Unité Algorithmes pour les séquences biologiques

Domaines scientifiques déclarés au RNSR

Mots-clés des publications HAL repérées

Publications HAL récentes repérées

• Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites · 2026

  Résumé de la publication : Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we identified and characterized the defence hotspots of thousands of P2-like phages and P4-like satellites to elucidate the origins and evolutionary dynamics of defence…

• Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites · 2026

  Résumé de la publication : Abstract Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we identified and characterized the defence hotspots of thousands of P2-like phages and P4-like satellites to elucidate the origins and evolutionary dynamics of…

• Lossless compression of k-mer matrices enabling random row access · 2026

  Résumé de la publication : Genomic search engines such as Logan-Search index petabytes of sequencing data as large binary matrices, called k-mer matrices, where each row encodes the presence of a k-mer across thousands to millions of genomic samples. Logan-Search contains a petabyte of binary matrices, and…

• BFVD—a large repository of predicted viral protein structures · 2025

  Résumé de la publication : The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences, severely limiting their study. To address this, we created…

• Fractional hitting sets for efficient multiset sketching · 2025

  Résumé de la publication : The exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashing techniques have successfully transformed large datasets into smaller, more manageable sketches while maintaining comparability using metrics such…