58311107 Seminar - Thousand Genomes Seminar (3 cr)

Structure of the Seminar (spring 2011)

- Seminar is lead by Prof. Esko Ukkonen (esko.ukkonen@cs.helsinki.fi)

- Seminar sessions: on Mondays at 14 - 16 in room B222

- Basic material: A map of human genome variation from population-scale sequencing, Nature 467, 1061--1073: (28 October 2010)

- Next session: February 14 at 14:15 B222

To pass the seminar, you need to do the following four tasks:
1. Write a seminar 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 (the first talk is a short overview of your planned paper, the second talk is a full 45 min presentation of your final paper); and
4. Participate actively 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 April-May.

Participants and their topics (from the list below)

Asan, B Hilal Topic: 5

Cervera, Alejandra Topic: 10

He, Liang Topic: 3

Ismail, Khadeeja Topic: 7

Kazi, Serikzhan Topic: 6

Korhonen, Pasi Topic: 4

Ng, Kim Topic: 8

Subramanian, Vigneshwari Topic: 11

Söderholm, Marcus

Vlachopoulou, Efthymia Topic: 9

Topics

1. RNA-Seq mappers: TopHat, G-Mo.R-Se, QPALMA

2. Resequencing and haplotyping: Genotype imputation, Local haplotype reconstruction

3. Resequencing and structural variation detection: Review, Combinatorial approach to structural variation detection, SNP detection (Atlas-SNP2)

4. ChIP-Seq analysis: review, CisGenome, SISSRs, ...

5. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature (2010)

6. Hugo Y K Lam, et al Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library Nature Biotechnology (2010)

Alexej Abyzov and Mark Gerstein AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision Bioinformatics (2011)

7. Can Alkan, et al Personalized copy number and segmental duplication maps using next-generation sequencing Nature Genetics (2009)

8. The International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations Nature (2010)

9. The Wellcome Trust Case Control Consortium Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature (2010)

10. Jun Wang, et al The diploid genome sequence of an Asian individual Nature (2008)

11. Samuel Levy, et al The Diploid Genome Sequence of an Individual Human PLoS Biology (2007)

12. L.J. McIver, et al Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is 2 indicative of the quality and utility of the raw data and alignments Genomics (2011)

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

Reviewer A Reviewer B

He, Liang Topic: 3 PK HA

Korhonen, Pasi Topic: 4 HA SK

Asan, B Hilal Topic: 5 SK KI

Kazi, Serikzhan Topic: 6 KI KN

Ismail, Khadeeja Topic: 7 KN EV

Ng, Kim Topic: 8 EV AC

Vlachopoulou, Efthymia Topic: 9 AC VS

Cervera, Alejandra Topic: 10 VS LH

Subramanian, Vigneshwari Topic: 11 LH PK

Söderholm, Marcus

Work plan (tentative)

Jan 17: introductions, organizing the work, planning the schedule

Jan 31: organizing (cont.), wikipage, seminar materials

Feb 7: selection of the topics and source materials for each student

Feb 14: re-allocation of topics if necessary

Feb 28:

- 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 28: check-point session: full draft seminar papers written and submitted to the wiki for review

April 5 (no session): HARD DEAD_LINE for submitting your full-draft seminar paper

April 14 (no session): dead-line for submitting your two review reports to the seminar wiki

April 20, 14-16:30 (normal session): Feed-back to the authors - each Reviewer A presents his/hers comments to the author & both reviewers give to the author the marked manuscript

May 2: Dead-line for submitting the final seminar paper

May 4, 12-18: Final presentations of the papers, Session I & II

May 5, 9-13: Final presentations of the papers, Session III

Final conference

Day I: Wednesday May 4 at 12 -18 in room B222

12:15 Liang

13:15 Pasi

14:15 Hilal

15:00 B R E A K

15:30 Serikzhan

16:30 Khadeeja

Day II: Thursday May 5 at 9 - 13 in room B222

9:15 Kim

10:15 Efthymia

11:15 Alejandra

12:15 Vigneshwari

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.