Conference reports

Michal Ozery-Flato, Yonit Halperin and Ofir Davidovich
TAU

Michal will report on RECOMB '07. She will present the paper "Framework for Identifying Common Aberrations in DNA Copy Number Data" by A. Ben-Dor, D. Lipson et al.
Abstract:
In this paper we present an efficient computational framework for identification of genomic aberrations that are common to multiple cancer samples in a CGH data set. We present and compare three different algorithmic approaches within the context of that framework. Finally, we apply our methods to two datasets: a collection of 20 breast cancer samples and a panel of 60 diverse human tumor cell lines (the NCI-60). Those analyses identified both known and novel common aberrations containing cancer-related genes.

Yonit and Ofir will report on ECCB '07 (January, Eilat).
Yonit will talk about two studies from Naama Barkai's lab:
  1. "A genetic signature of interspecies variations in gene expression" by I. Tirosh, A. Weinberger, M. Carmi and N Barkai (Nature Genetics 38, 2006).
  2. "The pattern and evolution of yeast promoter bendability" by I. Tirosh, J. Berman and N. Barkai (Trends in Genetics 23:7, 2007).
Abstract:
In the first paper, the authors show that many eukaryote genes containing a TATA box in their promoters show an increased interspecies variability in expression, independent of their functional association. The second paper displays an association between existence of a rigid DNA region in yeast promoters and lack of TATA box. The association is conserved in promoters from 11 yeast species.

Ofir will present a study on "A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data" by N. Yosef, Z. Yakhini, et al.
Abstract:
The authors have developed a graph theoretic approach for identifying discriminating patterns (DPs) for a given phenotype in a genotyped population. The method is based on representing the SNP data as a bipartite graph of individuals and their SNP states, and identifying fully connected subgraphs of this graph that relate individuals enriched for a given phenotypic group. I will present the method and results on simulated and real data.