I'm an Australian computer scientist based in Finland. I lead the Compressed Data Structures group at UH, within the Algorithmic Bioinformatics supergroup.

My research is on efficient algorithms and data structures for searching, storing, and manipulating sequences, trees and graphs, with particular focus on applications in genomics.

My group has been supported by the Research Council of Finland, the NSF, EU Horizon 2020, the Royal Society, the Australian Research Council, and the Japan Society for the Promotion of Science.

Email
simon.puglisi [at] helsinki.fi
Office
A238, Exactum, Kumpula Campus
Post
University of Helsinki
Department of Computer Science
P.O. Box 68
(Pietari Kalmin katu 5)
FI-00014
Finland

All publications

A fairly complete list is at DBLP, and there is also Google Scholar.

Selected

  • New space-time tradeoffs for subset rank and k-mer lookup. Anastasia C. Diseth, Simon J. Puglisi. ALENEX 2027, to appear. preprint
  • Finimizers: variable-length bounded-frequency minimizers for k-mer sets. Jarno N. Alanko, Elena Biagi, Simon J. Puglisi. IEEE Transactions on Computational Biology and Bioinformatics, 2025. doi preprint
  • Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes. Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi. Bioinformatics 39 (Suppl. 1): i260–i269, 2023 (ISMB 2023). doi
  • Small searchable k-spectra via subset rank queries on the spectral Burrows-Wheeler transform. Jarno N. Alanko, Simon J. Puglisi, Jaakko Vuohtoniemi. Proc. SIAM Conference on Applied and Computational Discrete Algorithms (ACDA), pp. 225–236, 2023. doi
  • Data structures based on k-mers for querying large collections of sequencing data sets. Camille Marchet, Christina Boucher, Simon J. Puglisi, Paul Medvedev, Mikaël Salson, Rayan Chikhi. Genome Research 31(1): 1–12, 2021. doi

Steering committees

  • ESA, European Symposium on Algorithms
  • SEA, Symposium on Experimental Algorithms
  • DSB, Workshop on Data Structures for Bioinformatics
  • Sequences in London

PC chairing

  • CPM 2024 (in Fukuoka, with Shunsuke Inenaga)
  • ESA 2023 (in Amsterdam, with Inge Li Gørtz and Martin Farach-Colton)
  • MFCS 2021 (in Tallinn, with Filippo Bonchi)
  • SPIRE 2019 (in Segovia, with Nieves Brisaboa)
  • SEA 2017 (in London, with Rajeev Raman and Solon Pissis)
  • IWOCA 2016 (in Helsinki, with Veli Mäkinen)
  • SPIRE 2015 (in London, with Emine Yilmaz and Costas Iliopoulos)

I have also served on many programme committees, including ALENEX, ISMB, ESA, CPM, SEA, IWOCA, and SPIRE.

Keynotes

ESA 2022 (Berlin), SEA 2018 (L'Aquila), PSC 2017 (Prague), MatBio 2016 (London)

Editorial

  • Associate Editor, ACM Journal of Experimental Algorithmics, 2014–2022
  • Steering committee, SPIRE, 2015–2022

Current

  • Jarno Alanko (Postdoc, U. Helsinki)
  • Lore Depuydt (Postdoc, U. Lille)
  • Elena Biagi (PhD, U. Helsinki)
  • Anastasia Diseth (PhD, U. Helsinki)
  • Saska Dönges (PhD, U. Helsinki)
  • Klára Sladečková (PhD, U. Lille)
  • Sehar Naveed (PhD, Goldsmiths, U. London)

Former

  • Bella Zhukova (U. Helsinki, 2024 — now at ePassi)
  • Christopher Hoobin (RMIT, 2015 — now at NASDAQ)
  • Jasbir Dhaliwal (RMIT, 2014 — now at Monash U.)
  • Shanika Kuruppu (U. Melbourne, 2013 — now at Google)

I travel lots.
I love reading.

I enjoy listening to Shintaro Sakamoto, Arvo Pärt, Colleen, Boards of Canada, and various other music.

Science at the Edge
The Long Now Foundation

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