bioconductor: methylKit | Projects

10.1038/s41598-021-89131-5

Systematic integrated analyses of methylomic and transcriptomic impacts of early combined botanicals on estrogen receptor-negative mammary cancer
Cited by: 4
Author(s): Itika Arora, Yuanyuan Li, Manvi Sharma, Michael R. Crowley, David K. Crossman, Shizhao Li, Trygve O. Tollefsbol
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms21051819

Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?
Cited by: 11
Author(s): Xiaoru Fan, Jingguang G. Chen, Yufeng Wu, Chee How Teo, Guohua Xu, Xing Fan
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22041838

Interspecific Variation in One-Carbon Metabolism within the Ovarian Follicle, Oocyte, and Preimplantation Embryo: Consequences for Epigenetic Programming of DNA Methylation
Cited by: 13
Author(s): Connie Clare, Valerie Pestinger, Wing Yee Kwong, Desmond Tutt, Juan Xu, Helen Byrne, David A. Barrett, Richard D. Emes, Kevin D. Sinclair
Software Mentions: 2
Published: almost 4 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

10.18632/oncotarget.20176

DNMT3B overexpression contributes to aberrant DNA methylation and MYC-driven tumor maintenance in T-ALL and Burkitt’s lymphoma
Cited by: 38
Author(s): Candace J. Poole, Wenli Zheng, Atul Lodh, Aleksey Yevtodiyenko, Daniel F. Liefwalker, Honglin Li, Dean W. Felsher, Jan van Riggelen
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-021-02358-3

Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa
Cited by: 14
Author(s): Tania Chakraborty, Timmy Kendall, Jeffrey W. Grover, Rebecca A. Mosher
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2020.00111

Age-Associated DNA Methylation Patterns Are Shared Between the Hippocampus and Peripheral Blood Cells
Cited by: 11
Author(s): Christopher Harris, Brett A. Davis, Jonathan A. Zweig, Kimberly A. Nevonen, Joseph F. Quinn, Lucia Carbone, Nora E. Gray
Software Mentions: 1
Published: over 4 years ago

10.1038/s41438-020-0298-0

DNA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya
Cited by: 17
Author(s): Ping Zhou, Xiaodan Zhang, Mahpara Fatima, Xinyi Ma, Hongqing Fang, Hansong Yan, Ray Ming
Software Mentions: 1
Published: over 4 years ago

10.18632/aging.103597

Epigenetic upregulation of HOXC10 in non-small lung cancer cells
Cited by: 7
Author(s): Miao Li, John Simon Alsager, Zhaokai Wang, Lin Cheng, Bin Shan
Software Mentions: 1
Published: over 4 years ago

10.1038/s41438-020-00348-3

Molecular memory of Flavescence dorée phytoplasma in recovering grapevines
Cited by: 16
Author(s): Chiara Pagliarani, Giorgio Gambino, Alessandra Ferrandino, Walter Chitarra, Urška Vrhovšek, Dario Cantu, Sabrina Palmano, Cristina Marzachı̀, Andrea Schubert
Software Mentions: 1
Published: over 4 years ago

10.1038/s41438-021-00633-9

DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus
Cited by: 12
Author(s): Shufen Li, Can-Can Lv, Liping Lan, Kai-Lu Jiang, Yulan Zhang, Ning Li, Chuan‐Liang Deng, Wu‐Jun Gao
Software Mentions: 1
Published: about 3 years ago

10.3389/fgene.2019.01263

Integrated Analysis of Methylome and Transcriptome Changes Reveals the Underlying Regulatory Signatures Driving Curly Wool Transformation in Chinese Zhongwei Goats
Cited by: 18
Author(s): Ping Xiao, Tao Zhong, Zhanfa Liu, Yangyang Ding, Weijun Guan, Xiaohong He, Yong‐Jin Pu, Lin Jiang, Yuehui Ma, Qianjun Zhao
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13072-017-0126-4

Differential DNA methylation at conserved non-genic elements and evidence for transgenerational inheritance following developmental exposure to mono(2-ethylhexyl) phthalate and 5-azacytidine in zebrafish
Cited by: 45
Author(s): Jorke H. Kamstra, L. Bastos Sales, Peter Alestrøm, Juliette Legler
Software Mentions: 1
Published: over 7 years ago

10.1002/ece3.7606

Epigenetic effects of parasites and pesticides on captive and wild nestling birds
Cited by: 6
Author(s): Sabrina M. McNew, M.T. Boquete, Sebastian Espinoza-Ulloa, José Á. Andrés, Cornelis A. M. Wagemaker, Sarah A. Knutie, Christina L. Richards, Dale H. Clayton
Software Mentions: 1
Published: over 3 years ago

10.1186/s13148-021-01108-3

Identification of DNA methylation biomarkers for risk of liver metastasis in early-stage colorectal cancer
Cited by: 7
Author(s): Weihua Li, Lei Guo, Wanxiangfu Tang, Yutong Ma, Xiaonan Wang, Yang Shao, Hong Zhao, Jianming Ying
Software Mentions: 1
Published: over 3 years ago

10.1186/s13148-020-00866-w

Single-cell DNA methylation sequencing reveals epigenetic alterations in mouse oocytes superovulated with different dosages of gonadotropins
Cited by: 16
Author(s): Ying Huo, Zhi Yan, Peng Yuan, Meng Qin, Ying Kuo, Rong Li, Yan Li, Huai L. Feng, Jie Qiao
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers11101466

Genome-Wide Methylation Profiling in Canine Mammary Tumor Reveals miRNA Candidates Associated with Human Breast Cancer
Cited by: 13
Author(s): Sujin Jeong, Kanghoon Lee, A-Reum Nam, Je‐Yoel Cho
Software Mentions: 1
Published: about 5 years ago

10.1038/srep38401

Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas
Cited by: 53
Author(s): Jun Li, Qian Huang, Mingwei Sun, Ziyang Wang, Hao Li, Biyun Chen, Kun Xu, Guizhen Gao, Feng Li, Guiqin Yan, Jiangwei Qiao, Cai Yongping, Xiaoming Wu
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-03837-z

Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
Cited by: 21
Author(s): Binhua Tang, Yufan Zhou, Chiou Miin Wang, Tim H.M. Huang, Victor X. Jin
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0186873

Hypomethylated Fgf3 is a potential biomarker for early detection of oral cancer in mice treated with the tobacco carcinogen dibenzo[def,p]chrysene
Cited by: 19
Author(s): Yuan Sun, Kun Ming Chen, Yuka Imamura Kawasawa, Anna C. Salzberg, Timothy K. Cooper, Carla Caruso, César Aliaga, Junjia Zhu, Raghavendra Gowda, Shantu Amin, Karam El‐Bayoumy
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.25374

Genome wide DNA differential methylation regions in colorectal cancer patients in relation to blood related family members, obese and non-obese controls - a preliminary report
Cited by: 2
Author(s): S. Pamela K. Shiao, Haiyan Xiao, Longlong Dong, Xiaoling Wang, Kebin Liu, Jin‐Xiong She, Huidong Shi
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0189581

Consequences of supplying methyl donors during pregnancy on the methylome of the offspring from lactating and non-lactating dairy cattle
Cited by: 7
Author(s): À. Bach, Anna Arı́s, I. Guasch
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-32975-1

In Utero Heat Stress Alters the Offspring Epigenome
Cited by: 63
Author(s): Amy L. Skibiel, Francisco Peñagaricano, Rocío Amorín, B. M. S. Ahmed, Geoffrey E. Dahl, Jimena Laporta
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0203147

Age-specific changes in genome-wide methylation enrich for Foxa2 and estrogen receptor alpha binding sites
Cited by: 3
Author(s): Nishanth Uli, Eduardo Michelen-Gómez, Enrique Ramos, Todd E. Druley
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-33817-w

Ionizing radiation induces transgenerational effects of DNA methylation in zebrafish
Cited by: 45
Author(s): Jorke H. Kamstra, Selma Hurem, Leonardo Martín, Leif C. Lindeman, Juliette Legler, Deborah Oughton, Brit Salbu, Dag Anders Brede, Jan Ludvig Lyche, Peter Alestrøm
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0135555

DNA-Methylation Patterns in Trisomy 21 Using Cells from Monozygotic Twins
Cited by: 45
Author(s): M. Reza Sailani, Federico Santoni, Audrey Letourneau, Christelle Borel, Periklis Makrythanasis, Youssef Hibaoui, Konstantin Popadin, Ximena Bonilla, Michel Guipponi, Corinne Gehrig, Anne Vannier, F. Carré-Pigeon, Anis Féki, Dean Nižetić, Stylianos E. Antonarakis
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-37895-8

Lifelong physical activity is associated with promoter hypomethylation of genes involved in metabolism, myogenesis, contractile properties and oxidative stress resistance in aged human skeletal muscle
Cited by: 57
Author(s): M. Reza Sailani, Jens Frey Halling, Henrik Devitt Møller, Hayan Lee, Peter Plomgaard, Henriette Pilegaard, M Snyder, Birgitte Regenberg
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.14042

Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis
Cited by: 51
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Antonio Ahn, Euan J. Rodger, Anna L. Leichter, Michael R. Eccles
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0003696

Alterations in DNA Methylation May Be the Key to Early Detection and Treatment of Schistosomal Bladder Cancer
Cited by: 14
Author(s): Simon Conti, Jared Honeycutt, Justin I. Odegaard, Mark L. Gonzalgo, Michael H. Hsieh
Software Mentions: 1
Published: over 9 years ago

10.1016/j.bonr.2017.04.001

Systemic analysis of osteoblast-specific DNA methylation marks reveals novel epigenetic basis of osteoblast differentiation
Cited by: 15
Author(s): Fangtang Yu, Hui Shen, Hong‐Wen Deng
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.27825

Selective amplification of hypermethylated DNA from diverse tumor types via MSRE-PCR
Cited by: 0
Author(s): Karen Chapman, Brandon W. Higgs
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41398-020-01186-6

DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life
Cited by: 4
Author(s): Aya Sasaki, M. Eng, Abigail H. Lee, Alisa Kostaki, Stephen G. Matthews
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.bone.2018.09.008

Demethylation of ITGAV accelerates osteogenic differentiation in a blast-induced heterotopic ossification in vitro cell culture model
Cited by: 10
Author(s): Niall Logan, Marie Camman, Greg Williams, Claire A. Higgins
Software Mentions: 1
Published: almost 6 years ago

10.1155/2019/2839614

Methylation Marks of Blood Leukocytes of Native Hucul Mares Differentiated in Age
Cited by: 1
Author(s): Tomasz Ząbek, Ewelina Semik-Gurgul, Tomasz Szmatoła, Artur Gurgul, Agnieszka Fornal, Monika Bugno‐Poniewierska
Software Mentions: 1
Published: over 5 years ago

10.1242/bio.034884

Human trophoblasts are primarily distinguished from somatic cells by differences in the pattern rather than the degree of global CpG methylation
Cited by: 6
Author(s): Teena Gamage, William Schierding, Peter Tsai, Jackie L. Ludgate, Larry Chamley, Robert J. Weeks, Erin C. Macaulay, Joanna L. James
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-021-03123-1

Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations
Cited by: 1
Author(s): Yuze Zhao, Yifan Zhong, Congting Ye, Pingping Liang, Xiaobao Pan, Yuanye Zhang, Yihui Zhang, Yingjia Shen
Software Mentions: 1
Published: over 3 years ago

10.1186/s12916-020-01896-0

Early maternal care restores LINE-1 methylation and enhances neurodevelopment in preterm infants
Cited by: 14
Author(s): Camilla Fontana, Federica Marasca, Livia Provitera, Sara Mancinelli, Nicola Pesenti, Shruti Sinha, Sofia Passera, Sergio Abrignani, Fabio Mosca, Simona Lodato, Beatrice Bodega, Monica Fumagalli
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-020-07329-9

Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons
Cited by: 24
Author(s): Melanie Lindner, Irene Verhagen, Heidi M. Viitaniemi, Veronika N. Laine, Marcel E. Visser, Arild Husby, Kees van Oers
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-020-06777-7

LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function
Cited by: 17
Author(s): Naveed Jhamat, Adnan Niazi, Yongkang Guo, M. Chanrot, Elena Ivanova, Gavin Kelsey, Erik Bongcam‐Rudloff, Gerhard Andersson, P. Humblot
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-018-4640-y

A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample
Cited by: 5
Author(s): Lisa Olohan, Laura‐Jayne Gardiner, Anita Lucaci, Burkhard Steuernagel, Brande B. H. Wulff, John Kenny, Neil Hall, Anthony Hall
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-021-07371-1

The effect of DNA methylation on bumblebee colony development
Cited by: 7
Author(s): María I. Pozo, Benjamin J. Hunt, Gaby van Kemenade, Jose M. Guerra-Sanz, Félix Wäckers, Eamonn B. Mallon
Software Mentions: 1
Published: almost 4 years ago

10.18632/oncotarget.22789

Detection of prognostic methylation markers by methylC-capture sequencing in acute myeloid leukemia
Cited by: 9
Author(s): Yan Li, Hongmei Zhao, Qingyu Xu, Na Lv, Jie Yu, Lili Wang, Xiaowen Wang, Jing Guo, Lei Zhou, Jing Liu, Guofeng Chen, Chongjian Chen, Yonghui Li, Li Yu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-3216-y

Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development
Cited by: 41
Author(s): Kyle M. Schachtschneider, Yingkai Liu, Laurie A. Rund, Ole Madsen, Rodney W. Johnson, M.A.M. Groenen, Lawrence B. Schook
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-020-03634-y

HPG-DHunter: an ultrafast, friendly tool for DMR detection and visualization
Cited by: 3
Author(s): Lisardo Fernández, Manuel Asensi Pérez, Ricardo Olanda, Juan M. Orduña, Joan Márquez-Molins
Software Mentions: 1
Published: over 4 years ago

10.1093/g3journal/jkab115

The boom and bust of the aphid’s essential amino acid metabolism across nymphal development
Cited by: 16
Author(s): Daniel Pers, Allison K. Hansen
Software Mentions: 1
Published: over 3 years ago

10.3390/genes9020075

Identification of Differentially Methylated Sites with Weak Methylation Effects
Cited by: 4
Author(s): Hong T. Tran, Hongxiao Zhu, Xiaowei Wu, Gunjune Kim, Christopher R. Clarke, Hailey Larose, David C. Haak, Shawn D. Askew, Jacob N. Barney, James H. Westwood, Liqing Zhang
Software Mentions: 1
Published: almost 7 years ago

10.3389/fphar.2020.612200

Role of GABRD Gene Methylation in the Nucleus Accumbens in Heroin-Seeking Behavior in Rats
Cited by: 9
Author(s): Qingxiao Hong, Wenjin Xu, Zhang Lin, Jing Liu, Weisheng Chen, Huaqiang Zhu, Ming-Kuen Lai, Dingding Zhuang, Zeyuan Xu, Dan Fu, Wenhua Zhou, Huifen Liu
Software Mentions: 1
Published: almost 4 years ago

10.3390/genes12010074

The Identification of a Novel Fucosidosis-Associated FUCA1 Mutation: A Case of a 5-Year-Old Polish Girl with Two Additional Rare Chromosomal Aberrations and Affected DNA Methylation Patterns
Cited by: 3
Author(s): Agnieszka Domin, Tomasz Ząbek, Aleksandra Kwiatkowska, Tomasz Szmatoła, Anna Deręgowska, Anna Lewińska, Artur Mazur, Maciej Wnuk
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms22115426

Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line
Cited by: 1
Author(s): YengMun Liaw, Yikun Liu, Chee How Teo, Petr Cápal, Naoki Wada, Kiichi Fukui, Jaroslav Doležel, Nobuko Ohmido
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms221910729

Hyperglycemia Altered DNA Methylation Status and Impaired Pancreatic Differentiation from Embryonic Stem Cells
Cited by: 4
Author(s): Andy Chun Hang Chen, Wen Huang, Sze Wan Fong, C. K. Chan, Kai Chuen Lee, William Shu Biu Yeung, Yin Lau Lee
Software Mentions: 1
Published: about 3 years ago

10.3389/fgene.2020.00627

Epigenetic Vulnerability of Insulator CTCF Motifs at Parkinson’s Disease-Associated Genes in Response to Neurotoxicant Rotenone
Cited by: 5
Author(s): Dana M. Freeman, Zhibin Wang
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2020.00224

Impact of ex vivo Sample Handling on DNA Methylation Profiles in Human Cord Blood and Neonatal Dried Blood Spots
Cited by: 6
Author(s): Aya Sasaki, Bona Kim, Kellie Murphy, Stephen G. Matthews
Software Mentions: 1
Published: over 4 years ago

10.1186/s12885-018-4221-0

The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes
Cited by: 11
Author(s): Junya Matsushita, Kazunori Okamura, Kazuhiko Nakabayashi, Takehiro Suzuki, Yu Horibe, Tomoko Kawai, Toshihiro Sakurai, Satoshi Yamashita, Yoshikazu Higami, Gaku Ichihara, Kenichiro Hata, Keiko Nohara
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2018.00719

Developmental Dioxin Exposure Alters the Methylome of Adult Male Zebrafish Gonads
Cited by: 12
Author(s): Camille Akemann, Danielle Meyer, Katherine Gurdziel, Tracie R. Baker
Software Mentions: 1
Published: almost 6 years ago

Projects: bioconductor: methylKit

Papers Mentioning methylKit 154