Publications 🗞️

Published Articles

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

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

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

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

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

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

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Talks

• "Deep likelihood-free inference of phylogenetic trees", juin 17 2025,
  CQSB Seminar , slides
• "Deep likelihood-free inference of phylogenetic trees", juin 13 2025,
  DEELOGENY meeting , slides
• "PhyloFormer and phylogenetic reconstruction with deep neural networks", novembre 21 2024,
  LISN Bioinfo seminar , slides , source
• "Phyloformer: fast, accurate and versatile phylogenetic reconstruction with deep neural networks", juin 20 2024,
  MCEB 2024 , slides , source
• "Mapping-friendly sequence reductions: Going beyond homopolymer compression", mai 21 2022,
  RECOMB-SEQ 2022 , slides
• "Can we improve analyses by transforming DNA ?", mai 21 2022,
  RECOMB-SEQ/CCB Joint COmmunication Session 2022 , slides
  *second place award for jargon-free scientific communication

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