Publications

  1. Andrej Baláž, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, and Jouni Sirén: Wheeler maps.
    Proc. LATIN 2024, Springer LNCS 14578, pp. 178-192, Puerto Varas, Chile, March 18--22, 2024.
    [Article] [Preprint] [Local copy]
  2. Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, and Benedict Paten:
    A draft human pangenome reference.
    Nature 617:312-324, 2023.
    [Article] [Preprint] [HPRC website]
  3. Jonas A. Sibbesen, Jordan M. Eizenga, Adam M. Novak, Jouni Sirén, Xian Chang, Erik Garrison, and Benedict Paten: Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.
    Nature Methods, 2023.
    [Article] [Preprint] [VG implementation] [RPVG implementation]
  4. Jouni Sirén and Benedict Paten: GBZ file format for pangenome graphs.
    Bioinformatics 38(22):5012-5018, 2022.
    [Article] [Preprint] [Local copy] [Supplement] [C++ implementation] [Rust implementation]
  5. Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, and Jouni Sirén:
    Computational graph pangenomics: a tutorial on data structures and their applications.
    Natural Computing 21:81-108, 2022.
    [Article] [Local copy]
  6. Jouni Sirén, Jean Monlong, Xian Chang, Adam M. Novak, Jordan M. Eizenga, Charles Markello, Jonas A. Sibbesen, Glenn Hickey, Pi-Chuan Chang, Andrew Carroll, Namrata Gupta, Stacey Gabriel, Thomas W. Blackwell, Aakrosh Ratan, Kent D. Taylor, Stephen S. Rich, Jerome I. Rotter, David Haussler, Erik Garrison, and Benedict Paten:
    Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
    Science 374(6574):abg8871, 2021.
    [Article] [Preprint] [Implementation]
  7. Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, and Christina Boucher: Efficiently Merging r-indexes.
    Proc. DCC 2021, IEEE, pp. 203-212, March 23-26, 2021.
    [Article] [Local copy] [Implementation]
  8. Jordan M. Eizenga, Adam M. Novak, Jonas A. Sibbesen, Simon Heumos, Ali Ghaffaari, Glenn Hickey, Xian Chang, Josiah D. Seaman, Robin Rounthwaite, Jana Ebler, Mikko Rautiainen, Shilpa Garg, Benedict Paten, Tobias Marschall, Jouni Sirén, and Erik Garrison: Pangenome Graphs.
    Annual Review of Genomics and Human Genetics 21:139-162, 2020.
    [Article] [Local copy]
  9. Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, and Benedict Paten: Distance indexing and seed clustering in sequence graphs.
    Bioinformatics 36(Supplement_1):i146-i153, 2020.
    [Article] [Preprint] [Local copy] [Implementation]
  10. Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, and Benedict Paten:
    Genotyping structural variants in pangenome graphs using the vg toolkit.
    Genome Biology 21:35, 2020.
    [Article] [Preprint] [Local copy] [Supplement] [Implementation]
  11. Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, and Richard Durbin: Haplotype-aware graph indexes.
    Bioinformatics 36(2):400-407, 2020.
    [Article] [Preprint] [Local copy] [Supplement] [Implementation]
  12. 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.
    [Article] [Preprint] [Implementation]
  13. 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.
    [Article] [Preprint] [Local copy] [Journal version] [Slides] [Implementation]
  14. Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, and Jouni Sirén: Relative Suffix Trees.
    The Computer Journal 61(5):773-788, 2018.
    [Article] [Preprint] [Local copy] [Implementation]
  15. Travis Gagie, Giovanni Manzini, and Jouni Sirén: Wheeler graphs: A framework for BWT-based data structures.
    Theoretical Computer Science 698:67-78, 2017.
    [Article] [Local copy]
  16. 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.
    [Article] [Preprint] [Local copy] [Implementation]
  17. Jouni Sirén: Indexing Variation Graphs.
    Proc. ALENEX 2017, SIAM, pp. 13-27, Barcelona, Spain, January 17-18, 2017.
    [Article] [Preprint] [Local copy] [Slides] [Implementation]
  18. 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.
    [Article] [Local copy] [Full version] [Implementation]
  19. Jouni Sirén: Burrows-Wheeler transform for terabases.
    Proc. DCC 2016, IEEE, pp. 211-220, Snowbird, UT, USA, March 29 - April 1, 2016.
    [Article] [Local copy] [Full version] [Slides] [Implementation]
  20. 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.
    [Article] [Preprint] [Local copy] [Slides] [Implementation]
  21. 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, UT, USA, April 7-9, 2015.
    [Article] [Local copy] [Full version] [Journal version] [Slides] [Implementation]
  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.
    Software: Practice and Experience 45(3):399-434, 2015.
    [Article] [Local copy]
  23. 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.
    [Article] [Preprint] [Local copy] [Slides] [Implementation]
  24. 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.
    [Article] [Local copy] [Full version] [Journal version] [Slides] [Implementation]
  25. 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.
    [Article] [Local copy] [Implementation]
  26. Paolo Ferragina, Jouni Sirén, and Rossano Venturini: Distribution-aware compressed full-text indexes.
    Algorithmica 67(4):529-546, 2013.
    [Article] [Local copy] [Implementation]
  27. 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.
    [Article] [Local copy] [Journal version] [Slides] [Implementation]
  28. 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.
    [Article] [Preprint] [Local copy] [Journal version] [Implementation]
  29. 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.
    [Article] [Preprint] [Local copy] [Full version] [Journal version] [Slides] [Implementation]
  30. Jouni Sirén: Sampled Longest Common Prefix Array.
    Proc. CPM 2010, Springer LNCS 6129, pp. 227-237, New York City, NY, USA, June 21-23, 2010.
    [Article] [Preprint] [Local copy] [Full version] [Slides] [Implementation]
  31. 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.
    [Article] [Preprint] [Local copy]
  32. 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.
    [Article] [Preprint] [Local copy] [Journal version]
  33. Jouni Sirén: Compressed Suffix Arrays for Massive Data.
    Proc. SPIRE 2009, Springer LNCS 5721, pp. 63-74, Saariselkä, Finland, August 25-27, 2009.
    [Article] [Preprint] [Local copy] [Slides] [Implementation]
  34. 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.
    [Article] [Preprint] [Local copy] [Journal version]
  35. 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.
    [Article] [Preprint] [Local copy] [Journal version] [Slides]

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