Teaching

SS 2010

Computational Genomics and Metagenomics (Block Seminar)

As more and more genomic data becomes available through high throughput sequencing novel techniques are necessary to process and handle this huge amount of information. This seminar focusses on presenting current problems in modern computational genomics and the methodologies developed to solve them. Topics comprise problems in the fields of metagenomics, viral evolution, function prediction, genome wide association studies and others.

General information

Lead by	Alice McHardy
Assistants	Sebastian Konietzny, Kaustubh Patil, Lars Steinbrück, Yulia Trukhina, Christina Tusche
Language	English

Time and location

Informal meeting	To be announced
Seminar	The seminar will be held as block event at the end of the semester. The exact date will be arranged with the students in the informal meeting.
Office hours	Assistants: by appointment

Details

This is an integrated seminar that can be attended by students at the Bachelor, as well as at the Master level in Bioinformatics and Computer Science. The seminar is going to take place as a Blockseminar (date not fixed yet) and will result in 5 CP for Bachelor students and 7 CP for Master students.

For a successful completion, every participant must:

Write a review on the selected topic. Bachelor students must summarize the results of the relevant publications in 2 to 3 pages. Master students must also comment on the advantages and the shortcomings of the methodologies, their reviews must be between 4 and 5 pages long. The review has to be submitted bevor the actual seminar. Every participant can (and is encouraged to) schedule a meeting with one of the assistants in the seminar, in order to discuss the review draft before submission.
Prepare and give a presentation on the selected topic. Every presentation is followed by a short discussion. For Bachelor students, the presentations must be no longer than 30 minutes; for Master students no longer than 40 minutes. Every participant can (and is encouraged to) schedule a meeting with one of the assistants in the seminar, in order to discuss the presentation slides before the seminar.
Actively participate in the discussions after the presentations. Attendance during the whole seminar is required.

Presentation guidelines

Guidelines for scientific presentations are provided by Department 3 and are available in English (Word PDF) and in German (Word PDF). Please read them carefully before you start working on our presentation.

WS 2009/2010

Phylogenies and viral evolution (2SWS lecture, 1 SWS practice)

This lecture comprises two parts: The first follows the book of Felsenstein on inferring phylogenies, covering parsimony, distance matrix, maximum likelihood and Bayesian methods for tree inference, techniques for searching for the best tree, models of DNA evolution, ancestral character state reconstruction and methods for testing trees and models. The second part focusses on the use of phylogenies to study the 'phylodynamics' of rapidly evolving RNA viruses. Phylodynamics studies analyse viral transmission behaviour based on whole genome sequence data using phylogenetic methods. Such techniques are becoming integral to prevention, control and understanding of viral diseases. The lecture will cover several examples, such as the reconstruction of the evolutionary origins of new emerging pathogens, such as the 2009 pandemic influenza A virus, timing evolutionary events, reconstructing viral transmission chains and identification of genetic sites under adaptive or purifying selection.

General information

Lecturer	Alice McHardy
Tutors	Lars Steinbrueck, Christina Tusche
Language	English

Time and location

Lecture	Mondays, 2 pm c.t., Campus E1.4 (MPI building), Room 024
Tutorial	Tuesday, 10 am c.t., Campus E1.4 (MPI building), Room 021 The exercises will take place every two weeks. Scheduled Dates: 17.11.2009; 1.12.2009; 15.12.2009; 12.01.2010; 26.01.2010; 02.02.2010
Office hours	Alice McHardy: after each lecture Lars Steinbrueck: Thursday, 13:00 - 15:00 or by appointment Christina Tusche: Thursday, 13:00 - 15:00 or by appointment

Requirements for the course certificate

You need at least 60% of the credits from the exercises to participate in the exam.

Literature

Inferring phylogenies by Joseph Felsenstein (Palgrave Macmillan, Sinauer Associates, Inc.; 2002).
Relevant publications from the field.

Course material

Lecture slides and tutorial handouts are available in the password protected area.