Algorithmic Bioinformatics

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
 

String Indices

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