csls2004 - second year seminar

second year seminar:

no date given by advisor topic links extra

1 26.3 Anat Afek Michal Linial Comparative genomics

Yeast rises again. pdf.
Sequencing and comparison of yeast species to identify genes and regulatory elements. pdf.
Conservation and evolution of cis-regulatory systems in ascomycete fungi. pdf.
presentation.

2 2.4 Elad Mezuman Michal Linial Protein-protein interactions

Protein\u2013protein interaction maps: a lead towards cellular functions. pdf.
Comparative assessment of large-scale data sets of protein-protein interactions. pdf.
Proteome survey reveals modularity of the yeast cell machinery. pdf.
Towards a proteome-scale map of the human protein-protein interaction network. pdf.
abstract, presentation

3 23.4 Yonatan Vaizman Hanah Margalit Gene expression

Cluster analysis and display of genome-wide expression patterns. pdf, online.
Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis. pdf, online.
Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. pdf, online.
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. pdf, online.
abstract, presentation1 , presentation2. a movie about mircoarray.

4 30.4 Yaar Reuveni Nir Friedman Transcription factor binding sites

Applied bioinformatics for the identification ofregulatory elements. pdf.
Predicting gene expression from sequence. pdf.
Identifying regulatory networks by combinatorial analysis of promoter elements. pdf.
abstract, presentation.

5 7.5 Dana Attias Nir Friedman Transcriptional regulation

A plethora of sites. pdf.
Genome-wide location and function of DNA binding proteins. pdf.
Transcriptional regulatory code of a eukaryotic genome. pdf.
Control of Pancreas and Liver Gene Expression by HNF Transcription Factors. pdf.
abstract, presentation.

6 14.5 Elhanan Elboher Nir Friedman Histone modification

The language of covalent histone modifications. pdf.
Mapping global histone acetylation patterns to gene expression. pdf.
Genomic maps and comparative analysis of histone modifications in human and mouse. pdf.
Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. pdf.
abstract, presentation.

7 28.5 Matan Hofree Hanah Margalit MicroRNAs

The functions of animal microRNAs. pdf.
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. pdf.
Combinatorial microRNA target predictions. pdf.
abstract, presentation.

8 4.6 Assaf Weiner Ora Furman Protein structure prediction

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. pdf.
Toward high-resolution de novo structure prediction for small proteins. pdf.
abstract, presentation.

9 11.6 Yosef Prat Ora Furman Protein function prediction

Predicting protein function from sequence and structural data. pdf.
Automated prediction of protein function and detection of functional sites from structure. pdf, online.
Switch-of-function mutants based on morphology classification of Ras superfamily small GTPases. pdf, online.
abstract, presentation.

no	date	given by	advisor	topic	links	extra
1	26.3	Anat Afek	Michal Linial	Comparative genomics	Yeast rises again. pdf. Sequencing and comparison of yeast species to identify genes and regulatory elements. pdf. Conservation and evolution of cis-regulatory systems in ascomycete fungi. pdf.	presentation.
2	2.4	Elad Mezuman	Michal Linial	Protein-protein interactions	Protein\u2013protein interaction maps: a lead towards cellular functions. pdf. Comparative assessment of large-scale data sets of protein-protein interactions. pdf. Proteome survey reveals modularity of the yeast cell machinery. pdf. Towards a proteome-scale map of the human protein-protein interaction network. pdf.	abstract, presentation
3	23.4	Yonatan Vaizman	Hanah Margalit	Gene expression	Cluster analysis and display of genome-wide expression patterns. pdf, online. Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis. pdf, online. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. pdf, online. Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. pdf, online.	abstract, presentation1 , presentation2. a movie about mircoarray.
4	30.4	Yaar Reuveni	Nir Friedman	Transcription factor binding sites	Applied bioinformatics for the identification ofregulatory elements. pdf. Predicting gene expression from sequence. pdf. Identifying regulatory networks by combinatorial analysis of promoter elements. pdf.	abstract, presentation.
5	7.5	Dana Attias	Nir Friedman	Transcriptional regulation	A plethora of sites. pdf. Genome-wide location and function of DNA binding proteins. pdf. Transcriptional regulatory code of a eukaryotic genome. pdf. Control of Pancreas and Liver Gene Expression by HNF Transcription Factors. pdf.	abstract, presentation.
6	14.5	Elhanan Elboher	Nir Friedman	Histone modification	The language of covalent histone modifications. pdf. Mapping global histone acetylation patterns to gene expression. pdf. Genomic maps and comparative analysis of histone modifications in human and mouse. pdf. Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. pdf.	abstract, presentation.
7	28.5	Matan Hofree	Hanah Margalit	MicroRNAs	The functions of animal microRNAs. pdf. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. pdf. Combinatorial microRNA target predictions. pdf.	abstract, presentation.
8	4.6	Assaf Weiner	Ora Furman	Protein structure prediction	A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. pdf. Toward high-resolution de novo structure prediction for small proteins. pdf.	abstract, presentation.
9	11.6	Yosef Prat	Ora Furman	Protein function prediction	Predicting protein function from sequence and structural data. pdf. Automated prediction of protein function and detection of functional sites from structure. pdf, online. Switch-of-function mutants based on morphology classification of Ras superfamily small GTPases. pdf, online.	abstract, presentation.