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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
◦ Roded Sharan’s lab – focus on networks
◦ Noam Shomron’s lab – focus on miRNA
◦ Eran Halperin’s lab – focus on genetics
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
“Histone code”: Chromatin modifications,
their function and regulation
Functional profiling of mammalian cells
Association studies for single-gene effects
Construction and modeling of synthetic
Digital gene expression from RNA-seq
Prediction of ncRNAs and their function
Global mapping of alternative splicing
Integration of multi-level signaling (TFs,
miRNA, chromatin)
Association studies for combinations of
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
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
Problems: few mutations are drivers most are
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
conservation to
uncover long noncoding RNAs
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