Bioinformatics Journal Club

Winter Semester 2006/2007

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

Jens Stoye

Topics:

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"	{{:teaching:2006winter:jclub:papers:alternative promoter paper.pdf \| summary }} {{:teaching:2006winter:jclub:papers:lan-mag-wil-2003.pdf \| paper 1 }} {{:teaching:2006winter:jclub:papers:kim-wak-suz-ota-xxx-2006.pdf \| 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.	{{:teaching:2006winter:jclub:papers:coh-kli-bou-nit-xxx-2006.pdf \| 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.	{{:teaching:2006winter:jclub:papers:mic-die-sto-2004.pdf \| 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.	{{:teaching:2006winter:jclub:papers:dav-gro-zha-2001.pdf \| pdf }}
21.11.06		---
28.11.06	Roland Wittler Jens Stoye	Introduction to "Rearrangement medians and gene clusters"	{{:teaching:2006winter:jclub:papers:san-sun-kec-1996.pdf \| paper 1 }} {{:teaching:2006winter:jclub:papers:hob-dur-2005.pdf \| paper 2 }}
05.12.06	Leo van Iersel	Caprara, The reversal median problem, INFORM J. Computing 15(1), 93-113, 2003.	{{:teaching:2006winter:jclub:papers:cap-2003.pdf \| 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.	{{:teaching:2006winter:jclub:papers:pee-sha-2000.pdf \| 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.	{{:teaching:2006winter:jclub:papers:sch-sto-2004.pdf \| pdf }}
09.01.07	Inke Hildebrandt	Bergeron et al. , The algorithmic of gene teams, Proceedings of WABI 2002, LNCS 2452, 464-476, 2002.	{{:teaching:2006winter:jclub:papers:ber-cor-raf-2002.pdf \| pdf }}
16.01.07	Tahir Ejaz	Chauve et al. , On common intervals with errors, Technical Report 2006-02, Technische Fakultät der Universität Bielefeld, 2006.	{{:teaching:2006winter:jclub:papers:cha-die-heb-mix-xxx-2006.pdf \| pdf }}
23.01.07	Sven Rahmann	Introduction to "Massively parallel DNA sequencing techniques"	{{:teaching:2006winter:jclub:papers:ber-tur-tai-dro-2006.pdf \| paper 1 }} {{:teaching:2006winter:jclub:papers:tau-tro-bek-goe-xxx-2006.pdf \| paper 2 }}
30.01.07	N.N.	Noonan et al. , Sequencing and analysis of Neanderthal genomic DNA, Science 314, 1113-1118, 2006.	{{:teaching:2006winter:jclub:papers:noo-coo-kud-smi-xxx-2006.pdf \| pdf }}
06.02.07	N.N.	Angly et al. , The marine viromes of four oceanic regions, PLoS Biology 4(11), e368, 2006.	{{:teaching:2006winter:jclub:papers:ang-fel-bre-sal-xxx-2006.pdf \| pdf }}