Publications

  1. Travis Gagie, Giovanni Manzini, and Jouni Sirén: Wheeler graphs: A framework for BWT-based data structures.
    Accepted to Theoretical Computer Science, 2017.
  2. Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, and Jouni Sirén: Document retrieval on repetitive string collections.
    Information Retrieval Journal 20(3):253-291, 2017.
  3. Jouni Sirén: Indexing Variation Graphs.
    Proc. ALENEX 2017, SIAM, pp. 13-27, Barcelona, Spain, January 17-18, 2017.
  4. Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, and Jouni Sirén: RLZAP: Relative Lempel-Ziv with Adaptive Pointers.
    Proc. SPIRE 2016, Springer LNCS 9954, pp. 1-14, Beppu, Japan, October 18-20, 2016.
  5. Jouni Sirén: Burrows-Wheeler transform for terabases.
    Proc. DCC 2016, IEEE, pp. 211-220, Snowbird, Utah, USA, March 29 - April 1, 2016.
  6. Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, and Jouni Sirén: Relative Select.
    Proc. SPIRE 2015, Springer LNCS 9309, pp. 149-155, London, UK, September 1-3, 2015.
  7. Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, and Jouni Sirén: Document Counting in Compressed Space.
    Proc. DCC 2015, IEEE, pp. 103-112, Snowbird, Utah, USA, April 7-9, 2015.
  8. Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyên, Jouni Sirén, and Niko Välimäki: Fast In-Memory XPath Search using Compressed Indexes.
    Software: Practice and Experience 45(3):399-434, 2015.
  9. Djamal Belazzougui, Travis Gagie, Simon Gog, Giovanni Manzini, and Jouni Sirén: Relative FM-indexes.
    Proc. SPIRE 2014, Springer LNCS 8799, pp. 52-65, Ouro Preto, Brazil, October 20-22, 2014.
  10. Gonzalo Navarro, Simon J. Puglisi, and Jouni Sirén: Document Retrieval on Repetitive Collections.
    Proc. ESA 2014, Springer LNCS 8737, pp. 725-736, Wroclaw, Poland, September 8-10, 2014.
  11. Jouni Sirén, Niko Välimäki, and Veli Mäkinen: Indexing Graphs for Path Queries with Applications in Genome Research.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 11(2):375-388, 2014.
  12. Paolo Ferragina, Jouni Sirén, and Rossano Venturini: Distribution-aware compressed full-text indexes.
    Algorithmica 67(4):529-546, 2013.
  13. Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, and Jouni Sirén: Document Listing on Repetitive Collections.
    Proc. CPM 2013, Springer LNCS 7922, pp. 107-119, Bad Herrenalb, Germany, June 17-19, 2013.
  14. Paolo Ferragina, Jouni Sirén, and Rossano Venturini: Distribution-Aware Compressed Full-Text Indexes.
    Proc. ESA 2011, Springer LNCS 6942, pp. 760-771, Saarbrücken, Germany, September 5-7, 2011.
  15. Jouni Sirén, Niko Välimäki, and Veli Mäkinen: Indexing Finite Language Representation of Population Genotypes.
    Proc. WABI 2011, Springer LNCS 6833, pp. 270-281, Saarbrücken, Germany, September 5-7, 2011.
  16. Jouni Sirén: Sampled Longest Common Prefix Array.
    Proc. CPM 2010, Springer LNCS 6129, pp. 227-237, New York, USA, June 21-23, 2010.
  17. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, and Niko Välimäki: Storage and Retrieval of Highly Repetitive Sequence Collections.
    Journal of Computational Biology 17(3):281-308, 2010.
  18. Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyên, Jouni Sirén, and Niko Välimäki: Fast In-Memory XPath Search using Compressed Indexes.
    Proc. ICDE 2010, IEEE, pp. 417-428, Long Beach, California, USA, March 1-6, 2010.
  19. Jouni Sirén: Compressed Suffix Arrays for Massive Data.
    Proc. SPIRE 2009, Springer LNCS 5721, pp. 63-74, Saariselkä, Finland, August 25-27, 2009.
  20. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, and Niko Välimäki: Storage and Retrieval of Individual Genomes.
    Proc. RECOMB 2009, Springer LNCS 5541, pp. 121-137, Tucson, Arizona, USA, May 18-21, 2009.
  21. Jouni Sirén, Niko Välimäki, Veli Mäkinen, and Gonzalo Navarro: Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections.
    Proc. SPIRE 2008, Springer LNCS 5280, pp. 164-175, Melbourne, Australia, November 10-12, 2008.