Ecosyste.ms: Papers

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: almost 5 years ago

10.3389/fgene.2014.00324

Statistical methods for detecting differentially methylated loci and regions
Cited by: 90
Author(s): Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Małgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou
Software Mentions: 9
Published: about 10 years ago

10.18632/oncotarget.12122

Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis
Cited by: 37
Author(s): Jing Hu, Jiu Hua Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Xu Chun, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 8 years ago

10.1038/sdata.2016.90

Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice
Cited by: 5
Author(s): Tonatiuh Peña Centeno, Orr Shomroni, Magali Hennion, Rashi Halder, Ramón Vidal, Raza-Ur Rahman, Stefan Bonn
Software Mentions: 7
Published: about 8 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

10.1038/s42003-021-02217-8

LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames
Cited by: 6
Author(s): Martin Blythe, Ayhan Kocer, Alejandro Rubio-Roldán, Tom Giles, Abdulkadir Abakir, Côme Ialy-Radio, Lee M. Wheldon, Oxana Bereshchenko, Stefano Bruscoli, Alexander Kondrashov, Joël R. Drevet, Richard D. Emes, Andrew D. Johnson, John R. McCarrey, Daniel Gackowski, Julie Cocquet, José L. García‐Pérez, Alexey Ruzov
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22010078

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts
Cited by: 10
Author(s): Paulina Kołodziej-Wojnar, Joanna Borkowska, Zofia Wicik, Anna Domaszewska-Szostek, Jacek Połosak, Marta Cąkała-Jakimowicz, Olga Bujanowska, Monika Puzianowska-Kuźnicka
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13148-015-0123-z

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: about 9 years ago

10.3389/fgene.2021.745284

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats
Cited by: 2
Author(s): Laure Denoyelle, Pierre de Villemereuil, Frédéric Boyer, Meidhi Khelifi, Clément Gaffet, Florian J. Alberto, Badr Benjelloun, François Pompanon
Software Mentions: 6
Published: about 3 years ago

10.3389/fgene.2019.00766

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: about 5 years ago

10.1186/2047-217X-1-3

Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
Cited by: 40
Author(s): Gareth A. Wilson, Pawandeep Dhami, Andrew Feber, Daniel Cortázar, Yuka Suzuki, Reiner Schulz, Primo Schär, Stephan Beck
Software Mentions: 5
Published: over 12 years ago

10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome
Cited by: 20
Author(s): Jie Du, Lin Zhang
Software Mentions: 5
Published: over 9 years ago

10.1186/s13148-020-00888-4

Alternative methylation of intron motifs is associated with cancer-related gene expression in both canine mammary tumor and human breast cancer
Cited by: 13
Author(s): A-Reum Nam, Kanghoon Lee, Hyeon-Ji Hwang, Johannes J. Schabort, Jaehoon An, Sungho Won, Je‐Yoel Cho
Software Mentions: 5
Published: over 4 years ago

10.1186/gb-2014-15-2-r35

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
Cited by: 26
Author(s): Andrea Riebler, Mirco Menigatti, Jenny Z. Song, Aaron L. Statham, Clare Stirzaker, Nadiya Mahmud, Charles A. Mein, Susan J. Clark, Mark D. Robinson
Software Mentions: 5
Published: almost 11 years ago

10.1186/gb-2014-15-4-r56

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder
Cited by: 84
Author(s): Matthew N. Davies, Lutz Krause, Jordana T. Bell, Fei Gao, Kirsten Ward, Honglong Wu, Hanlin Lu, Yuan Liu, Pei-Chien Tsai, David A. Collier, Therese M. Murphy, Emma Dempster, Jonathan Mill, Alexis Battle, Sara Mostafavi, Xiaowei Zhu, Anjali K. Henders, Enda M. Byrne, Naomi R. Wray, Nicholas G. Martin, Tim D. Spector, Jun Wang
Software Mentions: 5
Published: almost 11 years ago

10.7554/eLife.57683

EHMT2 epigenetically suppresses Wnt signaling and is a potential target in embryonal rhabdomyosarcoma
Cited by: 14
Author(s): Ananya Pal, Jia Yu Leung, Gareth Chin Khye Ang, Vinay Kumar Rao, Luca Pignata, Huey Jin Lim, Maxime Hebrard, Kenneth Tou En Chang, Victor Kwan Min Lee, Ernesto Guccione, Reshma Taneja
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-016-0911-6

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
Cited by: 15
Author(s): Tarmo Äijö, Yun Huang, Henrik Mannerström, Lukas Chávez, Ageliki Tsagaratou, Anjana Rao, Harri Lähdesmäki
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2017.00175

Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury
Cited by: 21
Author(s): Arko Sen, Katherine Gurdziel, Jenney Liu, Qian Wen, Oluwademi O Nuga, Rayanne B. Burl, Maik Hüttemann, Roger Piqué-Regi, Douglas M. Ruden
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-014-0513-0

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator
Cited by: 120
Author(s): Ya-Ping Tsai, Hsiao-Fan Chen, Sung-Yuan Chen, Wei‐Chung Cheng, Hsei‐Wei Wang, Zih-Jie Shen, Chun-Xiao Song, Shan-Yuan Teng, Chuan He, Kou-Juey Wu
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-016-1158-7

DISMISS: detection of stranded methylation in MeDIP-Seq data
Cited by: 6
Author(s): Umar Niazi, Kathrin K. Geyer, Martin Vickers, Karl F. Hoffmann, Martin Swain
Software Mentions: 4
Published: over 8 years ago

10.1186/s12920-015-0139-4

Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis
Cited by: 27
Author(s): Hongying Zhao, Jiu Hua Xu, Lin Pang, Yunpeng Zhang, Huihui Fan, Ling Liu, Tingting Liu, Fulong Yu, Guanxiong Zhang, Yujia Lan, Jing Bai, Xia Li, Yun Xiao
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0029450

Global Analysis of DNA Methylation by Methyl-Capture Sequencing Reveals Epigenetic Control of Cisplatin Resistance in Ovarian Cancer Cell
Cited by: 67
Author(s): Wei Yu, Chengmeng Jin, Xiaoyan Lou, Xu Han, Lisha Li, Yinghua He, Hongyu Zhang, Kelong Ma, Jingde Zhu, Li-Hua Cheng, Biaoyang Lin
Software Mentions: 3
Published: almost 13 years ago

10.3389/fgene.2021.620241

Integrated Transcriptomic and Epigenetic Study of PCOS: Impact of Map3k1 and Map1lc3a Promoter Methylation on Autophagy
Cited by: 11
Author(s): Yanmin Qin, Ting Li, Hui Zhao, Zhanrui Mao, Chunmei Ding, Yani Kang
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00220

The DNA Methylation Status of Wnt and Tgfβ Signals Is a Key Factor on Functional Regulation of Skeletal Muscle Satellite Cell Development
Cited by: 13
Author(s): Weiya Zhang, Saixian Zhang, Yongming Xu, Yunlong Ma, Dingxiao Zhang, Xinyun Li, Shuhong Zhao
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0201854

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice
Cited by: 21
Author(s): Xiang Li, Hang Yu, Yamin Jiao, Muhammad Qasim Shahid, Jinwen Wu, Xiangdong Liu
Software Mentions: 3
Published: over 6 years ago

10.1186/gm536

Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases
Cited by: 21
Author(s): Gareth A. Wilson, Lee M. Butcher, Holly R. Foster, Andrew Feber, Christian Roos, Lutz Walter, Grzegorz Woszczek, Stephan Beck, Christopher G. Bell
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13059-016-1023-z

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Cited by: 54
Author(s): Xiaoli Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lü, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zongshu Shao, Ji Wu, Xiaodong Zhao
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-016-1051-8

Novel regional age-associated DNA methylation changes within human common disease-associated loci
Cited by: 27
Author(s): Christopher G. Bell, Yudong Xia, Wei Yuan, Fei Gao, Kirsten Ward, Leonie Roos, Massimo Mangino, Pirro G. Hysi, Jordana T. Bell, Jun Wang, Timothy D. Spector
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-018-2574-7

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data
Cited by: 6
Author(s): Jingting Xu, Shimeng Liu, Ping Yin, Serdar E. Bulun, Yang Dai
Software Mentions: 3
Published: almost 6 years ago

10.1093/bioinformatics/btt650

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Cited by: 246
Author(s): Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chávez
Software Mentions: 3
Published: almost 11 years ago

10.1111/1759-7714.13497

Integrated analysis of <scp>miRNAs</scp> and <scp>DNA</scp> methylation identifies <scp>miR‐132‐3p</scp> as a tumor suppressor in lung adenocarcinoma
Cited by: 7
Author(s): Yun Su, Amol Shetty, Feng Jiang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-017-10648-9

Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C
Cited by: 31
Author(s): Haifei Wang, Jiying Wang, Chao Ning, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jianfeng Liu
Software Mentions: 3
Published: about 7 years ago

10.1038/s41420-020-0264-5

Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells
Cited by: 6
Author(s): Fei He, Hao Wu, Libing Zhou, Qing Lin, Yin Chen, Yi Sun
Software Mentions: 3
Published: over 4 years ago

10.1016/j.celrep.2015.11.040

Context-Specific Effects of TGF-β/SMAD3 in Cancer Are Modulated by the Epigenome
Cited by: 37
Author(s): Ana Tufegdžić Vidaković, Oscar M. Rueda, Stephin J. Vervoort, Ankita Batra, Mae A. Goldgraben, Santiago Uribe-Lewis, Wendy Greenwood, Paul J. Coffer, Alejandra Bruna, Carlos Caldas
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-13-S6-S14

Methods for high-throughput MethylCap-Seq data analysis
Cited by: 16
Author(s): Blanca Rodriguez, David Frankhouser, Mark W. Murphy, Michael Trimarchi, Hok Hei Tam, John Curfman, Rita Huang, Michael W.Y. Chan, Hung Cheng Lai, Deval Parikh, Bryan Ball, Sebastian Schwind, William Blum, Guido Marcucci, Pearlly S. Yan, Ralf Bundschuh
Software Mentions: 3
Published: about 12 years ago

10.1038/s42003-021-02242-7

A human isogenic iPSC-derived cell line panel identifies major regulators of aberrant astrocyte proliferation in Down syndrome
Cited by: 11
Author(s): Keiji Kawatani, Toshihiko Nambara, Nobutoshi Nawa, Hidetaka Yoshimatsu, Haruna Kusakabe, Katsuya Hirata, Akira Tanave, Kenta Sumiyama, Kimihiko Banno, Hidetoshi Taniguchi, Hitomi Arahori, Keiichi Ozono, Yasuji Kitabatake
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.18290

Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
Cited by: 109
Author(s): Chan-Wang Jerry Lio, Jiayuan Zhang, Edahí González-Avalos, Patrick G. Hogan, Xing Chang, Anjana Rao
Software Mentions: 3
Published: almost 8 years ago

10.4161/epi.26017

DNA methylation analysis of murine hematopoietic side population cells during aging
Cited by: 42
Author(s): Oluwatosin Taiwo, Gareth A. Wilson, Warren Emmett, Tiffany Morris, Dominique Bonnet, Eugene F. Schuster, Tomas Adejumo, Stephan Beck, Daniel J. Pearce
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-020-57919-6

Novel genes exhibiting DNA methylation alterations in Korean patients with chronic lymphocytic leukaemia: a methyl-CpG-binding domain sequencing study
Cited by: 2
Author(s): Miyoung Kim, Eun-Yup Lee, Dae Young Zang, Hyo Jung Kim, Ho Young Kim, Boram Han, Han-Sung Kim, Hee Jung Kang, Seungwoo Hwang, Young Kyung Lee
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13072-019-0281-x

Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation
Cited by: 23
Author(s): Ting Zhang, Xiangying Guan, Un Lam Choi, Qiang Dong, Melody M. T. Lam, Jianming Zeng, Jun Xiong, Xianju Wang, Terence Chuen Wai Poon, Hongjie Zhang, Xuanjun Zhang, Hailin Wang, Ruiyu Xie, Bing Zhu, Gang Li
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-49440-2

Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice
Cited by: 23
Author(s): Carlos Díaz-Castillo, Raquel Chamorro-García, Toshihiro Shioda, Bruce Blumberg
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0138524

Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for BMD Variation
Cited by: 22
Author(s): Jigang Zhang, Lijun Tan, Chao Xu, Hao He, Qing Tian, Yu Zhou, Chuan Qiu, Xiang-Ding Chen, Hong‐Wen Deng
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-016-2794-z

MBDDiff: an R package designed specifically for processing MBDcap-seq datasets
Cited by: 3
Author(s): Yuanhang Liu, Desiree Wilson, Robin J. Leach, Yidong Chen
Software Mentions: 2
Published: over 8 years ago

10.1186/s12870-017-1055-x

Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation
Cited by: 14
Author(s): Hongjun Liu, Langlang Ma, Xuerong Yang, Lin Zhang, Xing Zeng, Shupeng Xie, Huanwei Peng, Shibin Gao, Hung-Ching Lin, Guangtang Pan, Yongrui Wu, Yaou Shen
Software Mentions: 2
Published: over 7 years ago

10.1186/s12918-016-0356-2

Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines
Cited by: 12
Author(s): Han‐Jung Chae, Sangseon Lee, Kenneth P. Nephew, Sun Kim
Software Mentions: 2
Published: almost 8 years ago

10.3390/biom10121677

Cell-Free DNA-Methylation-Based Methods and Applications in Oncology
Cited by: 27
Author(s): Francesca Galardi, Francesca De Luca, Dario Romagnoli, Chiara Biagioni, Erica Moretti, Laura Biganzoli, Angelo Di Leo, Ilenia Migliaccio, Luca Malorni, Matteo Benelli
Software Mentions: 2
Published: almost 4 years ago

10.1002/cam4.1605

Epigenetic silencing of miR‐1271 enhances MEK1 and TEAD4 expression in gastric cancer
Cited by: 17
Author(s): Byungho Lim, Hee‐Jin Kim, Haejeong Heo, Nanhyung Huh, Su‐Jin Baek, Jong‐Hwan Kim, Donghyuck Bae, Eun‐Hye Seo, Sang Il Lee, Kyu‐Sang Song, Seon‐Young Kim, Yong‐Sung Kim, Mirang Kim
Software Mentions: 2
Published: over 6 years ago

10.14202/vetworld.2020.1113-1125

Differential DNA methylation analysis across the promoter regions using methylated DNA immunoprecipitation sequencing profiling of porcine loin muscle
Cited by: 2
Author(s): Kaj Chokeshaiusaha, Denis Puthier, Thanida Sananmuang, Em-on Olanratmanee, Catherine Nguyen, Roongtham Kedkovid
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1003250

DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer
Cited by: 41
Author(s): Christina Grimm, Lukas Chávez, Mireia Vilardell, Alexandra L. Farrall, Sascha Tierling, Julia Böhm, Phillip Grote, Matthias Lienhard, Jörn Dietrich, Bernd Timmermann, Jörn Walter, Michal R. Schweiger, Hans Lehrach, Ralf Herwig, Bernhard G. Herrmann, Markus Morkel
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0179141

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq
Cited by: 10
Author(s): Dou Liu, Xiaoyun Jia, Hengling Wei, Shuli Fan, Hantao Wang, Yanliang Guo, Shan Duan, Chaoyou Pang, Shuang Yu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0178535

Genome-wide alteration in DNA hydroxymethylation in the sperm from bisphenol A-exposed men
Cited by: 46
Author(s): Huajun Zheng, Xiaoyu Zhou, De-Kun Li, Fang Yang, Hongjie Pan, Tianqi Li, Maohua Miao, Li R, Wei Yuan
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0063407

Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed
Cited by: 17
Author(s): Fred P. Davis, Sean R. Eddy
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0201586

Methylation-level inferences and detection of differential methylation with MeDIP-seq data
Cited by: 2
Author(s): Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chun-Fu Jiang, Xiyan Yang
Software Mentions: 2
Published: about 6 years ago

10.1186/s13148-016-0242-1

Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
Cited by: 31
Author(s): Nicklas Heine Staunstrup, Anna Starnawska, Mette Nyegaard, Lene Christiansen, Anders Lade Nielsen, Anders D. Børglum, Ole Mors
Software Mentions: 2
Published: over 8 years ago

10.1186/s13148-017-0337-3

Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue
Cited by: 31
Author(s): Matthew Devall, Rebecca Smith, Aaron R. Jeffries, Eilís Hannon, Matthew N. Davies, Leonard C Schalkwyk, Jonathan Mill, Michael N. Weedon, Katie Lunnon
Software Mentions: 2
Published: over 7 years ago

10.1016/j.dib.2017.11.031

Data on novel DNA methylation changes induced by valproic acid in human hepatocytes
Cited by: 3
Author(s): Jarno E J Wolters, SimoneGJ van Breda, Sandra Claessen, T.D. Kok, J.C.S. Kleinjans
Software Mentions: 2
Published: almost 7 years ago

10.1155/2019/4108474

Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
Cited by: 32
Author(s): Wei Xu, Jun Lü, Qiang Zhao, Jun Wu, Jingyong Sun, Baohui Han, Xiaodong Zhao, Yani Kang
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2020.02131

Genome-Wide Characterization of Host Transcriptional and Epigenetic Alterations During HIV Infection of T Lymphocytes
Cited by: 5
Author(s): Xi Zeng, J Tsui, Mai Shi, Jie Peng, Cyanne Ye Cao, Lea Ling-Yu Kan, Carol Lau, Yonghao Liang, Lingyi Wang, Li Liu, Zhiwei Chen, Stephen Kwok-Wing Tsui
Software Mentions: 2
Published: about 4 years ago

10.1017/S0016672316000136

Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions
Cited by: 11
Author(s): Anna Keravnou, Marios Ioannides, Kyriakos Tsangaras, Charalambos Loizides, Michael D. Hadjidaniel, Elisavet A. Papageorgiou, Skevi Kyriakou, Pavlos Antoniou, Petros Mina, Achilleas Achilleos, Maria Neofytou, Elena Kypri, Carolina Sismani, George Koumbaris, Philippos C. Patsalis
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12711-018-0384-z

Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans
Cited by: 33
Author(s): Johan Bélteky, Beatrix Agnvall, Lejla Bektic, Andrey Höglund, Per Jensen, Carlos Guerrero-Bosagna
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evaa181

Between-Generation Phenotypic and Epigenetic Stability in a Clonal Snail
Cited by: 2
Author(s): Mark W. Smithson, Jennifer L. M. Thorson, Ingrid Sadler‐Riggleman, Daniel Beck, Michael K. Skinner, Mark F. Dybdahl
Software Mentions: 2
Published: about 4 years ago

10.1186/s13073-017-0413-5

DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation
Cited by: 46
Author(s): Juan Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D. Spector, Richard Saffery, Jeffrey M. Craig, Jordana T. Bell
Software Mentions: 2
Published: over 7 years ago

10.1002/jbm4.10383

TET1 Directs Chondrogenic Differentiation by Regulating SOX9 Dependent Activation of Col2a1 and Acan In Vitro
Cited by: 8
Author(s): Piera Smeriglio, Fiorella C. Grandi, Sarah Taylor, Antoine Zalc, Nidhi Bhutani
Software Mentions: 2
Published: over 4 years ago

10.1186/s40104-019-0316-y

Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia
Cited by: 27
Author(s): Bo Zhang, Dongmei Ban, Xin Gou, Yawen Zhang, Lin Yang, Yangzom Chamba
Software Mentions: 2
Published: over 5 years ago

10.1038/srep14699

MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq
Cited by: 11
Author(s): Yun Xiao, Fulong Yu, Lin Pang, Hongying Zhao, Ling Liu, Guanxiong Zhang, Tingting Liu, Hongyi Zhang, Huihui Fan, Yan Zhang, Bo Pang, Xia Li
Software Mentions: 2
Published: about 9 years ago

10.1038/srep15435

DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues
Cited by: 21
Author(s): Zhongyin Zhou, Aimin Li, Ligang Wang, David M. Irwin, Liu Yan-hu, Dan Xu, Xu-Man Han, Lu Wang, Shi-Fang Wu, Lixian Wang, Hailian Xie, Yaping Zhang
Software Mentions: 2
Published: about 9 years ago

10.1038/srep39883

Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs
Cited by: 35
Author(s): Yalan Yang, Guoming Liang, Guanglin Niu, Yuanyuan Zhang, Rong Zhou, Yanfang Wang, Yulian Mu, Zhonglin Tang, Kui Li
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms22158009

Prenatal Trimethyltin Exposure Induces Long-Term DNA Methylation Changes in the Male Mouse Hippocampus
Cited by: 4
Author(s): Soon-Ae Kim, Chai Junghoon, Eun-Hye Jang
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.8473

Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers
Cited by: 6
Author(s): Alan Chong, Jing Xian Teo, Kenneth Ban
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms22189716

Early Embryo Exposure to Assisted Reproductive Manipulation Induced Subtle Changes in Liver Epigenetics with No Apparent Negative Health Consequences in Rabbit
Cited by: 5
Author(s): Ximo García‐Domínguez, Gianfranco Diretto, David S. Peñaranda, Sarah Frusciante, Victor García‐Carpintero, Joaquı́n Cañizares, J.S. Vicente, Francisco Marco‐Jiménez
Software Mentions: 1
Published: about 3 years ago

10.3791/61617

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
Cited by: 1
Author(s): Justin Cayford, Sara Herrera-da la Mata, Benjamin Joachim Schmiedel, Vivek Chandra, Pandurangan Vijayanand, Grégory Seumois
Software Mentions: 1
Published: about 4 years ago

10.1111/acel.12513

Short‐term calorie restriction ameliorates genomewide, age‐related alterations in<scp>DNA</scp>methylation
Cited by: 51
Author(s): Chul Hong Kim, Eun Kyeong Lee, Yeon Ja Choi, Hye Jin An, Hyeong Oh Jeong, Daeui Park, Byoung Chul Kim, Byung Pal Yu, Jong Bhak, Hae Yung Chung
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-07405-3

Interplay between maternal Slc6a4 mutation and prenatal stress: a possible mechanism for autistic behavior development
Cited by: 24
Author(s): Calvin Sjaarda, Patrick M. Hecht, Amy J. M. McNaughton, Audrina Zhou, Melissa Hudson, Melissa L. Will, Garth Smith, Muhammad Ayub, Ping Liang, Nansheng Chen, David Q. Beversdorf, Xudong Li
Software Mentions: 1
Published: about 7 years ago

10.1186/s13072-017-0136-2

MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination
Cited by: 25
Author(s): S. Radhakrishnan, Robert Literman, Beatriz Mizoguchi, Nicole Valenzuela
Software Mentions: 1
Published: over 7 years ago

10.1186/1756-8935-5-9

Genome-wide DNA methylation profiling of non-small cell lung carcinomas
Cited by: 55
Author(s): Renata Carvalho, Vanja Haberle, Jun Hou, Teus van Gent, Supat Thongjuea, Wilfred F. J. van IJcken, Christel Kockx, Rutger W. W. Brouwer, Erikjan Rijkers, Anieta M. Sieuwerts, John A. Foekens, Mirjam van Vroonhoven, Joachim Aerts, Frank Grosveld, Boris Lenhard, Sjaak Philipsen
Software Mentions: 1
Published: over 12 years ago

10.1186/s13072-018-0223-z

Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours
Cited by: 29
Author(s): Xin Sun, Justin C. St. John
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0050233

A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling
Cited by: 85
Author(s): Christine Clark, Priit Palta, Christopher Joyce, Carol Scott, Elin Grundberg, Panos Deloukas, Aarno Palotie, Alison J. Coffey
Software Mentions: 1
Published: almost 12 years ago

10.1186/s40246-015-0036-0

SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing
Cited by: 14
Author(s): Luisa A. Wakeling, Laura J. Ions, Suzanne M Escolme, Simon Cockell, Tianhong Su, Madhurima Dey, Emily V Hampton, Gail Jenkins, Linda Wainwright, Jill A. McKay, Dianne Ford
Software Mentions: 1
Published: over 9 years ago

10.1186/1129-2377-15-S1-A6

EHMTI-0048. Epigenetic changes in a rat model of migraine with aura
Cited by: 4
Author(s): Marta Vila‐Pueyo, Noèlia Fernàndez‐Castillo, Bru Cormand, Patricia Pozo‐Rosich, Alfons Macaya
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0147514

A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells
Cited by: 27
Author(s): Basudev Chowdhury, Arun S. Seetharam, Zhiping Wang, Yunlong Liu, Amy C. Lossie, Jyothi Thimmapuram, Joseph Irudayaraj
Software Mentions: 1
Published: almost 9 years ago

10.1097/j.pain.0000000000000880

Genome-wide methylation analysis of a large population sample shows neurological pathways involvement in chronic widespread musculoskeletal pain
Cited by: 26
Author(s): Gregory Livshits, Ida Malkin, Maxim B. Freidin, Yudong Xia, Fei Gao, Jun Wang, Timothy D. Spector, Alexander Macgregor, Jordana T. Bell, Frances Williams
Software Mentions: 1
Published: over 7 years ago

10.1186/gm419

Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma
Cited by: 114
Author(s): Matthias Lechner, Tim R. Fenton, James D. West, Gareth A. Wilson, Andrew Feber, Stephen Henderson, Christina Thirlwell, Harpreet Dibra, Amrita Jay, Lee M. Butcher, Ankur Chakravarthy, Fiona Gratrix, Nirali M. Patel, Francis Vaz, Paul O’Flynn, Nicholas Kalavrezos, Andrew E. Teschendorff, Chris Boshoff, Stephan Beck
Software Mentions: 1
Published: almost 12 years ago

10.1186/gb-2012-13-6-r43

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
Cited by: 576
Author(s): Matthew N. Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R. Alan Harris, Aleksandar Milosavljevic, Claire Troakes, Safa Al‐Sarraj, Richard Dobson, Leonard C. Schalkwyk, Jonathan Mill
Software Mentions: 1
Published: almost 13 years ago

10.1097/j.pain.0000000000001364

Multi-OMICS analyses of frailty and chronic widespread musculoskeletal pain suggest involvement of shared neurological pathways
Cited by: 30
Author(s): Gregory Livshits, Ida Malkin, Ruth C E Bowyer, Serena Verdi, Jordana T. Bell, Cristina Menni, Frances Williams, Claire J. Steves
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2015.01161

Ammonium Inhibits Chromomethylase 3-Mediated Methylation of the Arabidopsis Nitrate Reductase Gene NIA2
Cited by: 9
Author(s): Jooyong Kim, Ye Jin Kwon, Sung-Il Kim, Do Youn Kim, Jong Tae Song, Hak Soo Seo
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-13-S8-S6

Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes
Cited by: 11
Author(s): Michael Trimarchi, Mark W. Murphy, David Frankhouser, Blanca Rodriguez, John Curfman, Guido Marcucci, Pearlly S. Yan, Ralf Bundschuh
Software Mentions: 1
Published: almost 12 years ago

10.18632/oncotarget.17078

Functional dissection of the role of UHRF1 in the regulation of retinoblastoma methylome
Cited by: 7
Author(s): Guangyan Kan, Heng He, Qi Zhao, Xiubo Li, Min Li, Huasheng Yang, Jong Kyong Kim
Software Mentions: 1
Published: over 7 years ago

10.1210/jc.2016-1219

Contribution of Heritability and Epigenetic Factors to Skeletal Muscle Mass Variation in United Kingdom Twins
Cited by: 40
Author(s): Gregory Livshits, Fei Gao, Ida Malkin, Maria Needhamsen, Yudong Xia, Wei Yuan, Christopher G. Bell, Kirsten Ward, Yuan Liu, Jun Wang, Jordana T. Bell, Tim D. Spector
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2020.596078

Genome-Wide Analysis of Cell-Free DNA Methylation Profiling for the Early Diagnosis of Pancreatic Cancer
Cited by: 18
Author(s): Shengyue Li, Lei Wang, Qiang Zhao, Wenwen Wang, Shuxian Lu, Yani Kang, Gang Jin, Jing Tian
Software Mentions: 1
Published: almost 4 years ago