Research Interests

Journal Papers

• Juha Kärkkäinen, Peter Sanders and Stefan Burkhardt.
  Linear work suffix array construction. J. ACM, 53 (6), 2006, pp. 918-936.
  [JACM] [preliminary version(pdf)]
• Stefan Burkhardt and Juha Kärkkäinen. Better filtering with gapped q-grams.
  Fundamenta Informaticae 56 (1-2), 2003, pp. 51-70. Special issue on Computing Patterns in Strings.
  [.ps]

Conference Papers

• Stefan Burkhardt and Kimmo Fredriksson and Tuomas Ojamies and Janne Ravantti and Esko Ukkonen.
  Local approximate 3D matching of proteins in viral cryo-EM density maps
  In Proc. 2nd International Symposium on 3D Data Processing, Visualization and Transmission (3DPVT '04), pp. 979-986.
  [.ps] [code]
• Marc Fontaine and Stefan Burkhardt and Juha Kärkkäinen.
  BDD-Based Analysis of Gapped q-Gram Filters
  In Prague Stringology Conference 2004 (PSC '04), pp. 56-68.
  [.ps]
• Stefan Burkhardt and Juha Kärkkäinen.
  Fast lightweight suffix array construction and checking
  In Proc. 14th Symposium on Combinatorial Pattern Matching (CPM '03), LNCS 2676, Springer, 2003, pp. 55-69.
  [.ps] [code] [conference presentation (pdf)]
• Stefan Burkhardt and Juha Kärkkäinen.
  One-gapped q-gram filters for Levenshtein distance
  In Proc. 13th Symposium on Combinatorial Pattern Matching (CPM '02), LNCS 2373, Springer 2002, pp. 225-234.
  [.ps]
• Stefan Burkhardt and Juha Kärkkäinen.
  Better filtering with gapped q-grams
  In Proc. 12th Symposium on Combinatorial Pattern Matching (CPM '01), LNCS 2089, Springer 2001, pp. 73-85.
  [.ps] [conference presentation (power point)]
• Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals and Martin Vingron.
  q-gram based database searching using a suffix array
  In Proc. 3rd Annual International Conference on Computational Molecular Biology (RECOMB '99), ACM Press 1999, pp. 77-83.
  [.ps] [conference presentation (power point)] [code] [example data for x86]

PhD Thesis

• Stefan Burkhardt.
  Filter Algorithms for Approximate String Matching
  Department of Computer Science, Saarland University, 2002.
  [.ps] [defense (power point)]