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Published bySibyl Berry Modified over 9 years ago
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Igor Ulitsky
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“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
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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
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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
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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
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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
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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
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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.
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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
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Using histone modifications and sequence conservation to uncover long non- coding RNAs (lincRNA)
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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
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