Download compgenomics

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 noncoding 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