Giosuè Lo Bosco, University of Palermo, Italy

Machine Learning Methods for Nucleosome Positioning
The basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped around a protein core
made of histone proteins. Nucleosome organization is critical for gene regulation, and  in living cells this organization is determined by multiple factors,
such as chromatin remodellers, competition with site specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. To measure nucleosome positions on a genomic scale both theoretical and experimental approaches have been recently developed. Such methodologies are mainly based on probabilistic models able to infer nucleosome positions basing purely on genomic sequence information or on genomic-scale hybridization data achieved by a tiled microarray approach. In this tutorial recent developed algorithms for nucleosome positioning  will be analyzed and discussed, giving also emphases to their comparison in terms of computational complexity and classification accuracy.

References:

G.-C. Yuan, Y.J. Liu, M.F. Dion, M.D. Slack, L.F. Wu, S.J. Altschuler, O.J. Rando, Genome-scale identification of nucleosome positions in S. cerevisiae, Science 309 (2005), 626–630.

E. Segal, Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I.K. Moore, J.P.Wang, J. Widom, A genomic code for nucleosome positioning, Nature 442 (2006), 772–778.

M. Yassour, T. Kaplan, A. Jaimovich, N. Friedman, Nucleosome positioning from tiling microarray data, Bioinformatics 24:13 (2008) i139–i146.

V. Di Gesù, G. Lo Bosco, L. Pinello, G.C. Yuan, D.F.V. Corona, “A Multi-Layer Method to Study Genome-Scale Positions of Nucleosomes”, Genomics 93:2 (2009), 140-145.

G-C Yuan , J.S. Liu, Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion, PLoS Comput Biol 4:1 (2008) , 164-174.