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Human DNA methylomes at base resolution show widespread epigenomic differences

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Cited by:

  1. Christopher G Bell & Sarah Finer & Cecilia M Lindgren & Gareth A Wilson & Vardhman K Rakyan & Andrew E Teschendorff & Pelin Akan & Elia Stupka & Thomas A Down & Inga Prokopenko & Ian M Morison & Jonat, 2010. "Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-12, November.
  2. Allegra Angeloni & Skye Fissette & Deniz Kaya & Jillian M. Hammond & Hasindu Gamaarachchi & Ira W. Deveson & Robert J. Klose & Weiming Li & Xiaotian Zhang & Ozren Bogdanovic, 2024. "Extensive DNA methylome rearrangement during early lamprey embryogenesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  3. Xusheng Zhang & Xintong Gao & Zhen Liu & Fei Shao & Dou Yu & Min Zhao & Xiwen Qin & Shuo Wang, 2024. "Microbiota regulates the TET1-mediated DNA hydroxymethylation program in innate lymphoid cell differentiation," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  4. Xuelong Yao & Zongyang Lu & Zhanying Feng & Lei Gao & Xin Zhou & Min Li & Suijuan Zhong & Qian Wu & Zhenbo Liu & Haofeng Zhang & Zeyuan Liu & Lizhi Yi & Tao Zhou & Xudong Zhao & Jun Zhang & Yong Wang , 2022. "Comparison of chromatin accessibility landscapes during early development of prefrontal cortex between rhesus macaque and human," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  5. Yongjun Piao & Wanxue Xu & Kwang Ho Park & Keun Ho Ryu & Rong Xiang, 2021. "Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data," IJERPH, MDPI, vol. 18(15), pages 1-15, July.
  6. Guodong Wu & Nengjun Yi & Devin Absher & Degui Zhi, 2011. "Statistical Quantification of Methylation Levels by Next-Generation Sequencing," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-12, June.
  7. Jamie L. Endicott & Paula A. Nolte & Hui Shen & Peter W. Laird, 2022. "Cell division drives DNA methylation loss in late-replicating domains in primary human cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  8. Olbricht Gayla R. & Craig Bruce A. & Doerge Rebecca W., 2012. "Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-37, November.
  9. Singer Meromit & Engström Alexander & Schönhuth Alexander & Pachter Lior, 2011. "Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-27, September.
  10. Rakesh Chettier & Lesa Nelson & James W Ogilvie & Hans M Albertsen & Kenneth Ward, 2015. "Haplotypes at LBX1 Have Distinct Inheritance Patterns with Opposite Effects in Adolescent Idiopathic Scoliosis," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-11, February.
  11. Jason A. Carter & Léonie Strömich & Matthew Peacey & Sarah R. Chapin & Lars Velten & Lars M. Steinmetz & Benedikt Brors & Sheena Pinto & Hannah V. Meyer, 2022. "Transcriptomic diversity in human medullary thymic epithelial cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  12. Zengyu Shao & Jiuwei Lu & Nelli Khudaverdyan & Jikui Song, 2024. "Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  13. Brendan Evano & Diljeet Gill & Irene Hernando-Herraez & Glenda Comai & Thomas M Stubbs & Pierre-Henri Commere & Wolf Reik & Shahragim Tajbakhsh, 2020. "Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation," PLOS Genetics, Public Library of Science, vol. 16(10), pages 1-21, October.
  14. Sun Shuying & Yu Xiaoqing, 2016. "HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 55-67, March.
  15. Lacey Michelle R. & Baribault Carl & Ehrlich Melanie, 2013. "Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(6), pages 723-742, December.
  16. Jiang Li & Fangxu Han & Tongqi Yuan & Wei Li & Yue Li & Harry X. Wu & Hairong Wei & Shihui Niu, 2023. "The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  17. Ruth V. Nichols & Brendan L. O’Connell & Ryan M. Mulqueen & Jerushah Thomas & Ashley R. Woodfin & Sonia Acharya & Gail Mandel & Dmitry Pokholok & Frank J. Steemers & Andrew C. Adey, 2022. "High-throughput robust single-cell DNA methylation profiling with sciMETv2," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  18. Jian Fang & Jianjun Jiang & Sarah M. Leichter & Jie Liu & Mahamaya Biswal & Nelli Khudaverdyan & Xuehua Zhong & Jikui Song, 2022. "Mechanistic basis for maintenance of CHG DNA methylation in plants," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  19. Xue Yue & Zhiyuan Xie & Moran Li & Kai Wang & Xiaojing Li & Xiaoqing Zhang & Jian Yan & Yimeng Yin, 2022. "Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  20. Kaiqiong Zhao & Karim Oualkacha & Lajmi Lakhal‐Chaieb & Aurélie Labbe & Kathleen Klein & Antonio Ciampi & Marie Hudson & Inés Colmegna & Tomi Pastinen & Tieyuan Zhang & Denise Daley & Celia M.T. Green, 2021. "A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation," Biometrics, The International Biometric Society, vol. 77(2), pages 424-438, June.
  21. Yu Xiaoqing & Sun Shuying, 2016. "Comparing five statistical methods of differential methylation identification using bisulfite sequencing data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(2), pages 173-191, April.
  22. Emanuele Raineri & Marc Dabad & Simon Heath, 2014. "A Note on Exact Differences between Beta Distributions in Genomic (Methylation) Studies," PLOS ONE, Public Library of Science, vol. 9(5), pages 1-5, May.
  23. Yu Xiaoqing & Sun Shuying, 2016. "HMM-DM: identifying differentially methylated regions using a hidden Markov model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 69-81, March.
  24. David Cheishvili & Chifat Wong & Mohammad Mahbubul Karim & Mohammad Golam Kibria & Nusrat Jahan & Pappu Chandra Das & Md. Abul Khair Yousuf & Md. Atikul Islam & Dulal Chandra Das & Sheikh Mohammad Noo, 2023. "A high-throughput test enables specific detection of hepatocellular carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  25. Anyou Wang & Ying Du & Qianchuan He & Chunxiao Zhou, 2013. "A Quantitative System for Discriminating Induced Pluripotent Stem Cells, Embryonic Stem Cells and Somatic Cells," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-10, February.
  26. Ihab Ansari & Llorenç Solé-Boldo & Meshi Ridnik & Julian Gutekunst & Oliver Gilliam & Maria Korshko & Timur Liwinski & Birgit Jickeli & Noa Weinberg-Corem & Michal Shoshkes-Carmel & Eli Pikarsky & Era, 2023. "TET2 and TET3 loss disrupts small intestine differentiation and homeostasis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  27. Romain O. Georges & Hugo Sepulveda & J. Carlos Angel & Eric Johnson & Susan Palomino & Roberta B. Nowak & Arshad Desai & Isaac F. López-Moyado & Anjana Rao, 2022. "Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
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