEF2A Expression Regulated by Its Enhancer Methylation Inhibits Autophagy and May Play an Important Role in the Progression of Alzheimer’s Disease
Cited by: 8
Author(s): Hui Li, Rui Wang, Xuqi Guo, Yugang Jiang
Software Mentions: 7
Published: about 3 years ago

10.1136/jitc-2021-002467

Tumor microenvironment evaluation promotes precise checkpoint immunotherapy of advanced gastric cancer
Cited by: 75
Author(s): Dongqiang Zeng, Jiani Wu, Hongyu Luo, Yong Li, Jian Xiao, Jianjun Peng, Zilan Ye, Rui Zhou, Yunfang Yu, Gaofeng Wang, Na Huang, Jianhua Wu, Xiaoxiang Rong, Li Sun, Huiying Sun, Wenjun Qiu, Yuting Xue, Jianping Bin, Yulin Liao, Li N, Min Shi, Kyoung‐Mee Kim, Wangjun Liao
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12859-015-0568-2

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns
Cited by: 95
Author(s): Tiphaine Martin, İdil Yet, Pei-Chien Tsai, Jordana T. Bell
Software Mentions: 7
Published: over 9 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: over 3 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

10.1186/1756-8935-8-6

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

10.1038/s41598-020-64794-8

Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes
Cited by: 12
Author(s): Hanna Engqvist, Toshima Z. Parris, Jana Biermann, Elisabeth Werner Rönnerman, Peter Larsson, Karin Sundfeldt, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 7
Published: about 4 years ago

10.3389/fimmu.2020.02149

CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro
Cited by: 23
Author(s): Sandra Silva-Cardoso, Weiyang Tao, Chiara Angiolilli, Ana P Lopes, Cornelis P. J. Bekker, Abhinandan Devaprasad, Barbara Giovannone, Jaap van Laar, Marta Cossu, Wioleta Marut, Erik Hack, Rob J. de Boer, Marianne Boes, Timothy R D J Radstake, Aridaman Pandit
Software Mentions: 7
Published: almost 4 years ago

10.1002/cam4.3447

Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes
Cited by: 13
Author(s): Tobias Keßler, Anne Berberich, Ahmed Sadik, Felix Sahm, Thierry Gorlia, Christoph Meisner, Dirk C. Hoffmann, Antje Wick, Philipp Kickingereder, Petra Rübmann, Martin Bendszus, Christiane A. Opitz, Michael Weller, Martin van den Bent, Roger Stupp, Frank Winkler, Alba Ariela Brandes, Andreas von Deimling, Michael Platten, Wolfgang Wick
Software Mentions: 7
Published: almost 4 years ago

10.3389/fgene.2020.00634

Construction of a Comprehensive Multiomics Map of Hepatocellular Carcinoma and Screening of Possible Driver Genes
Cited by: 6
Author(s): Ziyu Liu, Yan Lin, Xing Gao, Rongyun Mai, Xuemin Piao, Jiazhou Ye, Rong Liang
Software Mentions: 7
Published: about 4 years ago

10.1002/jcsm.12556

An epigenetic clock for human skeletal muscle
Cited by: 58
Author(s): Sarah Voisin, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Kevin J. Ashton, Vernon G. Coffey, Thomas Doering, Jamie-Lee M Thompson, Christian Benedict, Jonathan Cedernaes, Maléne E. Lindholm, Jeffrey M. Craig, David S. Rowlands, Adam P. Sharples, Steve Horvath, Nir Eynon
Software Mentions: 7
Published: over 4 years ago

10.1186/s40478-020-00908-7

Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients
Cited by: 18
Author(s): Rasmus Rydbirk, Jonas Folke, Florence Busato, Elodie Roché, Alisha Shahzad Chauhan, Annemette Løkkegaard, Anne Mette Hejl, Matthias Bode, Morten Blaabjerg, Mette Møller, Erik Hvid Danielsen, Tomasz Brudek, Bente Pakkenberg, Jörg Tost, Susana Aznar
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-019-55453-8

MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
Cited by: 2
Author(s): Andigoni Malousi, Sofia Kouidou, Maria Tsagiopoulou, Nikos Papakonstantinou, Emmanouil Bouras, Elisavet Georgiou, Georgios Tzimagiorgis, Kostas Stamatopoulos
Software Mentions: 7
Published: over 4 years ago

10.3390/cancers12061461

PDX1 DNA Methylation Distinguishes Two Subtypes of Pancreatic Neuroendocrine Neoplasms with a Different Prognosis
Cited by: 19
Author(s): Gitta Boons, Timon Vandamme, Joe Ibrahim, Geert Roeyen, Ann Driessen, Dieter Peeters, Ben Lawrence, Cristin G. Print, Maria C. W. Peeters, Guy Van Camp, Ken Op de Beeck
Software Mentions: 6
Published: about 4 years ago

10.1007/s00401-018-1821-3

5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma
Cited by: 10
Author(s): Wioletta K. Glowacka, Harshika Jain, Makiko Okura, Abulizi Maimaitiming, Yasin Mamatjan, Romina Nejad, Hamza Farooq, Michael D. Taylor, Kenneth Aldape, Paul Kongkham
Software Mentions: 6
Published: over 6 years ago

10.1186/s12967-018-1751-9

Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
Cited by: 37
Author(s): Raúl Fernández Pérez, Pablo Santamarina, Juan Ramón Tejedor, Rocío G. Urdinguio, Julio Álvarez, P. Redon, Agustín F. Fernández, Mario F. Fraga, Empar Lurbe
Software Mentions: 6
Published: over 5 years ago

10.18632/oncotarget.10962

Epigenetic reprogramming and aberrant expression of PRAME are associated with increased metastatic risk in Class 1 and Class 2 uveal melanomas
Cited by: 85
Author(s): Matthew G. Field, Michael A. Durante, Christina L. Decatur, Berçin Tarlan, Kristen M. Oelschlager, John F. Stone, Jeffim N. Kuznetsov, Anne M. Bowcock, Stefan Kurtenbach, J. William Harbour
Software Mentions: 6
Published: almost 8 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: about 3 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: about 8 years ago

10.1002/1878-0261.12709

HPV‐related methylation‐based reclassification and risk stratification of cervical cancer
Cited by: 25
Author(s): Shuanying Yang, Ying Wu, Shuqian Wang, Peng Xu, Yao Deng, Meng Wang, Kang Liu, Tian Tian, Yuyao Zhu, Na Li, Linghui Zhou, Zhijun Dai, Huafeng Kang
Software Mentions: 6
Published: about 4 years ago

10.1186/s13148-018-0463-6

Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia
Cited by: 60
Author(s): Katherine Leavey, Samantha L. Wilson, Shannon Bainbridge, Wendy P. Robinson, Brian Cox
Software Mentions: 6
Published: over 6 years ago

10.1038/s42003-020-01479-y

Epigenetic landscape of pancreatic neuroendocrine tumours reveals distinct cells of origin and means of tumour progression
Cited by: 48
Author(s): Annunziata Di Domenico, Christodoulos P. Pipinikas, Renaud Maire, Konstantin Bräutigam, Cédric Simillion, Matthias S. Dettmer, Erik Vassella, Chrissie Thirlwell, Aurel Perren, Ilaria Marinoni
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2020.634634

A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers
Cited by: 17
Author(s): Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Qin Xiong, Menghuan Zhang
Software Mentions: 6
Published: over 3 years ago

10.1242/bio.058222

RNA-Seq reveals changes in human placental metabolism, transport and endocrinology across the first–second trimester transition
Cited by: 15
Author(s): Malwina Prater, Russell S. Hamilton, Hong Wa Yung, Andrew Sharkey, Paul Robson, N. Erlyani Abd Hamid, Eric Jauniaux, D. Stephen Charnock-Jones, Graham J. Burton, Tereza Cindrová‐Davies
Software Mentions: 6
Published: about 3 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: almost 8 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: almost 5 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: about 4 years ago

10.1093/gigascience/giaa066

CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes
Cited by: 5
Author(s): Sara-Jayne Thursby, Darin K Lobo, Kristina Pentieva, Shudong Zhang, Rachelle E Irwin, Colum P. Walsh
Software Mentions: 5
Published: about 4 years ago

10.1186/s12885-021-08645-3

Gene-associated methylation status of ST14 as a predictor of survival and hormone receptor positivity in breast Cancer
Cited by: 3
Author(s): Yang-Hong Dai, Ying-Fu Wang, Po-Chien Shen, Cheng‐Hsiang Lo, Juxiang Yang, Chun‐Shu Lin, Hsing‐Lung Chao, Weimin Huang
Software Mentions: 5
Published: almost 3 years ago

10.3389/fimmu.2021.590742

High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery
Cited by: 30
Author(s): Jessica Zielinski, Jason J. Luke, Silvia Guglietta, Carsten Krieg
Software Mentions: 5
Published: over 3 years ago

10.3389/fmed.2021.674338

Role of Immune Cell-Specific Hypermethylation Signatures in Classification and Risk Stratification of Breast Cancer
Cited by: 0
Author(s): Yong Chen, Fada Xia, Bo Jiang, Wenlong Wang, Xinying Li
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13072-015-0045-1

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay
Cited by: 11
Author(s): Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
Software Mentions: 5
Published: over 8 years ago

10.1080/15592294.2019.1656157

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

10.3390/cancers13123014

Upper Aerodigestive Tract Squamous Cell Carcinomas Show Distinct Overall DNA Methylation Profiles and Different Molecular Mechanisms behind WNT Signaling Disruption
Cited by: 6
Author(s): Sheila Coelho Soares-Lima, Hisham Mehanna, Diego Camuzi, Paulo Thiago de Souza-Santos, Tatiana de Almeida Simão, Pedro Nicolau-Neto, Monique de Souza Almeida Lopes, Cyrille Cuenin, Fazlur Rahman Talukdar, Nikolaos Batis, Izabella Costa, Fernando Luiz Dias, Davide Degli Esposti, Mariana Boroni, Zdenko Herceg, Luís Felipe Ribeiro Pinto
Software Mentions: 5
Published: about 3 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

10.3389/fgene.2021.676449

MeImmS: Predict Clinical Benefit of Anti-PD-1/PD-L1 Treatments Based on DNA Methylation in Non-small Cell Lung Cancer
Cited by: 8
Author(s): Shuai Shang, Xin Li, Yue Gao, Shuang Guo, Di Sun, Hongliang Zhou, Yue Sun, Peng Wang, Hui Zhi, Jing Bai, Shangwei Ning
Software Mentions: 5
Published: about 3 years ago

10.18632/oncotarget.26032

Comprehensive analysis identifying aberrant DNA methylation in rectal mucosa from ulcerative colitis patients with neoplasia
Cited by: 6
Author(s): Yuji Toiyama, Yoshinaga Okugawa, Satoru Kondo, Yoshiki Okita, Toshimitsu Araki, Kurando Kusunoki, Motoi Uchino, Hiroki Ikeuchi, Seiichi Hirota, Akira Mitsui, Kenji Takehana, Tsutomu Umezawa, Masato Kusunoki
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13148-021-01083-9

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

10.1186/s13148-021-01149-8

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

10.3390/ijms22073735

Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders
Cited by: 6
Author(s): Guillaume Velasco, Damien Ulveling, Sophie Rondeau, Pauline Marzin, Motoko Unoki, Valérie Cormier‐Daire, Claire Francastel
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2020.00557

Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer
Cited by: 10
Author(s): Nan Xiao, Yang Hu, Liran Juan
Software Mentions: 5
Published: about 4 years ago

10.3389/fphar.2021.616529

Systematic Investigation of DNA Methylation Associated With Platinum Chemotherapy Resistance Across 13 Cancer Types
Cited by: 4
Author(s): Ruizheng Sun, Chao Du, Jiaxin Li, Yanhong Zhou, Xiong Wang, Juanjuan Xiang, Jiheng Liu, Zhifeng Xiao, Fang Li, Li Zheng
Software Mentions: 5
Published: about 3 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: about 3 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: almost 7 years ago

10.3390/ijms21186853

DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa
Cited by: 7
Author(s): Nina Milutin Gašperov, Ivan Sabol, Ksenija Božinović, Emil Dediol, Marinka Mravak‐Stipetić, Danilo Licastro, Simeone Dal Monego, Magdalena Grce
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13073-018-0575-9

Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins
Cited by: 60
Author(s): Amy P Webster, Darren Plant, Simone Ecker, Flore Zufferey, Jordana T. Bell, Andrew Feber, Dirk S. Paul, Stephan Beck, Anne Barton, Frances Williams, Jane Worthington
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13148-021-01115-4

Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells
Cited by: 7
Author(s): Johanna Huoman, David Martínez-Enguita, Elin Olsson, Jan Ernerudh, Lennart Nilsson, Karel Duchén, Mika Gustafsson, Maria C. Jenmalm
Software Mentions: 4
Published: about 3 years ago

10.3390/cancers12030680

Global RNA Expression and DNA Methylation Patterns in Primary Anaplastic Thyroid Cancer
Cited by: 14
Author(s): Naveen Ravi, Minjun Yang, Nektaria Mylona, Johan Wennerberg, Kajsa Paulsson
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02230-w

Comprehensive integrative profiling of upper tract urothelial carcinomas
Cited by: 27
Author(s): Xiaoping Su, Xiaofan Lu, Sehrish K. Bazai, Éva Compérat, Roger Mouawad, Hui Yao, Morgan Rouprêt, Jean Philippe Spano, David Khayat, Irwin Davidson, Nizar Tannir, Fangrong Yan, Gabriel G. Malouf
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.640266

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

10.3389/fgene.2021.563051

Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: over 3 years ago

10.1016/j.heliyon.2021.e06000

Unsupervised subtyping and methylation landscape of pancreatic ductal adenocarcinoma
Cited by: 9
Author(s): Shikha Roy, Amar Singh, Dinesh Gupta
Software Mentions: 4
Published: over 3 years ago

10.15252/embj.2019103790

Microglia promote glioblastoma via mTOR‐mediated immunosuppression of the tumour microenvironment
Cited by: 69
Author(s): Anaëlle Dumas, Nicola Pomella, Gabriel Rosser, Loredana Guglielmi, Claire Vinel, Thomas O Millner, Jeremy Rees, Natasha Aley, Denise Sheer, Jun Wei, Anantha Marisetty, Amy B. Heimberger, Robert L. Bowman, Sebastian Brandner, Johanna A. Joyce, Silvia Marino
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-020-06886-3

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data
Cited by: 8
Author(s): Yadollah Shahryary, Rashmi R. Hazarika, Frank Johannes
Software Mentions: 4
Published: about 4 years ago

10.3389/fendo.2021.690648

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

10.7717/peerj.7107

Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
Cited by: 8
Author(s): Juchuanli Tu, Xiaolu Li, Jianjun Wang
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2019.00801

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

10.1186/s13148-018-0530-z

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

10.1186/gb-2014-15-2-r30

Using high-density DNA methylation arrays to profile copy number alterations
Cited by: 109
Author(s): Andrew Feber, Paul Guilhamon, Matthias Lechner, Tim R. Fenton, Gareth A. Wilson, Christina Thirlwell, Tiffany Morris, Adrienne M. Flanagan, Andrew E. Teschendorff, John D. Kelly, Stephan Beck
Software Mentions: 4
Published: over 10 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: over 3 years ago

10.1038/s41597-019-0205-4

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

10.1371/journal.ppat.1009785

Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART
Cited by: 9
Author(s): Michael J. Corley, Carlo Sacdalan, Alina P.S. Pang, Nitiya Chomchey, Nisakorn Ratnaratorn, Victor Valcour, Eugène Kroon, Kyu S. Cho, Andrew C. Belden, Donn Colby, Merlin L. Robb, Denise C. Hsu, Serena Spudich, Robert Paul, Sandhya Vasan, Lishomwa C. Ndhlovu, Rv study groups
Software Mentions: 4
Published: almost 3 years ago

10.1038/s42003-020-01469-0

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association
Cited by: 27
Author(s): Vanessa Lakis, Rita T. Lawlor, Felicity Newell, Ann‐Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michèle Milella, David K. Chang, Peter J. Bailey, Nigel B. Jamieson, Fraser Duthie, Marie‐Claude Gingras, Donna M. Muzny, David A. Wheeler, Richard A. Gibbs, Massimo Milione, Apgi, ARC-Net, Paolo Pederzoli, Jaswinder S. Samra, Anthony J. Gill, Amber Johns, John V. Pearson, Andrew V. Biankin, Sean M. Grimmond, Nicola Waddell, Kátia Nones, Aldo Scarpa
Software Mentions: 4
Published: over 3 years ago

10.1186/s13148-021-01161-y

Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes
Cited by: 12
Author(s): Lyndsey E. Shorey‐Kendrick, Cindy T. McEvoy, Shannon M. O’Sullivan, Kristin Milner, Brittany Vuylsteke, Robert S. Tepper, David M. Haas, Byung Park, Lina Gao, Annette Vu, Cynthia D. Morris, Eliot R. Spindel
Software Mentions: 4
Published: almost 3 years ago

10.3389/fphys.2019.00917

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

10.1186/s13014-021-01853-y

Complete response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT mutations and high tumour mutational burden
Cited by: 4
Author(s): Joanne Stockton, Louise Tee, Celina M. Whalley, Jonathan James, Mark Dilworth, Rachel Wheat, Thomas Nieto, Ian Geh, João D. Barros-Silva, Andrew D Beggs
Software Mentions: 4
Published: about 3 years ago

10.1186/s13148-020-0822-y

Epigenetic age acceleration of cervical squamous cell carcinoma converged to human papillomavirus 16/18 expression, immunoactivation, and favourable prognosis
Cited by: 13
Author(s): Xiaofan Lu, Yu Jie Zhou, Jialin Meng, Liyun Jiang, Jun Gao, Xiaohu Fan, Yanfeng Chen, Changhong Yu, Yang Wang, Bing Zhang, Hangyu Yan, Fangrong Yan
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-020-00847-z

The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation
Cited by: 14
Author(s): Kang Li, Ling Qin, Sanjie Jiang, Ang Li, Chi Zhang, Guihai Liu, Jianping Sun, Haolin Sun, Yan Zhao, Ning Li, Yonghong Zhang
Software Mentions: 3
Published: about 4 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: almost 7 years ago

10.3390/cancers11111650

The Role of Aberrant DNA Methylation in Misregulation of Gene Expression in Gonadotroph Nonfunctioning Pituitary Tumors
Cited by: 10
Author(s): Paulina Kober, Joanna Boresowicz, Natalia Rusetska, Maria Maksymowicz, Agnieszka Paziewska, Michalina Dąbrowska, Jacek Kunicki, Wiesław Bonicki, Jerzy Ostrowski, Janusz A. Siedlecki, Mateusz Bujko
Software Mentions: 3
Published: almost 5 years ago

10.18632/aging.101992

Investigation of bidirectional longitudinal associations between advanced epigenetic age and peripheral biomarkers of inflammation and metabolic syndrome
Cited by: 13
Author(s): Filomene G. Morrison, Mark W. Logue, Dafne Guetta, Hannah Maniates, Annjanette Stone, Steven A. Schichman, Regina E. McGlinchey, William Milberg, Mark W. Miller, Erika J. Wolf
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0171694

An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology
Cited by: 2
Author(s): Buğra Özer, Uğur Sezerman
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-020-03559-6

Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies
Cited by: 38
Author(s): Tristan Zindler, Helge Frieling, Alexandra Neyazi, Stefan Bleich, Eva Friedel
Software Mentions: 3
Published: about 4 years ago

10.1155/2021/6697848

Identification of Molecular Regulatory Features and Markers for Acute Type A Aortic Dissection
Cited by: 5
Author(s): Rui Li, Guochao Zhang, Shaomin Yan, Lichao Sun, Guoqiang Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00301

Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer
Cited by: 12
Author(s): Yanshen Kuang, Ying Wang, Wanli Zhai, Xuning Wang, Bingdong Zhang, Maolin Xu, Shaohua Guo, Mu Ke, Baoqing Jia, Hongyi Liu
Software Mentions: 3
Published: over 4 years ago

10.3390/genes12091433

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

10.3390/genes12091408

Years of Schooling Could Reduce Epigenetic Aging: A Study of a Mexican Cohort
Cited by: 1
Author(s): Juan Carlos Gómez-Verján, Marcelino Esparza-Aguilar, Verónica Martín-Martín, Cecilia Salazar-Pérez, Cinthya Cadena-Trejo, Luis Miguel Gutiérrez‐Robledo, José Jaime Martínez‐Magaña, Humberto Nicolini, Pedro Arroyo
Software Mentions: 3
Published: almost 3 years ago

Projects: bioconductor: ChAMP

Papers Mentioning ChAMP 208