Identification and computational analysis of gene regulatory elements

Leila Taher, Leelavati Narlikar, Ivan Ovcharenko

Research output: Contribution to journalReview articleResearchpeer-review

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.

Original languageEnglish
Pages (from-to)pdb.top083642
JournalCold Spring Harbor Protocols
Volume2015
Issue number1
DOIs
Publication statusPublished - 5 Jan 2015

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Keywords

  • Animals
  • Computational Biology
  • Epigenesis, Genetic
  • Genome/genetics
  • Genomics/methods
  • Humans
  • Regulatory Elements, Transcriptional/genetics

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