# Bioinformatics Seminar (MTAT.03.242)

### Course info

- The first meeting will take place on February 19.
**Seminars:**Monday 10:15 - 12:00, J. Liivi 2 -**512****Contacts:**Ahto Salumets (ahto.salumets [at] ut.ee), Kaur Alasoo (kaur.alasoo [at] ut.ee), room 311 in J. Liivi 2- BIIT (Bioinformatics, Algorithmics, and Data Mining group) group website : http://biit.cs.ut.ee/

Bioinformatics is an interdisciplinary field that combines computer science, biology, statistics and mathematics for understanding biological data.

### Aims of the course:

The broad aim of the seminar is to provide basic introduction into the biological questions, introduce common measurement techniques and data types and demonstrate how combining rich data with clever computational approaches can lead to new scientific insight. This semester's seminar is complementary to the Bioinformatics course and topics will be chosen to roughly match the course schedule.

The seminar is open for students from **all backgrounds**. However, for those familiar with the field, here are some keywords that might (or might not) be covered during the semester:

**Experimental:** transcription factors, enhancers, gene expression, chromatin accessibility, ChIP-seq, ATAC-seq.

**Computational:** clustering, principal component analysis, k-mers, missing data, differential expression, deep learning.

As a bonus you will get a great experience in functional reading of a scientific paper and improve your presentation and teaching skills.

### Seminar organisations

- We will have one seminar in every two weeks. The first seminar will take place on the 19th of February.
- In each seminar, two students will make two short (15-20 minutes) presentations about two related scientific papers (see Topics). These could be, for example, two different computational approaches to solve a particular biological problem.
- The presentations will be followed by discussion, with the aim of comparing and contrasting the two different papers in order to understand their relative strengths and weaknesses. To aid the discussion, 2 students (reviewers) will fulfil specific roles.
- For the next sessions, presenters will write a report (400-500 words), comparing the two methods and summarising the discussion. Each report will be reviewed by two students who grade them.
- We expect
**every**student to be familiar with the papers presented in each seminar.

### Roles for reviewers

- One of the reviewers will lead discussion (or they can share this role). This means introducing the papers, moderating the discussion and making sure that everyone will get a word.
**Skeptic**- asks at least 3 questions that reveal potential shortcomings of the methods.**Optimist**- asks at least 3 questions about potential applications of the method or potential future directions.

Others will get points for each questions that was asked.

### Requirements to pass the course:

The seminar is a non-differentiated course (pass/fail). You need to collect **70 points out of 100** in order to pass the course.

- Presenting an article/topic gives maximum
**30 points**. The presentation points are scaled according to listener feedback which evaluates both clearness and presentation skills. - Writing a report
**20 points**(20*average points from two reviewers) - Being a reviewer (also leading discussion) gives
**20 points** - Asking questions
**1 point**per question (up to 5 per seminar, needs to be meaningful!) - Attending all the seminars gives
**20 points**

Current state of the points can be seen here