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Bioinformatics Advance Access originally published online on November 17, 2007
Bioinformatics 2008 24(1):1-10; doi:10.1093/bioinformatics/btm546
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational epigenetics

Christoph Bock * and Thomas Lengauer

Max-Planck-Institut für Informatik, Saarbrücken, Germany

*To whom correspondence should be addressed.


  Abstract

Epigenetic research aims to understand heritable gene regulation that is not directly encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and histone modifications modulate the packaging of the DNA in the nucleus and thereby influence gene expression. Patterns of epigenetic information are faithfully propagated over multiple cell divisions, which makes epigenetic regulation a key mechanism for cellular differentiation and cell fate decisions. In addition, incomplete erasure of epigenetic information can lead to complex patterns of non-Mendelian inheritance. Stochastic and environment-induced epigenetic defects are known to play a major role in cancer and ageing, and they may also contribute to mental disorders and autoimmune diseases. Recent technical advances such as ChIP-on-chip and ChIP-seq have started to convert epigenetic research into a high-throughput endeavor, to which bioinformatics is expected to make significant contributions. Here, we review pioneering computational studies that have contributed to epigenetic research. In addition, we give a brief introduction into epigenetics—targeted at bioinformaticians who are new to the field—and we outline future challenges in computational epigenetics.

Contact: cbock{at}mpi-inf.mpg.de

Associate Editor: Jonathan Wren

Received on August 25, 2007; revised on October 28, 2007; accepted on October 28, 2007

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