Igor Ulitsky
“the branch of genetics that studies organisms in terms of their genomes (their full DNA sequences)” Computational genomics in TAU ◦ Ron Shamir’s lab – focus on gene expression and regulatory networks ◦ Eithan Ruppin’s lab – focus on metabolism ◦ Tal Pupko’s and Benny Chor’s labs – focus on phylogeny ◦ Roded Sharan’s lab – focus on networks ◦ Noam Shomron’s lab – focus on miRNA ◦ Eran Halperin’s lab – focus on genetics
Alignment Protein coding gene finding Assembly of long reads Basic microarray data analysis Mapping of transcriptional regulation in simple organisms Functional profiling in simple organisms
Determining protein abundance Assembly of short reads Transcriptional regulation in higher eukaryotes “Histone code”: Chromatin modifications, their function and regulation Functional profiling of mammalian cells Association studies for single-gene effects Construction and modeling of synthetic circuits
Digital gene expression from RNA-seq studies Prediction of ncRNAs and their function Global mapping of alternative splicing regulation Integration of multi-level signaling (TFs, miRNA, chromatin) Association studies for combinations of alleles
All microbial genomes are sequenced in E. coli Each sequencing efforts basically introduces genes (3-8Kb fragments) into E. coli Sometimes sequencing fails Idea: sequencing fails barrier to horizontal gene transfer
Even sequencing of reads with 100s of bp will no identify many indels Idea: sequence pairs of sequences at some distance apart from each other
High-throughput sequencing can identify all the mutations in different cancers 20,857 transcripts from 18,191 human genes sequenced in 11 breast and 11 colorectal cancers.
Problems: few mutations are drivers most are passangers Most studies did not identify high frequent risk allels But: members of some pathways are affected in almost any tumour Network biology needed
Using histone modifications and sequence conservation to uncover long non- coding RNAs (lincRNA)
12 fly species were sequenced to identify ◦ Evolution of genes and chromosome ◦ Evolutionary constrained sequence elements in promoters and 3’ UTRs Starting point – genome-wide alignment of the genomes