News
25.12.2012: Details for the oral exam on January,11th are online.
17.12.2012: Link for Chapter 7 in weekly notes for week 50 fixed.
26.11.2012: Preliminary second mandatory assignment was published.
15.11.2012: The score in Testcase 3 (global alignment) was wrong. I added the correct solution.
06.11.2009: First mandatory assignment was published.
06.11.2012: Access to the Blackboard material is provided via WebDav folders. See the Weekly Notes for how to access the material.
05.11.2012: Site Launch.
Schedule
All lectures are in the IMADA seminar room. (The schedule might be modified.)
Lecture | 45 | 46 | 47 | 48 | 49 | 50 | 51 |
---|---|---|---|---|---|---|---|
Tue 10-12 | Lecture | Lecture | Lecture | Lecture | Lecture | Lecture | Lecture |
Thu 16-18 | Lecture | Lecture | Lecture | (Lecture) | |||
Fri 12-14 | Lecture | Lecture | Lecture (13:15 - 14:00) | Lecture (12:15 - 13:00) | |||
Weekly Notes
The slides (and additional material) presented in the lectures can be found in the Blackboard System.
Date | Topic | Reading | Weekly Notes |
---|---|---|---|
Week 45 | Central Dogma, Scoring Matrices, Local and Global Sequence Alignment, Smith-Watermann, Needleman-Wunsch | Chapters 1, 4.1, 5.1, and 5.2 from [3] | Week 45 |
Week 46 | Substitution and scoring matrices, PAM, BLOSUM; Indexing Techniques, BLAST, FASTA | Chapter 5.1 and 5.3 from [3] | Week 46 |
Week 47 | Coevolution, Dynamic Programming for coevolution reconstructions, ILP formulation for tanglegram layout, ILP formulation for fixing estimated orthology matrices | Chapter 1 from [3] + original articles (see Weekly Notes) | Week 47 |
Week 48 | Coevolution, orthology relations, gene and species tree reconciliation, an ILP formulation for fixing estimated orthology matrices, Pattern Profiles and Multiple Alignments | see Weekly Notes, Chapter 6 from [3] | Week 48 |
Week 49 | Hidden Markov Models, Genome Rearrangements - PQ Trees / Sorting / Median Problem | [3], details see Weekly Notes | Week 49 |
Week 50 | Reversal Median Problem, Phylogenetics (distance correction) | Chapter 7 and 8 from [3], see Weekly Notes | Week 50 |
Week 51 | Phylogenetics, inferring phylogenetic trees, parsimony and likelihood methods | Chapter 8 from [3] | tba |
Office Hours
Just write a short mail, and come by.
- Office: IMADA, Ø14-602b-2 map.
- Phone: 2322
- E-mail: daniel
Literature
Books used for the Lecture
- [1] Bioinformatics and Functional Genomics, 2009, Second Edition, by Jonathan Pevsner
- [2] Combinatorics of Genome Rearrangements, 2009, by Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier and Stéphane Vialette
- [3] Understanding Bioinformatics, 2008 by Marketa Zvelebil and Jeremy O. Baum, Chapter 1, Chapter 4, Chapter 7
- [4] Tangled Trees - Phylogeny, Cospeciation, and Coevolution, 2003, edited by Roderic D. M. Page
In addition to the books we will use original articles as a source of information (see blackboard).
Original Articles
- [5] BLOSUM62 miscalculations improve search performance. Mark P Styczynski; Kyle L Jensen, Isidore Rigoutsos, Gregory Stephanopoulos (2008). Nat. Biotech. 26: 274-275. doi:10.1038/nbt0308-274.