Bioinformatics Journal Club, Winter 2005/2006

18.10.05 Vorbesprechung
08.11.05 Constantin Bannert Introduction HIV {{:teaching:2005winter:jclub:paper:2005-11_jclub_hiv.pdf | Talk }}
15.11.05 Sebastian Oehm HIV: Computational design of antiviral RNA interference strategies {{:teaching:2005winter:jclub:paper:hiv_computational_design_of_antiviral_rna_interference_strategies.pdf | Paper }}
22.11.05 Sven Rahmann HIV: Learning Multiple Evolutionary Pathways from Cross-Sectional Data {{:teaching:2005winter:jclub:paper:jclub-beerenwinkel-hiv.pdf | Paper1 }} ,
{{:teaching:2005winter:jclub:paper:beerenwinkel-jcb-trees.pdf | Paper2 }}
29.11.05 Sridhar Hariharaputran HIV: Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes {{:teaching:2005winter:jclub:paper:geno2pheno.pdf | Paper }}
06.12.05 Klaus-Bernd Schürmann Introduction: A tutorial of recent developments in the seeding of local alignment. Brown et al. {{:teaching:2005winter:jclub:paper:tutorial_brown.pdf | Paper }}
13.12.05 -- Christmas party
20.12.05 Jens Stoye
Wolfgang Gerlach
Efficient q-Gram Filters for Finding epsilon-Matches
Better filtering with gapped q-grams, Burkhardt and Kärkkäinen
{{:teaching:2005winter:jclub:paper:swiftfinal.pdf | Paper1 }}
{{:teaching:2005winter:jclub:paper:qgram_bur_kar.pdf | Paper2 }}
10.01.06 José Augusto Amgarten Quitzau Designing seeds, Buhler et al. {{:teaching:2005winter:jclub:paper:buhler-seeds.pdf | Paper }}
17.01.06 Brona Brejová Knowing more about alignments helps in finding them {{:teaching:2005winter:jclub:paper:04seedscoding.pdf | Paper1 }} {{:teaching:2005winter:jclub:paper:bre-bro-vin-2003.pdf | Paper2 }}
24.01.06 Lars Ulveland Introduction to Parameterized Complexity:
"Parameterized complexity for the skeptic", read chapters 1, 2, 3.2 and 4.3.1
"Ubiquitous parameterization...", read chapters 1, 2, 3, 4.2.


{{:teaching:2005winter:jclub:paper:ccc.pdf | Downey }}
{{:teaching:2005winter:jclub:paper:mfcs04.pdf | Niedermeier }}

31.01.06 Ferdinando Cicalese Peter Damaschke:
On the fixed parameter enumerability of Cluster Editing
in proceeding of WG 2005, LNCS 3787 pp. 283-294, 2005.

Peter Damaschke:
Parametrized Enumeration, Transversals, and Imperfect Phylogeny Reconstruction
to appear in Theoretical Computer Science Special Issue IWPEC 2004 ,
Preliminary version in LNCS 3162, pp. 1-12.






{{:teaching:2005winter:jclub:paper:damaschke_cluster.pdf | Damaschke1 }}


{{:teaching:2005winter:jclub:paper:tcs_version_of_ppfptsj.pdf | Damaschke2 }}


07.02.06 Sebastian Böcker Jens Gramm and Rolf Niedermeier:
Breakpoint Medians and Breakpoint Phylogenies: A Fixed-Parameter Approach
Bioinformatics 18 (Suppl. 2), S128-S139, 2002. (Proceedings of ECCB 2002)

{{:teaching:2005winter:jclub:paper:breakpointphylogenies-fpt-eccb02.pdf | GrammNiedermeier }}