2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2026
List of papers

• Lotfi, Jalal, Sayed. plsMD: a plasmid reconstruction tool from short-read assemblies. BMC Bioinformatics, 2026.
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• Jana Ebler, Timofey Prodanov, Andrew Blair, Samuel K. Lee, Peter Ebert, Human Pangenome Reference Consortium, Benedict Paten, Tobias Marschall. Scalable and rare-variant aware genome inference across the 1kGP cohort. bioRxiv, 2026.
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• Garyk Brixi, Matthew G. Durrant, Jerome Ku et al. Genome modelling and design across all domains of life with Evo 2. Nature, 652:1349–1361. 2026.
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• Xian Chang et al.. Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. bioRxiv, 2025.
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• Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer. nPhase: an accurate and contiguous phasing method for polyploids. Genome Biology, 2021.
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• Etienne Conchon-Kerjan, Timothe Rouzé, Lucas Robidou, Florian Ingels, Antoine Limasset. Super Bloom: Fast and precise filter for streaming k-mer queries. bioRxiv, 2026.
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• Ryan D. Doughty, Michael J. Tisza, Todd J. Treangen. bronko: ultrafast, alignment-free detection of viral genome variation. bioRxiv, 2026.
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• Jaebeom Kim,Martin Steinegger. Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers. bioRxiv, 2026.
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• Albert Jiménez-Blanco, Lorién López-Villellas, Juan Carlos Moure, Miquel Moreto, Santiago Marco-Sola. Theseus: fast and optimal affine-gap sequence-to-graph alignment. Bioinformatics, 2026.
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• Authors: Jarno N. Alanko, Lore Depuydt, Camille Marchet, Simon J. Puglisi . Fast Set Operations for Compact k-mer Sets. In 2026.
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• Molly Borowiak, Yun William Yu. KuPID: Kmer-based Upstream Preprocessing of Long Reads for Isoform Discovery. bioRxiv, 2026.
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• Jamshed Khan, Laxman Dhulipala, Rob Patro. Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3. bioRxiv, 2025.
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• Nicola Rizzo, Ragnar Groot Koerkamp. Revisiting O(nloglogn) chaining for anchored edit distance. In 2026.
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• Jarno N. Alanko, Elena Biagi, Simon J. Puglisi. Finimap: fast and accurate single-species bacterial pseudoalignment with finimizers. In 2026.
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