Publications 🗞️

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Published Articles

1. (2025) - Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau & Laurent Jacob.
   "Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks"
   in Molecular Biology and Evolution : p.msaf051. 10.1093/molbev/msaf051

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2. (2022) - Luc Blassel, Paul Medvedev & Rayan Chikhi.
   "Mapping-friendly sequence reductions: going beyond homopolymer compression"
   in iScience : p.105305. 10.1016/j.isci.2022.105305

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3. (2021) - Luc Blassel, Anna Zhukova, Christian J Villabona-Arenas, Katherine E Atkins, Stéphane Hué & Olivier Gascuel.
   "Drug resistance mutations in HIV: new bioinformatics approaches and challenges"
   in Current Opinion in Virology (51) : p.56-64. 10.1016/j.coviro.2021.09.009

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4. (2021) - Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué & Olivier Gascuel.
   "Using machine learning and big data to explore the drug resistance landscape in HIV"
   in PLOS Computational Biology (17) : p.e1008873. 10.1371/journal.pcbi.1008873

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5. (2021) - Anna Zhukova, Luc Blassel, Frédéric Lemoine, Marie Morel, Jakub Voznica & Olivier Gascuel.
   "Origin, evolution and global spread of SARS-CoV-2"
   in Comptes Rendus. Biologies (344) : p.57-75. 10.5802/crbiol.29

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6. (2020) - Frédéric Lemoine, Luc Blassel, Jakub Voznica & Olivier Gascuel.
   "COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM"
   in Bioinformatics (37) : p.1761-1762. 10.1093/bioinformatics/btaa871

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Preprints & Submitted Articles

1. (2026) - Vincent Garot, Luc Blassel, Luca Nesterenko, Anna Zhukova, Samuel Alizon & Laurent Jacob.
   "Teddy: neural inference of epidemiological parameters from viral sequences"
   in bioRxiv : p.2026.01.05.697728. 10.64898/2026.01.05.697728

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2. (2025) - Luc Blassel, Bastien Boussau, Nicolas Lartillot & Laurent Jacob.
   "Likelihood-free inference of phylogenetic tree posterior distributions"
   in arXiv 10.48550/arXiv.2510.12976

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Talks

• "Likelihood-free inference of phylogenetic tree posterior distributions", December 11 2025,
  LEGEND 2025 , slides
• "Likelihood-free inference of phylogenetic tree posterior distributions", November 27 2025,
  LEGO 2025 , slides
• "Deep end-to-end likelihood-free inference of phylogenetic trees", September 11 2025,
  MLCB 2025 , slides
• "Deep likelihood-free inference of phylogenetic trees", September 8 2025,
  MASAMB 2025 , slides
• "Deep likelihood-free inference of phylogenetic trees", June 17 2025,
  CQSB Seminar , slides
• "Deep likelihood-free inference of phylogenetic trees", June 13 2025,
  DEELOGENY meeting , slides
• "PhyloFormer and phylogenetic reconstruction with deep neural networks", November 21 2024,
  LISN Bioinfo seminar , slides , source
• "Phyloformer: fast, accurate and versatile phylogenetic reconstruction with deep neural networks", June 20 2024,
  MCEB 2024 , slides , source
• "Mapping-friendly sequence reductions: Going beyond homopolymer compression", May 21 2022,
  RECOMB-SEQ 2022 , slides
• "Can we improve analyses by transforming DNA ?", May 21 2022,
  RECOMB-SEQ/CCB Joint COmmunication Session 2022 , slides
  *second place award for jargon-free scientific communication