Bioinformatics of Gene Regulation -seminar (3AP)

Jaak Vilo -

Bioinformatics of Gene Regulation (seminar MTAT.03.192, 3AP) 2005 fall
Tuesday 16.15-18.00, J. Liivi 2 - room 315
Jaak Vilo

NB! Seminar will be held in English

NB! Seminar will continue also during the Spring 2006 semester (another 3cu!)

Geeniregulatsiooni Bioinformaatika (eestikeelne kirjeldus)

Geenide regulatsiooni mehhanismide väljaselgitamine on modernse molekulaarbioloogia üks olulisi probleeme. Seoses probleemi keerukusega ei ole selle lahendamine ilma bioinformaatika abita aga realistlik. Seminaris tutvume erinevate aspektidega viimaste aastate teadusuurimustest, mis tegelevad antud valdkonnaga. Esindatud on nii puhtalt arvutuslikud ülesanded ja probleemid kui ka relevantsed bioloogilised aspektid.

Töö käigus on oluline iseseisev uurimuslik töö - otsida artikleid, materjale, lugeda ja süstematiseerida see referaadiks ja seminariettekandeks.

Description

Understanding the mechanisms of gene regulation remains one of the key problems the molecular biology and bioinformatics are tackling currently. Due the scale of the problem the need for bioinformatics is growing. We will be studying the recent scientific literature about the subject - both computational as well as biological aspects.

This seminar aims to bring together students and researchers interested in bioinformatics. The topics will vary from algorithmic (motif discovery) to networks analysis to biological problems and interpretations.

Seminar will be held in the in the "Journal club" style. Every week someone will present the research articles about a specific topic. Each presentation will be accompanied by a written 5-12 page overview of that topic.

Participants and their final reports

Priit Adler - T02: Examples of gene reg. networks
Juri Gavshin - Large scale gene regulation networks
Jaanus Hansen - Random Projections (Challenge problem)
Sten Ilmjärv - Organisation of promoters ...
Raivo Kolde - MONKEY
Darja Kruševskaja - T13 - systematic approach to S. cerevisae network reconstruction
Meelis Kull - (1) Alternative Splicing Specificity ; (2) Motif discovery
Kristo Käärmann - Haplotype inference with segment overlapping
Anton Litvinenko - Estimator of gene expression similarity significance
Ilja Livenson - Structural properties of TF-DNA interactions and the inference of sequence specificity
Hendrik Nigul - PWM discovery algorithms
Priit Palta - Statistical analysis of overrepresented words
Pavlos Pavlidis - Microarray class prediction ; Graph Mining
Jüri Reimand - SOMBRERO (why not GO?)
Sergei Sitov - Databases for gene regulatory data
Jelena Zaitseva - Gene expression coherence score and it's modifications...
Asko Tiidumaa - Methods for finding TF modules ...
Konstantin Tretjakov - RVM & EPONINE
Andres Veidenberg - T12 Seqvista

Time Schedule

6.09 Opening, topics, ...
13.09 Π ; MK
20.09 JH (MK, RK) ; HN ( MK, PA )
27.09 SI (KK, PA) ; JZ (KK, AT)
4.10 PP (IK, RK) ; JV?
11.10 DK () ; JR ()
18.10 --- no seminar!!!
25.10 PA (DK, Π ) ; AV (SI, JR)
1.11 -- no seminar
8.11 RK (HN, Π )
15.11 SR (SI, AV); JG (IL, SR)
22.11 KT (Π , JG ) ; KK ( )
29.11 IL (AV, PP) ;
6.12 Kristo Käärmann
13.12 Meelis Kull
20.12 Igor Kuzmitshov AND Deadline for all written reports!

Topics

Biological aspects of gene regulation and problem satetements for bioinformatics

T01: Organization of promoters, cis-regulatory sequences, miRNA targets, alternative splice sites etc.
T02: Specific examples of gene regulation networks
T03: ...

Pattern discovery algorithms and their usage for dissecting gene regulation mechanisms

T05: Relevance Vector Machine and Eponine algorithm (Down & Hubbard).
T06: PWM discovery algorithms (COMODO, MEME, ...)
T07: Statistical Analysis of overrepresented words
T08: The Challenge problem and random projections
T09: Assessing pattern discovery methods
T091 MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model Alan M Moses1, 2 , Derek Y Chiang3 , Daniel A Pollard1 , Venky N Iyer4 and Michael B Eisen
T092 SOMBRERO http://bioinf.nuigalway.ie/sombrero/

Construction and analysis of small or large-scale gene regulation networks

T10: Construction of large-scale networks and their analysis Google Search; Google Scholar search
T11: Graph minging techniques for gene regulatory networks (Uri Alon)
T12: SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
T13: A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae Wei Wang*, J. Michael Cherry*, David Botstein* , and Hao Li (PNAS).
T14: Yeast promoter analysis papers and thesis from M. Eisen lab

Reconstruction of higher-order dependencies within regulatory sequences

T15: Modules of transcriprion factor binding sites (articles by Thomas Werner, tools by Genomatix)
T16: Modules of TF sites, Synergistic motifs, coherence score
T17: Modules: GoogleScholar: Eran Segal
T18: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
Benjamin P. Berman, Yutaka Nibu, Barret D. Pfeiffer, Pavel Tomancak, Susan E. Celniker, Michael Levine, Gerald M. Rubin , and Michael B. Eisen
T19: Dieterich C, Rahmann S, Vingron M (2004). Functional inference from non-random distributions of conserved predicted transcription factor binding sites. Bioinformatics 20 (Suppl.1) 2004: i109-i115 (Proceedings of ISMB 2004)

Databases for storing Gene Regulatory data

Google Scholar Search
T20: Which databases exist, what are their main features, and useful aspects
T21: What are the key problems in developing such databases
T22: DRAGON: Disease Explorer and other tools

Jaak Vilo,

Bioinformatics of Gene Regulation (seminar MTAT.03.192, 3AP) 2005 fall Tuesday 16.15-18.00, J. Liivi 2 - room 315 Jaak Vilo