bioconductor: methylKit | Projects

10.1186/s13072-021-00390-y

Molecular and computational approaches to map regulatory elements in 3D chromatin structure
Cited by: 7
Author(s): Beoung Hun Lee, Suhn Kyong Rhie
Software Mentions: 21
Published: over 3 years ago

Epigenetic inheritance of circadian period in clonal cells
Cited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: over 4 years ago

10.1111/pbi.13299

Learning from methylomes: epigenomic correlates ofPopulus balsamiferatraits based on deep learning models of natural DNA methylation
Cited by: 9
Author(s): Marc J. Champigny, Faride Unda, Oleksandr Skyba, Raju Soolanayakanahally, Shawn D. Mansfield, Malcolm M. Campbell
Software Mentions: 10
Published: almost 5 years ago

10.7554/eLife.39380

Intergenerational epigenetic inheritance of cancer susceptibility in mammals
Cited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: over 5 years ago

10.26508/lsa.202000794

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
Cited by: 5
Author(s): Elisa Redl, Raheleh Sheibani-Tezerji, Crhistian de Jesus Cardona, Patricia Hamminger, Gerald Timelthaler, Melanie R. Hassler, Maša Zrimšek, Sabine Lagger, Thomas Dillinger, Lorena Hofbauer, Kristina Draganić, Andreas Tiefenbacher, Michael Kothmayer, C. Dietz, Bernard Ramsahoye, Lukas Kenner, Christoph Bock, Christian Seiser, Wilfried Ellmeier, Gabriele Schweikert, Gerda Egger
Software Mentions: 9
Published: almost 4 years ago

10.1126/sciadv.aaz1138

Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation
Cited by: 76
Author(s): Melanie J. Heckwolf, Britta Meyer, Robert Häsler, Marc P. Höppner, Christophe Eizaguirre, Thorsten B. H. Reusch
Software Mentions: 9
Published: over 4 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

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: about 6 years ago

10.1038/srep35903

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: about 8 years ago

10.1186/s13059-019-1664-9

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

10.3389/fimmu.2021.617592

Phenotypic and Epigenetic Adaptations of Cord Blood CD4+ T Cells to Maternal Obesity
Cited by: 11
Author(s): Suhas Sureshchandra, Norma Mendoza, Allen Jankeel, Randall M. Wilson, Nicole Marshall, Ilhem Messaoudi
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-015-0742-6

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
Cited by: 60
Author(s): Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J. Morelli, Valerio Bianchi, Bruno Amati, Joseph R. Ecker, Mattia Pelizzola
Software Mentions: 7
Published: about 9 years ago

10.1186/s13229-017-0119-y

Exaggerated CpH methylation in the autism-affected brain
Cited by: 30
Author(s): Shannon Ellis, Saloni Gupta, Anna Moes, Andrew B. West, Dan E. Arking
Software Mentions: 7
Published: almost 8 years ago

10.1186/s12864-016-3326-6

TEA: the epigenome platform for Arabidopsis methylome study
Cited by: 3
Author(s): Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yubin Wang, Pao‐Yang Chen, Chung‐Yen Lin
Software Mentions: 7
Published: almost 8 years ago

10.7554/eLife.34031

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Cited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-019-6415-5

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex
Cited by: 19
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Michael E. Pfrender, James Brown, John K. Colbourne, Leda Mirbahai
Software Mentions: 7
Published: almost 5 years ago

10.1002/ctm2.234

Epigenetic consequences of hormonal interactions between opposite‐sex twin fetuses
Cited by: 4
Author(s): Siming Kong, Yong Peng, Wei Chen, Xinyi Ma, Wei Yuan, Yangyu Zhao, Rong Li, Jie Qiao, Liying Yan
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41416-018-0236-1

Phenotype-independent DNA methylation changes in prostate cancer
Cited by: 11
Author(s): Davide Pellacani, Alastair Droop, Fiona M. Frame, Matthew Simms, Vincent M. Mann, Anne T. Collins, Connie J. Eaves, Norman J. Maitland
Software Mentions: 6
Published: about 6 years ago

10.1186/s13072-018-0205-1

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
Cited by: 243
Author(s): Dafni Anastasiadi, Anna Esteve‐Codina, Francesc Piferrer
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2105-14-S5-S10

An optimized algorithm for detecting and annotating regional differential methylation
Cited by: 101
Author(s): Shengyong Li, Francine E. Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross L. Levine, Bik To, Ian D. Lewis, Anna L. Brown, Richard J. D’Andrea, Ari Melnick, Christopher E. Mason
Software Mentions: 6
Published: over 11 years ago

10.15252/embj.2018100882

Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Cited by: 11
Author(s): Solomiia Korchynska, Maria Krassnitzer, Katarzyna Maleńczyk, Rashmi B. Prasad, Evgenii Tretiakov, Sabah Rehman, Valentina Cinquina, Victoria Gernedl, Matthias Farlik, Julian Petersen, S Hannes, Julia Schachenhofer, Sonali N. Reisinger, Alice Zambon, Olof Asplund, Isabella Artner, Erik Keimpema, Gert Lübec, Jan Mulder, Christoph Bock, Daniela D. Pollak, Roman A. Romanov, Christian Pifl, Leif Groop, Tomas Hökfelt, Tibor Harkany
Software Mentions: 6
Published: about 5 years ago

10.1186/s12870-017-1070-y

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions
Cited by: 12
Author(s): Martin Schmidt, Michiel Van Bel, Magdalena Wołoszyńska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
Software Mentions: 6
Published: over 7 years ago

10.1186/1471-2105-15-337

Bison: bisulfite alignment on nodes of a cluster
Cited by: 12
Author(s): Devon P. Ryan, Dan Ehninger
Software Mentions: 6
Published: about 10 years ago

10.15252/embj.2020107100

De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis
Cited by: 17
Author(s): Sara Zocher, Rupert W. Overall, Gabriel Berdugo-Vega, Nicole Rund, Anne Karasinsky, Vijay S. Adusumilli, Christina Steinhauer, Sina Scheibenstock, Kristian Händler, Joachim L. Schultze, Federico Calegari, Gerd Kempermann
Software Mentions: 6
Published: over 3 years ago

10.18632/oncotarget.22942

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells
Cited by: 33
Author(s): Yan Wang, Zhong Sheng Sun, Moshe Szyf
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12859-020-3470-5

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
Cited by: 8
Author(s): Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder
Software Mentions: 5
Published: over 4 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: about 3 years ago

10.7554/eLife.05255

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Cited by: 402
Author(s): Manu Dubin, Pei Zhang, Dong Meng, Marie Stanislas Remigereau, Edward J. Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Géraldine Jean, Bjarni J. Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver Stegle, Richard M. Clark, Magnus Nordborg
Software Mentions: 5
Published: over 9 years ago

10.1002/evl3.129

Methylation and gene expression differences between reproductive and sterile bumblebee workers
Cited by: 48
Author(s): Hollie Marshall, Zoë N. Lonsdale, Eamonn B. Mallon
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-019-5578-4

Genome-wide methylation is modified by caloric restriction in Daphnia magna
Cited by: 20
Author(s): Jack Hearn, Marianne Pearson, Mark Blaxter, Philip J. Wilson, Tom J. Little
Software Mentions: 5
Published: over 5 years ago

10.3390/cells9061436

Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver
Cited by: 14
Author(s): Qinwei Kim-Wee Zhuang, José Héctor Gálvez, Qian Xiao, Najla AlOgayil, Jeffrey Hyacinthe, Teruko Taketo, Guillaume Bourque, Anna K. Naumova
Software Mentions: 5
Published: over 4 years ago

10.1186/s12915-020-00769-5

Multiple links between 5-methylcytosine content of mRNA and translation
Cited by: 71
Author(s): Ulrike Schümann, He-Na Zhang, Tennille Sibbritt, Anyu Pan, Attila Horváth, Simon Gross, Susan J. Clark, Li Yang, Thomas Preiß
Software Mentions: 5
Published: over 4 years ago

10.1534/g3.119.400152

Early Developmental Stress Affects Subsequent Gene Expression Response to an Acute Stress in Atlantic Salmon: An Approach for Creating Robust Fish for Aquaculture?
Cited by: 23
Author(s): Nick Robinson, Hanne Johnsen, Hooman K. Moghadam, Øivind Andersen, Helge Tveiten
Software Mentions: 4
Published: over 5 years ago

10.1093/gbe/evy155

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective
Cited by: 43
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Omid Shams Solari, James Brown, John K. Colbourne, Michael E. Pfrender, Leda Mirbahai
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.566320

Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection
Cited by: 11
Author(s): Hongmei Li-Byarlay, Humberto Boncristiani, Gary W. Howell, Jacob Herman, Lindsay V. Clark, Micheline K. Strand, David R. Tarpy, Olav Rueppell
Software Mentions: 4
Published: about 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.2019.00184

Associations Between Behavioral Effects of Bisphenol A and DNA Methylation in Zebrafish Embryos
Cited by: 38
Author(s): Pål A. Olsvik, Paul Whatmore, Samuel Penglase, Kaja H. Skjærven, Marc Anglès d’Auriac, Ståle Ellingsen
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20215343

Discrimination of DNA Methylation Signal from Background Variation for Clinical Diagnostics
Cited by: 8
Author(s): Robersy Sánchez, Xiaodong Yang, Thomas A. Maher, Sally A. Mackenzie
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2086-5

An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
Cited by: 23
Author(s): W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.36435

Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters
Cited by: 8
Author(s): Ryo Nabeshima, Osamu Nishimura, Takako Maeda, Nobujiro Shimizu, Takahiro Ide, Kenta Yashiro, Yasuo Sakai, Chikara Meno, Mitsutaka Kadota, Hidetaka Shiratori, Shigehiro Kuraku, Hiroshi Hamada
Software Mentions: 4
Published: over 6 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: over 3 years ago

10.1155/2019/9565794

A Pathway Analysis Based on Genome-Wide DNA Methylation of Chinese Patients with Graves’ Orbitopathy
Cited by: 10
Author(s): Xin Zhong, Lin Hua, Yilin Yang, Tingting Shi, Wei Liu, Xiu Tuo, Li Yu, Xi Cao, Fengying Yang
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-83851-4

Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice
Cited by: 30
Author(s): Payel Kundu, Eileen Ruth S. Torres, Keaton Stagaman, Kristin B. Kasschau, Mariam Okhovat, Sarah Holden, Samantha Ward, Kimberly A. Nevonen, Brett A. Davis, Takashi Saito, Takaomi C. Saido, Lucia Carbone, Thomas J. Sharpton, Jacob Raber
Software Mentions: 4
Published: over 3 years ago

10.26508/lsa.202000848

Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis
Cited by: 19
Author(s): Martin Rougée, Leandro Quadrana, Jérôme Zervudacki, Valentin Hure, Vincent Colot, Lionel Navarro, Angélique Deleris
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1006964

rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline
Cited by: 56
Author(s): Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Nathalie Lailler, Christopher E. Mason, Kathryn V. Anderson, Scott Keeney
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-51423-2

Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes
Cited by: 12
Author(s): G. Marconi, Stefano Capomaccio, Cinzia Comino, Alberto Acquadro, Ezio Portis, Andrea Porceddu, Emidio Albertini
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-32448-5

The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis
Cited by: 51
Author(s): Joost H. M. Stassen, Ana López, Ritushree Jain, David Pascual-Pardo, Estrella Luna, Lisa M. Smith, Jurriaan Ton
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-27979-w

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea
Cited by: 22
Author(s): Himanshi Bhatia, Niraj Khemka, Mukesh Jain, Rohini Garg
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers12113425

The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma
Cited by: 29
Author(s): Zigui Chen, Pak-Kin Wong, Cherrie W K Ng, Linda Lan, S. Fung, Jing W Li, Liuyang Cai, Pu Liao, Qianqian Mou, Sunny H. Wong, William Ka Kei Wu, Ryan J. Li, Katie Meehan, Vivian Wai Yan Lui, Chit Chow, Kwok Wai Lo, Amy B.W. Chan, Siaw Shi Boon, Eric S. H. Lau, Zenon W C Yeung, K.C. Allen Chan, Eddy W.Y. Wong, Alfred Sze‐Lok Cheng, Jun Yu, Paul Kay Sheung Chan, Jason Ying Kuen Chan
Software Mentions: 4
Published: about 4 years ago

10.1186/s13148-021-01127-0

DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies
Cited by: 7
Author(s): Julien Morival, Halida P. Widyastuti, Christopher Nguyen, Michael V. Zaragoza, Timothy L. Downing
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-018-0190-4

“Same difference”: comprehensive evaluation of four DNA methylation measurement platforms
Cited by: 26
Author(s): Thadeous J. Kacmarczyk, Mame P. Fall, Xihui Zhang, Xin Yuan, Yushan Li, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 6 years ago

10.1083/jcb.201804042

Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities
Cited by: 33
Author(s): Alison E. Casey, Ankit Sinha, Rajat Singhania, Julie Livingstone, Paul Waterhouse, Pirashaanthy Tharmapalan, Jennifer Cruickshank, Mona Shehata, Erik Drysdale, Hui Fang, Hye-Yeon Kim, Ruth Isserlin, Swneke D. Bailey, Tiago da Silva Medina, Geneviève Deblois, Yu-Jia Shiah, Dalia Baršytė-Lovejoy, Stefan Höfer, Gary D. Bader, Mathieu Lupien, C.H. Arrowsmith, S. Knapp, Daniel D De Carvalho, Hal K. Berman, Paul C. Boutros, Thomas Kislinger, Rama Khokha
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0182638

Epigenetic differences between monozygotic twins discordant for amyotrophic lateral sclerosis (ALS) provide clues to disease pathogenesis
Cited by: 35
Author(s): Paul E. Young, Stephen Kum Jew, Michael E. Buckland, Roger Pamphlett, Catherine M. Suter
Software Mentions: 3
Published: over 7 years ago

10.1038/srep31014

The CD4+ T cell methylome contributes to a distinct CD4+ T cell transcriptional signature in Mycobacterium bovis-infected cattle
Cited by: 20
Author(s): Rachael Doherty, Ronan Whiston, Paul Cormican, Emma K. Finlay, Christine Couldrey, Christopher S. Brady, Cliona O’Farrelly, Kieran G. Meade
Software Mentions: 3
Published: over 8 years ago

10.1186/s13148-015-0135-8

Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer
Cited by: 68
Author(s): Christophe Legendre, Gerald C. Gooden, Kyle N. Johnson, Rae Anne Martinez, Winnie S. Liang, Bodour Salhia
Software Mentions: 3
Published: about 9 years ago

10.3389/fgene.2020.00922

Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls
Cited by: 8
Author(s): Abdolrahman Khezri, Birgitte Narud, Else‐Berit Stenseth, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Robert Wilson, Rafi Ahmad, Elisabeth Kommisrud
Software Mentions: 3
Published: over 4 years ago

10.1038/sdata.2016.19

Genome-scale DNA methylome and transcriptome profiling of human neutrophils
Cited by: 17
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Euan J. Rodger, Ian M. Morison
Software Mentions: 3
Published: over 8 years ago

10.1016/j.isci.2021.103148

Epigenetic and transcriptional responses underlying mangrove adaptation to UV-B
Cited by: 3
Author(s): Yushuai Wang, Chenglong Huang, Weishun Zeng, Tianyuan Zhang, Cairong Zhong, Shulin Deng, Tian Tang
Software Mentions: 3
Published: about 3 years ago

10.1186/s13148-021-01121-6

Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements
Cited by: 1
Author(s): Sayaka Kawashima, Atsushi Hattori, Erina Suzuki, Kazuo Matsubara, Machiko Toki, Rika Kosaki, Yukihiro Hasegawa, Kazuhiko Nakabayashi, Maki Fukami, Masayo Kagami
Software Mentions: 3
Published: over 3 years ago

10.3390/life10080121

Parental Selenium Nutrition Affects the One-Carbon Metabolism and the Hepatic DNA Methylation Pattern of Rainbow Trout (Oncorhynchus mykiss) in the Progeny
Cited by: 9
Author(s): Pauline Wischhusen, Takaya Saito, Cécile Héraud, Sadasivam Kaushik, Benoı̂t Fauconneau, P. Antony Jesu Prabhu, Stéphanie Fontagné-Dicharry, Kaja H. Skjærven
Software Mentions: 3
Published: over 4 years ago

10.1155/2019/6212681

Identifying and Validating Genes with DNA Methylation Data in the Context of Biological Network for Chinese Patients with Graves’ Orbitopathy
Cited by: 6
Author(s): Tingting Shi, Lin Hua, Xin Zhong, Li Yu, Wei Liu, Yilin Yang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-018-2593-4

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
Cited by: 44
Author(s): Qiangwei Zhou, Jing-Quan Lim, Wing-Kin Sung, Guoliang Li
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-6307-8

DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation
Cited by: 22
Author(s): Abdolrahman Khezri, Birgitte Narud, Else‐Berit Stenseth, Anders Johannisson, Frøydis Deinboll Myromslien, Ann Helen Gaustad, Robert Wilson, Robert Lyle, Jane M. Morrell, Elisabeth Kommisrud, Rafi Ahmad
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.118.200297

Key Transport and Ammonia Recycling Genes Involved in Aphid Symbiosis Respond to Host-Plant Specialization
Cited by: 17
Author(s): Dohyup Kim, Bushra Fazal Minhas, Hongmei Li-Byarlay, Allison K. Hansen
Software Mentions: 3
Published: over 6 years ago

10.1186/s13072-020-00338-8

The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure
Cited by: 6
Author(s): Dana M. Freeman, Dan Lou, Yanqiang Li, Suzanne N. Martos, Zhibin Wang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41438-021-00505-2

Genome of a citrus rootstock and global DNA demethylation caused by heterografting
Cited by: 43
Author(s): Yue Huang, Yuantao Xu, Xiaolin Jiang, Huang Yu, Hui-Hui Jia, Chunming Tan, Gang Hu, Yibo Hu, Muhammad Junaid Rao, Xiuxin Deng, Qiang Xu
Software Mentions: 3
Published: over 3 years ago

10.1093/jxb/eraa132

Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects
Cited by: 43
Author(s): Tom J. M. Van Dooren, Amanda Bortolini Silveira, Elodie Gilbault, José M. Jiménez‐Gómez, Antoine Martin, Liên Bach, Sébastien Tisné, Leandro Quadrana, Olivier Loudet, Vincent Colot
Software Mentions: 3
Published: over 4 years ago

10.1186/s13072-016-0105-1

Targeted bisulfite sequencing of the dynamic DNA methylome
Cited by: 21
Author(s): Michael J. Ziller, Elena K. Stamenova, Hongcang Gu, Andreas Gnirke, Alexander Meissner
Software Mentions: 3
Published: almost 8 years ago

10.3390/genes11080850

Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk
Cited by: 11
Author(s): Marcello Del Corvo, Silvia Bongiorni, Bruno Stefanon, Sandy Sgorlon, Alessio Valentini, Paolo Ajmone‐Marsan, Giovanni Chillemi
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-014-0472-5

Dynamic evolution of clonal epialleles revealed by methclone
Cited by: 60
Author(s): Sheng Li, Francine E. Garrett-Bakelman, Alexander E. Perl, Selina M. Luger, Chao Zhang, Bik To, Ian D. Lewis, Anna L. Brown, Richard J. D’Andrea, M. Elizabeth Ross, Ross L. Levine, Martin Carroll, Ari Melnick, Christopher E. Mason
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2020.597943

The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep
Cited by: 14
Author(s): Nicole Groß, Todd D. Taylor, Thomas D. Crenshaw, Hasan Khatib
Software Mentions: 3
Published: about 4 years ago

10.1111/eva.12912

Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico
Cited by: 35
Author(s): Kevin M. Johnson, Morgan W. Kelly
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-017-05222-2

Impacts of Early Life Stress on the Methylome and Transcriptome of Atlantic Salmon
Cited by: 41
Author(s): Hooman K. Moghadam, Hanne Johnsen, Nick Robinson, Øivind Andersen, Even H. Jørgensen, Hanne Johnsen, Vegar J. Bæhr, Helge Tveiten
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-019-0687-8

Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations
Cited by: 45
Author(s): Lingzhao Fang, Shuli Liu, Mei Liu, Xiaolong Kang, Shudai Lin, Bingjie Li, Erin E. Connor, VI Ransom L. Baldwin, Albert Tenesa, Li Ma, George E. Liu, Congjun Li
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms21186700

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
Cited by: 13
Author(s): Aleksandra Skalska, Christoph Stritt, Michele Wyler, H. Williams, Martin Vickers, Jungong Han, Metin Tuna, Gülsemin Savaş Tuna, Karolina Susek, Martin Swain, Rafał Wóycicki, Saurabh Chaudhary, Fiona Corke, John H. Doonan, Anne Roulin, Robert Hasterok, Luis A. J. Mur
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-37618-z

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis
Cited by: 9
Author(s): Alan M. O’Doherty, Kévin Rue-Albrecht, David A. Magee, Simone Ahting, Rachelle E Irwin, Thomas Jonathan Hall, John A. Browne, Nicolas C. Nalpas, Colum P. Walsh, Stephen V. Gordon, Marcin W. Wojewodzic, David E. MacHugh
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.558189

Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels
Cited by: 10
Author(s): Ryan J. Corbett, M.F.W. te Pas, H. van den Brand, M.A.M. Groenen, R.P.M.A. Crooijmans, Catherine W. Ernst, Ole Madsen
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-020-03865-z

A novel computational strategy for DNA methylation imputation using mixture regression model (MRM)
Cited by: 9
Author(s): Fangtang Yu, Chao Xu, Hong‐Wen Deng, Hui Shen
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12864-019-5880-1

Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs
Cited by: 23
Author(s): Siriluck Ponsuksili, Nares Trakooljul, Basavaraj Sajjanar, Frieder Hadlich, Eduard Muráni, Klaus Wimmers
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-4350-x

Isogenic mice exhibit sexually-dimorphic DNA methylation patterns across multiple tissues
Cited by: 26
Author(s): Helen McCormick, Paul E. Young, Suzy S J Hur, Keith Booher, Hunter Chung, Jennifer E. Cropley, Eleni Giannoulatou, Catherine M. Suter
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13104-020-4883-y

DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)
Cited by: 6
Author(s): Ramesh Bhat, Jonathan Rockey, Kenta Shirasawa, I. S. Tilak, M. P. Brijesh Patil, V. B. Reddy Lachagari
Software Mentions: 2
Published: almost 5 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

10.1242/bio.035196

Epigenetic modifications by polyphenolic compounds alter gene expression in the hippocampus
Cited by: 13
Author(s): Tal Frolinger, Francis Herman, Abhijeet Sharma, Steven Sims, Jun Wang, Giulio Maria Pasinetti
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41375-018-0092-2

Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia
Cited by: 5
Author(s): R Gunnarsson, Sebastian DiLorenzo, Kristina B. Lundin-Ström, Linda Olsson, Andrea Biloglav, Henrik Lilljebjörn, Marianne Rissler, Per Wahlberg, Anders Lundmark, Anders Castor, Mikael Behrendtz, Thoas Fioretos, Kajsa Paulsson, Anders Isaksson, Bertil Johansson
Software Mentions: 2
Published: over 6 years ago

10.3390/molecules23112879

Identification of Epigenetic Mechanisms Involved in the Anti-Asthmatic Effects of Descurainia sophia Seed Extract Based on a Multi-Omics Approach
Cited by: 12
Author(s): Su‐Jin Baek, Jin Mi Chun, Tae-Wook Kang, Yun‐Soo Seo, Sung‐Bae Kim, Boseok Seong, Yunji Jang, Ga-Hee Shin, Chul Kim
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0166575

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation
Cited by: 13
Author(s): David K. Kranzhöfer, Ralf Gilsbach, Björn Grüning, Rolf Backofen, Thomas Nührenberg, Lutz Hein
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0086707

WBSA: Web Service for Bisulfite Sequencing Data Analysis
Cited by: 21
Author(s): Liang Fang, Bixia Tang, Yanqing Wang, Jianfeng Wang, Chao Yu, Chen Xu, Junwei Zhu, Jiangwei Yan, Wenming Zhao, Rujiao Li
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13148-019-0657-6

DNA methylome profiling of granulosa cells reveals altered methylation in genes regulating vital ovarian functions in polycystic ovary syndrome
Cited by: 53
Author(s): Pooja Sagvekar, Pankaj Kumar, Vijay Mangoli, Shashvat Desai, Srabani Mukherjee
Software Mentions: 2
Published: over 5 years ago

10.1111/eva.13160

Urbanization is associated with modifications in DNA methylation in a small passerine bird
Cited by: 23
Author(s): Hannah Watson, Daniel Powell, Pablo Salmón, Arne Jacobs, Caroline Isaksson
Software Mentions: 2
Published: about 4 years ago

10.1111/eva.13153

Insecticide exposure affects intergenerational patterns of DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata
Cited by: 26
Author(s): Kristian Brevik, Erika Bueno, Stephanie McKay, Sean D. Schoville, Yolanda H. Chen
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2019.00694

Investigation of Gene Expression and DNA Methylation From Seven Different Brain Regions of a Crab-Eating Monkey as Determined by RNA-Seq and Whole-Genome Bisulfite Sequencing
Cited by: 4
Author(s): Won-Jun Lim, Kyoung Hyoun Kim, Jaeyoon Kim, Hee‐Jin Kim, Mirang Kim, Jong‐Lyul Park, Seokjoo Yoon, Jung‐Hwa Oh, Jae-Woo Cho, Yong‐Sung Kim, Namshin Kim
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.633132

Methylome Patterns of Cattle Adaptation to Heat Stress
Cited by: 19
Author(s): Marcello Del Corvo, Barbara Lazzari, Emanuele Capra, Ludmilla Balbo Zavarez, Marco Milanesi, Yuri Tani Utsunomiya, Adam Taiti Harth Utsunomiya, Alessandra Stella, Guilherme de Paula Nogueira, José Fernando Garcia, Paolo Ajmone‐Marsan
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.626536

Characterization of Genome-Wide DNA Methylation and Hydroxymethylation in Mouse Arcuate Nucleus of Hypothalamus During Puberty Process
Cited by: 13
Author(s): Yihang Shen, Shasha Zhou, Xiaodong Zhao, Hua Li, Jingyong Sun
Software Mentions: 2
Published: almost 4 years ago

10.3389/fnmol.2019.00182

DNA Methylation Dynamics During the Differentiation of Retinal Progenitor Cells Into Retinal Neurons Reveal a Role for the DNA Demethylation Pathway
Cited by: 11
Author(s): Galina Dvoriantchikova, Rajeev J. Seemungal, Dmitry Ivanov
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.00694

A Cost Reduced Variant of Epi-Genotyping by Sequencing for Studying DNA Methylation in Non-model Organisms
Cited by: 12
Author(s): Olaf Werner, Ángela S. Prudencio, Elena de la Cruz-Martínez, Marta Nieto‐Lugilde, P. Martínez-Gómez, Rosa M. Ros
Software Mentions: 2
Published: over 4 years ago

10.1016/j.gdata.2014.10.008

Base-resolution DNA methylation landscape of zebrafish brain and liver
Cited by: 21
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Julia A. Horsfield, Ian M. Morison, Shinichi Nakagawa
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2012-13-10-r87

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
Cited by: 1,321
Author(s): Altuna Akalin, Matthías Kormáksson, Sheng Li, Francine E. Garrett-Bakelman, María E. Figueroa, Ari Melnick, Christopher E. Mason
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13059-017-1266-3

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network
Cited by: 30
Author(s): Priyanka Dhingra, Alexander Martínez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, De Li Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin, Ekta Khurana
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-06351-4

Integrin α6β4 Upregulates Amphiregulin and Epiregulin through Base Excision Repair-Mediated DNA Demethylation and Promotes Genome-wide DNA Hypomethylation
Cited by: 9
Author(s): Brittany L. Carpenter, Jinpeng Liu, Lei Qi, Chi Wang, Kathleen L. O’Connor
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-40262-w

The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue
Cited by: 21
Author(s): Galina Dvoriantchikova, Rajeev J. Seemungal, Dmitry Ivanov
Software Mentions: 2
Published: over 5 years ago

Projects: bioconductor: methylKit

Papers Mentioning methylKit 154