Seminar Gene Regulatory Networks

Structure of the Seminar (spring 2010)

- Seminar is lead by Prof. Esko Ukkonen

- Seminar sessions: on Mondays at 14 - 16 in room C222

- Seminar textbook: Hamid Bolouri: Computational modeling of gene regulatory networks. Imperial College Press 2008

- Next session: February 8

To pass the seminar, you need to do the following four tasks:
1. Write a paper about a topic agreed during the first meetings,
2. Review two papers written by other students (a written review plus discussions),
3. Prepare and present two oral presentations and discuss them with the other students (first talk is a short overview of your planned paper, second talk is a full 45 min presentation of your final paper); and
4. Participate in the seminar sessions by asking questions, raising discussions on the topic, and reviewing other students' work.

During Period I all students write their papers in English. The length of the paper is about 8-12 pages. The feedback from other students on your paper is given during period II. The papers are then revised, and the oral presentations of the final papers are given in May.

Participants and seminar topics (the chapters are from Bolouri's textbook)

Al-Hello, Muhammed H Topic: Chap 8 (Singel-cell model of transcriptional regulation)

Brilhante, Virginia Topic: Chap 10 (Boolean and multi-valued logic)

Fitsum, Tamene Topic: Chap 11 (Bayesian networks) , second part: constructing BNs from data etc (pages 156-166)

Gutierrez Cardenas, Juan Topic: Chap 13 (Network inference in practice), first part: intro + learning logic models + REVEAL algorithm + intro to ARACNE (pages 175-181 + S Liang et al article on the REVEAL algorithm (page 178) + AA Margolin et al paper on ARACNE (page 182))

He, Liang Topic: Chap 6, subtopic Evolutionary conserved network topologies (pages 55-56 + the three articles listed on page 55)

K. V. Naga Poojitha Topic: Chap 18 (Robustness analysis), Intro & sensitivity (pages 265-275)

Kumar, Ajay A Topic: Chap 7 (Biochemical basis of gene regulation)

Langohr, Laura Topic: Chap 18 (Robustness analysis), Evolution of robustness (pages 275-277 + some suitable original articles)

Narayanasamy, Shaman Topic: Chap 13 (Network inference in practice), second part: learning continuous valued networks + recalling ARACNE + learning module netvorks (pages 182-187 + AA Margolin et al paper on ARACNE (page 182) + E Segal et al article on Module networks (page 183))

Prakash, Kirti Topic: Chap 9 (Mass-action kinetics) NOTE: This chapter is VERY technical; your seminar paper should cover concepts and results but not mathematical derivations

Seise, Matti J Topic: Chap 5 (Graphical representations)

Wong, Swee Topic: Chap 12 (Relationship between logic and bayesian networks) NOTE: Some material from the three papers listed on page 172 should be included in your seminar paper

Xiong, Jie Topic: Chap 11 (Bayesian networks) , first part: definition and use (pages 143-155)

Zhao, Yan Topic: Chap 6 (Interaction network maps)

Guidelines for writing your seminar paper

The goal of writing a seminar paper is to learn by experience the process of writing scientific text that is based on the knowledge you can obtain from open sources but that you have to present in your own words. You learn a lot in this process!

It is important to give proper credit to the original inventors of the content by using literature references.

NOTE: You can easily find from internet different guidelines of writing a paper (say 'writing a term paper' to Google).

Guidelines for making your reviews

The goal of writing a review is to give constructive feedback to the author such that he or she can improve the paper. A good review can consider all aspects of the paper starting from the content and organization to the language style, lay-out, grammatical correctness and typing errors.

Content

- Is the level of exposition suitable? Is something important missing? Is something elaborated in too much detail? Does the paper give enough background material such that the content is understandable without reading the references (assuming that the reader has basic knowledge in the field)?

Organization

- Is the content of the paper presented in a natural order (for example, the central concepts should be defined before they are used)? Does the introduction of the paper give a clear picture to the reader of what is going to happen in the paper? Is the exposition consistent throughout?

- Is the list of references adequate? Are literature references used in the text in a proper way?

Language

- Is the message of each sentence clear? Is the usage of language precise and readable? Is the language grammatically correct? Is the spelling of words correct? Is the punctuation correct?

- Is mathematical and other formal notation elegant and consistently used?

Lay-out

- Is the lay-out of the pages of the paper such that it supports readability: good font size (not too small, not too large), good size of figures and diagrams and the embedded text, a suitable amount of material per page, etc?

NOTE: In your review, you should be constructive. This means that when you think that, say, something is missing in the paper, then you should say in the review, what is missing. Or if you think that a sentence is unclear, you should say as precisely as possible what you don't understand in this specific sentence. E.t.c.

NOTE': The detailed comments concerning typos and small local grammatical improvements etc are easiest to make as hand-written markings to a paper copy of the article. You should prepare such a marked copy and give it to the author.

Presentation order and reviewer allocation

0. Seise, Matti J

1. Zhao, Yan

2. He, Liang

3. Kumar, Ajay A

4. Al-Hello, Muhammed H

5. Prakash, Kirti

6. Brilhante, Virginia

7. Xiong, Jie

8. Fitsum, Tamene

9. Wong, Swee

10. Gutierrez Cardenas, Juan

11. Narayanasamy, Shaman

12. K. V. Naga Poojitha

13. Langohr, Laura

NOTE: Student i in the above list has to serve as the reviewer for students i-1 mod 14 and i-2 mod 14

Work plan (tentative)

Jan 18: introductions, organizing the work, planning the schedule

Feb 8: selection of the topics and source materials for each student

Feb 15: re-allocation of topics if necessary

Feb 22:

- short presentations (max 2 slides!) by each student of the topic area and planned content of the report

- nomination of two reviewers for each student

Mar 22: check-point session: full draft reports written and submitted for review

Apr 12: check-point session: review reports submitted

Apr 19: review session I

Apr 26: review session II

May 17-18: final conference: presentations of final papers (45 min per paper)

Final conference May 17 & May 20, room B119

Day I: Monday May 17 at 10 -14 in room B119

10:15 Kirti Prakash

11:15 Liang

12:15 Swee

13:15 Matti Seise

14:00 End of Day I

Day II: Thursday May 20 at 9 - 18 in room B119

9:15 Zhao Yan

10:15 Al-Hello Muhammed Hassan

11:15 Xiong Jie

12:15 Ajay Anand Kumar

13:00 LUNCH BREAK

14:15 Poojitha

15:15 Laura

16:15 Juan Manuel

17:15 Shaman

18:00 The End

Students' working areas

Instructions on how to create a link to your pdf file

First log in using the University account and press the edit button
to go to edit mode.

Modify the text "<create here a link to your paper (pdf file)>" next to your
name to a more descriptive name. Then select this piece of text with mouse,
and press the link button (the one with a globe and chain link on it) to make
a link to your document. If you have stored your document somewhere in the Internet,
you can give its URL in the link field. Otherwise you need to upload your
document to the wiki server. You can do this by selecting the attachment
tab. Then select your file using the browse button. Once the file is chosen
click it so it appears in the link-field. Then press OK or equivalent
button.

After any modifications to the wiki page use the save button to store the
new version.

If you have any problems, you can ask Jarkko Toivonen.