Publications, manuscripts and presentations

Publications

2008

• The effect of sequence quality on sequence alignments.
  Ketil Malde.
  Bioinformatics, accepted for publication.
• Repeats and EST analysis for new organisms.
  Ketil Malde and Inge Jonassen.
  BMC Bioinformatics, 9:23

2006

• RBR: Library-less Repeat Detection in ESTs.
  Ketil Malde, Korbinian Schneeberger, Eivind Coward, and Inge Jonassen.
  Bioinformatics, 22(18):2232-2236.
• Calculating PSSM Probabilities with Lazy Dynamic Programming.
  Ketil Malde and Robert Giegerich.
  Journal of Functional Programming, 16(1):75-81.

2005

• Masking Repeats while Clustering ESTs.
  Korbinian Schneeberger, Ketil Malde, Eivind Coward and Inge Jonassen.
  Nucleic Acids Research, 33(7):2176-2180.
• Algorithms for the Analysis of Expressed Sequence Tags.
  Ketil Malde
  Thesis for the degree of dr. scient.
  Department of Informatics, University of Bergen.
• A graph based algorithm for generating EST consensus sequences.
  Ketil Malde, Eivind Coward, and Inge Jonassen.
  Bioinformatics, 21(8):1371-1375.

2004

• Space-efficient incremental single-linkage clustering.
  Ketil Malde.
  (unpublished)

2003

• Fast sequence clustering using a suffix array algorithm.
  Ketil Malde, Eivind Coward, and Inge Jonassen:
  Bioinformatics , 19(10):1221-1226.

Presentations

• Thesis defense, introduction
• Thesis defense, closing words
• Computing the high-end distribution from lazy permutations (AGPI seminar)
• Sequence clustering and other string related problems in bioinformatics (CBU seminar)
• A tool for constructing EST splice graphs and consensus sequence assembly - abstract and poster from RECOMB2004
• Sequence Clustering with Suffix Arrays - abstract, slides and photos from the BREW03 workshop in Bielefeld.
• Presentation at the BFYS meeting at Vatnahalsen in March 2003, including the (silly) poster The Genome Puzzle and the the slides from my presentation there
• The abstract for my presentation at WABI2002, and the corresponding slides.

Other

• The Lazy Back Door - a small Haskell tutorial on how to report progress from pure code. Published in The Monad Reader.