Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume 44, Issue 1, Pages 75-94
Publisher
Oxford University Press (OUP)
Online
2015-12-04
DOI
10.1093/nar/gkv1332
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency
- (2015) Davide Cacchiarelli et al. CELL
- Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin
- (2015) Xiaofei Yang et al. HUMAN MOLECULAR GENETICS
- Integrative analysis of 111 reference human epigenomes
- (2015) Anshul Kundaje et al. NATURE
- Human body epigenome maps reveal noncanonical DNA methylation variation
- (2015) Matthew D. Schultz et al. NATURE
- Transcription factor binding dynamics during human ES cell differentiation
- (2015) Alexander M. Tsankov et al. NATURE
- Modeling the relationship of epigenetic modifications to transcription factor binding
- (2015) Liang Liu et al. NUCLEIC ACIDS RESEARCH
- Deconstruction of DNA Methylation Patterns During Myogenesis Reveals Specific Epigenetic Events in the Establishment of the Skeletal Muscle Lineage
- (2015) Elvira carrió et al. STEM CELLS
- Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics
- (2015) Matthias Farlik et al. Cell Reports
- Effects of cytosine methylation on transcription factor binding sites
- (2014) Yulia A Medvedeva et al. BMC GENOMICS
- ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
- (2014) Li Shen et al. BMC GENOMICS
- MetaImprint: an information repository of mammalian imprinted genes
- (2014) Y. Wei et al. DEVELOPMENT
- Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- (2014) F. Court et al. GENOME RESEARCH
- Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma
- (2014) M Affer et al. LEUKEMIA
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers
- (2013) Jakob Lovén et al. CELL
- Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
- (2013) Warren A. Whyte et al. CELL
- Super-Enhancers in the Control of Cell Identity and Disease
- (2013) Denes Hnisz et al. CELL
- Mapping Human Epigenomes
- (2013) Chloe M. Rivera et al. CELL
- Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells
- (2013) Wei Xie et al. CELL
- Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- (2013) B. Zhang et al. GENOME RESEARCH
- Charting a dynamic DNA methylation landscape of the human genome
- (2013) Michael J. Ziller et al. NATURE
- Large conserved domains of low DNA methylation maintained by Dnmt3a
- (2013) Mira Jeong et al. NATURE GENETICS
- Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
- (2013) Gary C Hon et al. NATURE GENETICS
- Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes
- (2013) Hongbo Liu et al. Scientific Reports
- DNA methylation presents distinct binding sites for human transcription factors
- (2013) Shaohui Hu et al. eLife
- Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development
- (2013) Yi-An Ko et al. GENOME BIOLOGY
- Widespread plasticity in CTCF occupancy linked to DNA methylation
- (2012) H. Wang et al. GENOME RESEARCH
- Analysing and interpreting DNA methylation data
- (2012) Christoph Bock NATURE REVIEWS GENETICS
- CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data
- (2012) Jianzhong Su et al. NUCLEIC ACIDS RESEARCH
- DNA methylation status predicts cell type-specific enhancer activity
- (2011) Malgorzata Wiench et al. EMBO JOURNAL
- CpG islands and the regulation of transcription
- (2011) A. M. Deaton et al. GENES & DEVELOPMENT
- Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
- (2011) M. N. Cabili et al. GENES & DEVELOPMENT
- Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
- (2011) Ryan Lister et al. NATURE
- Mapping and analysis of chromatin state dynamics in nine human cell types
- (2011) Jason Ernst et al. NATURE
- Enhancer function: new insights into the regulation of tissue-specific gene expression
- (2011) Chin-Tong Ong et al. NATURE REVIEWS GENETICS
- DiseaseMeth: a human disease methylation database
- (2011) J. Lv et al. NUCLEIC ACIDS RESEARCH
- QDMR: a quantitative method for identification of differentially methylated regions by entropy
- (2011) Yan Zhang et al. NUCLEIC ACIDS RESEARCH
- DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
- (2011) Jordana T Bell et al. GENOME BIOLOGY
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- CpG islands influence chromatin structure via the CpG-binding protein Cfp1
- (2010) John P. Thomson et al. NATURE
- GREAT improves functional interpretation of cis-regulatory regions
- (2010) Cory Y McLean et al. NATURE BIOTECHNOLOGY
- Principles and challenges of genome-wide DNA methylation analysis
- (2010) Peter W. Laird NATURE REVIEWS GENETICS
- Histone H3K27ac separates active from poised enhancers and predicts developmental state
- (2010) M. P. Creyghton et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation
- (2010) A. Zemach et al. SCIENCE
- Identifying novel constrained elements by exploiting biased substitution patterns
- (2009) Manuel Garber et al. BIOINFORMATICS
- Human DNA methylomes at base resolution show widespread epigenomic differences
- (2009) Ryan Lister et al. NATURE
- The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
- (2009) Rafael A Irizarry et al. NATURE GENETICS
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- A census of human transcription factors: function, expression and evolution
- (2009) Juan M. Vaquerizas et al. NATURE REVIEWS GENETICS
- DNA hypomethylation in cancer cells
- (2009) Melanie Ehrlich Epigenomics
- Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
- (2008) Ryan Lister et al. CELL
- An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- (2008) V. K. Rakyan et al. GENOME RESEARCH
- Epigenetics in Cancer
- (2008) Manel Esteller NEW ENGLAND JOURNAL OF MEDICINE
- Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies
- (2008) D. P. Genereux et al. NUCLEIC ACIDS RESEARCH
- On the nature of human housekeeping genes
- (2008) Jiang Zhu et al. TRENDS IN GENETICS
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now