Bioinformatics Journal Club (AG Genome Informatics)

Bioinformatics Journal Club

Winter Semester 2006/2007

Every Tuesday, 18.00 c.t., U10-146

Jens Stoye


  • Prediction of transcription start sites and alternative promoters
  • Genome rearrangement: gene clusters and rearrangement medians
  • Massively parallel DNA sequencing techniques

Time table:

17.10.06 Preliminaries
24.10.06 Sten Ilmjärv Introduction to "Prediction of transcription start sites and alternative promoters" summary
paper 1
paper 2

31.10.06 Katharina Pernhorst Cohen et al. , Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins, PNAS 103(15), 5682-5687, 2006. pdf
07.11.06 Jens Stoye Michael et al. , Suboptimal local alignments across multiple scoring schemes, Proceedings of WABI 2004, LNBI 3240, 99-110, 2004. pdf
14.11.06 Jan Baumbach Davuluri et al. , Computational identification of promoters and first exons in the human genome, Nature Genetics 29, 412-417, 2001. pdf
21.11.06 ---
28.11.06 Roland Wittler
Jens Stoye
Introduction to "Rearrangement medians and gene clusters" paper 1
paper 2
05.12.06 Leo van Iersel Caprara, The reversal median problem, INFORM J. Computing 15(1), 93-113, 2003. pdf
12.12.06 Søren Besenbacher Pe'er and Shamir, Approximation algorithms for the permutations median problem in the breakpoint model in comparative genomics, in Sankoff and Nadeau: Comparative Genomics, 225-241, Kluwer Academic Publisher, 2000. pdf
19.12.06 Katharina Jahn Schmidt and Stoye, Quadratic time algorithms for finding common intervals in two and more sequences, Proceedings of CPM 2004, LNCS 3109, 347-358, 2004. pdf
09.01.07 Inke Hildebrandt Bergeron et al. , The algorithmic of gene teams, Proceedings of WABI 2002, LNCS 2452, 464-476, 2002. pdf
16.01.07 Tahir Ejaz Chauve et al. , On common intervals with errors, Technical Report 2006-02, Technische Fakultät der Universität Bielefeld, 2006. pdf
23.01.07 Sven Rahmann Introduction to "Massively parallel DNA sequencing techniques" paper 1
paper 2
30.01.07 N.N. Noonan et al. , Sequencing and analysis of Neanderthal genomic DNA, Science 314, 1113-1118, 2006. pdf
06.02.07 N.N. Angly et al. , The marine viromes of four oceanic regions, PLoS Biology 4(11), e368, 2006. pdf