Putting epigenome comparison into practice.

NIH Epigenomics Roadmap Data Analysis and Coordination Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, USA.
Nature Biotechnology (Impact Factor: 39.08). 10/2010; 28(10):1053-6. DOI: 10.1038/nbt1010-1053
Source: PubMed

ABSTRACT Comparative analysis of epigenomes offers new opportunities to understand cellular differentiation, mutation effects and disease processes. But the scale and heterogeneity of epigenetic data present numerous computational challenges.

  • [Show abstract] [Hide abstract]
    ABSTRACT: Cell reprogramming has been known to accompany cell type-specific epigenetic alterations of the genome. Chromatin structure and dynamics influenced by epigenetic factors such as covalent histone modifications, histone variants, DNA methylation, ncRNAs and chromatin remodeling play an important role in determining cell fate. The rapid progress made with the development of high-throughput technology and the systematic assessment of accumulated data has enabled the identification of previously unknown biological processes and disease states in terms of whole-genome profiles of epigenetic signatures at a high resolution. In this article, we discuss the fundamental advances and challenges over the past several years in our knowledge of chromatin state and gene transcription programs associated with epigenetic changes during cell reprogramming processes. In particular, histone modifications, DNA methylation and transcriptome analyses in genome-scale studies will be reviewed to characterize a functional cross-talk between epigenetic and transcriptional regulations in cell reprogramming.
    Epigenomics 02/2011; 3(1):73-81. DOI:10.2217/epi.10.72 · 5.22 Impact Factor
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. Availability: CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
    Bioinformatics 03/2013; 29(9). DOI:10.1093/bioinformatics/btt114 · 4.62 Impact Factor

Preview (2 Sources)

Available from