Giosuè Lo Bosco, University of Palermo, Italy

Computational models for Epigenomic Analyis
Epigenetic mechanisms include nucleosome positioning, histone modifications, and DNA methylation. They play an important role in the regulation of cell-type specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators, so that several methods based on such information have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles.
Here we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison, and prediction models.
Computational studies using these methods have provided important insights into the epigenetic regulatory mechanisms.

References
  1. Yuan GC. Linking genome to epigenome. Wiley interdisciplinary reviews. Systems biology and medicine. 2012;4(3):297--309.

  2. Pham TH, Ho TB, Tran DH et al. Prediction of Histone Modifications in DNA. 2007 959--966.

  3. Yang Y, Nephew K, Kim S. A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. BMC Bioinformatics. 2009;12(Suppl 3).

  4. Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology. 2008;4(1).

  5. Pinello L, Lo Bosco G, Hanlon B et al. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011;12.