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:
- "A genetic signature of interspecies variations in gene expression"
by I. Tirosh, A. Weinberger, M. Carmi and N Barkai (Nature Genetics 38, 2006).
- "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.