Publications

  1. Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, and Richard Durbin: Haplotype-aware graph indexes.
    Accepted to Bioinformatics, 2019.
  2. Erik Garrison, Jouni Sirén, Adam M. Novak, Glenn Hickey, Jordan M. Eizenga, Eric T. Dawson, William Jones, Shilpa Garg, Michael F. Lin, Benedict Paten, and Richard Durbin:
    Variation graph toolkit improves read mapping by representing genetic variation in the reference.
    Nature Biotechnology 36(9):875-879, 2018.
  3. Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, and Richard Durbin: Haplotype-aware graph indexes.
    Proc. WABI 2018, LIPIcs 113, pp. 4:1-4:13, Helsinki, Finland, August 20-22, 2018.
  4. Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, and Jouni Sirén: Relative Suffix Trees.
    The Computer Journal 61(5):773-788, 2018.
  5. Travis Gagie, Giovanni Manzini, and Jouni Sirén: Wheeler graphs: A framework for BWT-based data structures.
    Theoretical Computer Science 698:67-78, 2017.
  6. 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.
  7. Jouni Sirén: Indexing Variation Graphs.
    Proc. ALENEX 2017, SIAM, pp. 13-27, Barcelona, Spain, January 17-18, 2017.
  8. 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.
  9. Jouni Sirén: Burrows-Wheeler transform for terabases.
    Proc. DCC 2016, IEEE, pp. 211-220, Snowbird, Utah, USA, March 29 - April 1, 2016.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Paolo Ferragina, Jouni Sirén, and Rossano Venturini: Distribution-aware compressed full-text indexes.
    Algorithmica 67(4):529-546, 2013.
  17. 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.
  18. 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.
  19. 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.
  20. Jouni Sirén: Sampled Longest Common Prefix Array.
    Proc. CPM 2010, Springer LNCS 6129, pp. 227-237, New York, USA, June 21-23, 2010.
  21. 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.
  22. 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.
  23. Jouni Sirén: Compressed Suffix Arrays for Massive Data.
    Proc. SPIRE 2009, Springer LNCS 5721, pp. 63-74, Saariselkä, Finland, August 25-27, 2009.
  24. 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.
  25. 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.