Sequence Analysis and Molecular Evolution
In the seminar we discuss important and recent research results in the field of algorithmic genome comparison. The seminar can be accounted under "Studienbereich" C or D. In the new MSC Regulations it is W2 B. The goal of the seminar is twofold: 1. The participants should get an insight of the current research in the field 2. The participants will practice to read original research articles, work through them and present the gist of it in a coherent form to the other participants. The mark will be given according to the quality of the slides, the oral representation and the level of participation.
(19579)
| Type | Seminar |
|---|---|
| Instructor | Knut Reinert, Andreas Döring |
| Room | Takustr. 9 SR 055 |
| Time | Thursday 16-18 |
Student Profile
MSc students
Time Table
| 23-Oct-08 | Knut Reinert | SeqAn Library Overview |
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String Indices |
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| 06-Nov-08 | René Märker | Giegerich, Kurtz, Stoye (2003) Efficient implementation of lazy suffix trees |
| Genome Comparison Tools | ||
| 13-Nov-08 | Martin Riese | Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cedric Notredame, Knut Reinert (2008) Segment-based multiple sequence alignment |
| Ricardo Raspe | Michael Brudno et Al (2003) LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA | |
| Next-Gen Sequencing | ||
| 20-Nov-08 | Nicolas Balcazar | Ali Mortazavi, Brian A. Williams, Kenneth McCue, Lorian Schaeffer, Barara Wold (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq |
| Johannes Röhr | Zerbino, Birney (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs | |
| 27-Nov-08 | Jochen Singer | Tobias Wittkop, Jan Baumbach, Francisco P Lobo, Sven Rahmann (2007) Large scale clustering of protein sequences with FORCE -A layout |
| Miscellaneous | ||
| 04-Dec-08 | Jian Li | Marc Fontaine, Stefan Burkhardt, Juha Kärkkäinen (2005) BDD-Based Analysis of Gapped q-Gram Filters |
| Algorithms on Real Hardware | ||
| 18-Dec-08 | Alexander Rose | Schatz, Trapnell, Delcher, Varshney (2007) High-throughput sequence alignment using Graphics Processing Units |
| Lars Langner | Chowdhury, Ramachandran (2006) Cache-Oblivious Dynamic Programming | |