title: Identification and computational analysis of gene regulatory elements.
abstract: Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research. Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences. Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements. A mix of comparative genomics, high-throughput biological experiments, and machine learning approaches has played a major role in this truly global effort. Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome. We also present overviews of different publicly available, large-scale experimental data sets and computational tools, which we hope will prove beneficial for researchers working with large and complex genomes.
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, 18051 Rostock, Germany.
authors.forename: Leila
authors.initials: L
authors.lastname: Taher
authors.affiliation: Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India.
authors.forename: Leelavati
authors.initials: L
authors.lastname: Narlikar
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
mesh_terms: D000818:Animals; D019295:Computational Biology; D044127:Epigenesis, Genetic; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*