Bioinformatics of Gene Regulation (seminar MTAT.03.192, 3AP) 2006 Spring
Thursday 10.15-12.00, J. Liivi 2 - room 404
Jaak Vilo

NB! Seminar will be held in English

WiKi pages contain up-to date information about time schedule.

Look at the first part's homepage: Fall 2005

Description

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.

• Journal club style combined with problem-oriented research seminar
• Choice of the topic by next week
• Choice of the topic is a 1-page abstract (key questions, problems, references)
• We have to avoid collisions - via e-mail?

Requirements

• Written article (on the Monday of the presentation week)
• Oral presentations: 1 or 2 per meeting
• Everyone has to write twice a 1-2 page reviews about other persons article and presentation (opponent)
• From your own research topic - identify 1-2 aspects of infoirmation that would be needed to be saved in the database, or be taken into account in bioinformatics prediction or analysis (how?).
• Active participation at every meeting

1. Priit Adler
2. Juri Gavshin -
3. Jaanus Hansen -
4. Sten Ilmjärv -
5. Raivo Kolde -
6. Darja Kruševskaja -
7. Kaie Kubjas
8. Meelis Kull -
9. Igor Kuzmitšov -
10. Ilja Livenson
11. Hendrik Nigul -
12. Pavlos Pavlidis
13. Jüri Reimand
14. Sergei Sitov
15. Jelena Zaitseva
16. Asko Tiidumaa -
17. Konstantin Tretjakov
18. Andres Veidenberg

Time Schedule

• 9.2 Opening, topics, ...
• 16.2 Ilja Livenson - Estonian GRID
• 23.2

Topics

1. What is the reason, influence or effect of the directionality of TF binding sites or signals.
2. Study an example of a feed-forward loop and demonstrate that effect on some expression data sets
3. Study an example of a negative feedback loop and demonstrate its effect on the expression data
4. (Andres Veidenberg) What is known about methylation of the DNA . and acetylation and other artefacts controlling histones that control gene activity
5. Provide examples from literature about the study of binding site combinations (clustering) in upstream regions
6. The formation of DNA-Protein (TF) complexes
7. Role of protein-protein interactions in gene regulation
8. What is the role of alternative promoters
9. "Enhancers - how they regulate transcription?"
10. "How to use different species for the discovery of TFBS in human?"
11. "The functions of highly conserved non-coding sequences"
12. (Sergei Shitov) Study the systems biology markup language (SBML) sbml.org
    • What aspects of transcription control can be described?
    • Are there any models available?
    • ...
13. Systematic discovery of regulatory motifs in human promoters and 3 0 UTRs by comparison of several ?
    X Xie, J Lu, EJ Kulbokas, TR Golub, V Mootha, K ? - Nature, 2005 - nature.com
14. Sequencing and comparison of yeast species to identify genes and regulatory elements - group of 33 »
    M Kellis, N Patterson, M Endrizzi, B Birren, ES ? - Nature, 2003 - nature.com
15. For systems biology type modeling of gene expression regulation, what aspecs should be taken into account in the model? Propose a model.
16. Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters
    Stefan Roepcke, Degui Zhi, Martin Vingron and Peter F. Arndt
17. Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen and Jussi Taipale. CELL 124(1), 13 January 2006, Pages 47-59.
18. Thornburg B.G., V. Gotea & W. Makalowski (2006): Transposable elements as a significant source of transcription regulating signals. Gene 365, 104-10.
19. "A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation"
    Dutilh, Huynen, Snel
20. "A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of TF binding profiles"
    Chang, Nagarajan, Magee, Milbrandt, Stormo
21. "Comprehensive analysis of transcriptional promoter structure & function in 1% of the human genome"
    Cooper, Trinklein, Anton, Nguyen, Myers
22. "The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates"
    Ettwiller, Paten, Souren, Loosli, Wittbrodt, Birney
23. "A network of transcriptionally coordinated functional modules in S.cerevisiae"
    Petti, Church

Jaak Vilo,