Bioinformatics Journal Club (AG Genome Informatics)

Bioinformatics Journal Club

Summer Semester 2007

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

Jens Stoye and Klaus-Bernd Schürmann


  • Algorithms for MassSpectrometry (responsible: Jens Stoye)
  • String indexing without suffix trees or suffix arrays (responsible: Peter Husemann)
  • Approximation Algorithms for Gene Glusters (responsible: Tahir Ejaz)

Time table:

03.04.07 Jens Stoye, Klaus-Bernd Schürmann Preliminaries
16.04.07 Nils, Heiko und Jens Listgarten and Andrew, Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry, Molecular and Cellular Proteomics 4(4), 419-434, 2006. pdf
23.04.07 Heiko Neuweger Truong et al. , Learning a Complex Metabolomic Dataset using Random Forests and Support Vector Machines, In Proceedings of the tenth ACM international conference on Knowledge discovery and data mining (SIGKDD 2004) , 835-840, 2004. pdf
07.05.07 Wiebke Timm Mallick et al. , Computational prediction of proteotypic peptides for quantitative proteomics, Nature Biotechnology 25(1), 125-131, 2007. pdf
14.05.07 Nils Hoffmann Salvador and Chan, FastDTW: Toward Accurate Dynamic Time Warping in Linear Time and Space; Technical Report, Florida Institute of Technology, Melbourne, 2004. pdf
21.05.07 Peter Husemann Kärkkäinen, Suffix Cactus: A cross between suffix tree and suffix array; In Proceedings of the 6th Annual Symposium on Combinatorial Pattern Matching (CPM 1995) , 191-204, 1995. pdf
04.06.07 Klaus-Bernd Schürmann Allauzen et al. , Factor Oracle: a new structure for pattern matching, In Proceedings of the 26th Conference on Current Trends in Theory and Practice of Informatics on Theory and Practice of Informatics (SOFSEM 1999) , 295-310, 1999. pdf
11.06.07 José Augusto Amgarten Quitzau Rasmussen et al. , Efficient q-Gram Filters for Finding All Epsilon-Matches over a Given Length, Journal of Computational Biology 13(2), 296-308, 2006. pdf
18.06.07 Tahir Ejaz Caprara, Sorting Permutations by Reversals and Eulerian Cycle Decompositions, SIAM Journal on Discrete Mathematics 12(1), 91-110, 1999. pdf
25.06.07 Roland Wittler Elias and Hartman, A 1.375-Approximation Algorithm for Sorting by Transpositions, IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(4), 369-379, 2006. pdf
02.07.07 Katharina Jahn Rahman et al. , An Approximation Algorithm for Sorting by Reversals and Transpositions, In Proceedings of the Workshop on Algorithms and Computation (WALCOM 2007) , 97-108, 2007. pdf
09.07.07 Roland Wittler Knuth, The Toilet Paper Problem, The American Mathematical Monthly 91(8), 465-470, 1984. pdf