News
06.01.2011: Exam Information online.
06.01.2011: Final slides (including week 50, 51) are online.
01.12.2010: Slides update (week 49/50). Book chapter (Chapter 1 and 2 from [2]) online.
03.12.2010: Chapter 8 from [3] can be found in blackboard. (Chapter 7 can be found on the publishers webpage)
01.12.2010: Slides for week 48 are online.
01.12.2010: Chapter 6 from [3] can be found in blackboard.
23.11.2010: Second mandatory assignment online.
23.11.2010: Weekly notes for week 47 are online.
15.11.2010: Weekly notes for week 46 are online.
13.11.2010: Slides for Chapter 4 and 5 are online.
01.11.2010: Site Launch.
Schedule
All lectures are in the IMADA seminar room. (The schedule might be modified, but I'll try to not have lectures on Fridays).
Lecture | 45 | 46 | 47 | 48 | 49 | 50 | 51 |
---|---|---|---|---|---|---|---|
Wed 08-10 | Lecture | Lecture | Lecture | Lecture | Lecture | Lecture | Lecture |
Thu 10-12 | Lecture | Lecture | Lecture | Lecture | Lecture | Lecture | (Lecture) |
Fri 10-12 | |||||||
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 | Reading: 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 (BLOSUM); Indexing Techniques, BLAST, FASTA. Multiple sequence alignments. | Chapter 5.2-5.4 from [3] and [5] | Week 46 |
Week 47 | Cophylogenetics, Coevolution, Tanglegram Layout. | Reading: See weekly notes | Week 47 |
Week 48 | Patterns, Profiles, and Multiple Sequence Alignments. | Chapter 6 from from [3] | Week 48 | Week 49 | Phylogenetics. | Selected parts from Chapters 7 and 8 from [3] |
Week 50 | Continue with Phylogenetics. Start with genome rearrangements. | Still Chapters 7 and 8 (focus on Chapter 8) from [3], [6] | |
Week 51 | Continue with genome rearrangements. | [6] |
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:
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.
- [6] Solving the Preserving Reversal Median Problem,IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 3, 332-347, 2008.