Classical Bioinformatics Papers

Classical Bioinformatics Papers

In this proseminar/seminar that is exclusively offered for Bioinformatics students (B.Sc. or M.Sc.), we will read historical original groundbreaking Bioinformatics papers, and in addition complement them with book chapters that offer a more modern treatment of the same subject. A certain focus will be on molecular evolution and phylogenetics, which were not treated in the Bioinformatics 1 lecture in much depth.

The papers we will discuss can be partitioned into four categories:

1. Classical edit distance and alignment (e.g. original Levenshtein paper; Needleman-Wunsch; Smith-Waterman)
2. Database search and read mapping (e.g. original BLAST paper)
3. Comparative genomics and genome rearrangements (e.g. the unifying DCJ framework, which is less classical than Hannenhalli-Pevzner theory but much nicer)
4. Molecular evolution and phylogenetic trees (e.g. Maximum parsimony, UPGMA, Neighbor Joining, Jukes-Cantor model, Kimura model, etc.)

 

Registration Rules

You cannot register directly here. Also, this course is NOT in the CS seminar system.
To express interest in registration for this seminar, please contact Inês Alves Ferreira (see Information > Team) until Friday 10.04. and provide

• your name, matriculation number, student email (not a private email)
• which program (BSc or MSc Bioinformatics) you are enrolled in and in which semester (1,2,3, ...)
• a statement why you want to take this seminar and whether you passed Bioinformatics 1 here, or an equivalent lecture elsewhere (see topics in last semester's Bioinformatics 1 course in the CMS). This may and probably should include some detail about the course (if not the one from Saarbrücken).
• additional helpful information (e.g. having passed BioStatsLab helps with some of the papers, but is not a strict requirement; any other relevant experience)

There is a limit of 15 people for the seminar [M.Sc.] and a limit of 15 people for the proseminar [B.Sc.].

 

Workload and Grading

The workload for the seminar [7 CP] is 210 hours over the semester; the workload for the proseminar [5 CP] is 150 hours over the semester, including preparation; reading; meetings; preparing a talk; providing feedback; refining your talk; preparing and refining your final report.

You will pass if your final presentation and you final report are acceptable (i.e., 4,0 or better). The responsible instructor has been known for relatively strict grading and not handing out good grades (2,0 or 1,0) for nothing. If you are trying to strategically optimize your grade at low workload, more than wanting to learn and explore classical bioinformatics, it is advised to stay away from this course.

 

Schedule

Attendance is mandatory. The following milestones are planned.

● Kick-off Meeting - 24th April (today)
● Choose a paper - 27th April (monday)
● Paper assignment - 28th April (tuesday)
● LSF registration - 15th May (friday)
● Meeting to talk about how to write and present - Second week of May
● Deadline for draft slides - 17th May (sunday)
● Deadline for slides feedback - 24th May (sunday) (M.Sc. only)
● Presentations for topic A - Second week of June
● Presentations for topics B and C - Third week of June
● Presentations for topic D - Fourth week of June
● Deadline for draft report - 28th of June (sunday)
● Deadline for report feedback - 5th July (sunday) (M.Sc. only)
● Deadline for final report - 12th July (sunday)