Research Articleposted 2025-06-13 04:34:20
Computing Double-Pushout GraphTransformation Rules and Atom-to-Atom Mapsfrom KEGG RCLASS Data
Nora Beier, Thomas Gatter, Jakob Lykke Andersen, Peter Florian Stadler
Under Review
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Research Articleposted 2024-12-05 07:43:23
Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation
Tsuyoshi Urata, Manato Yokoyama, Haruki Miyaji, Momoko Hayamizu
Under Review
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Research Articleposted 2024-11-18 05:40:46
b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier
Published
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Research Articleposted 2024-11-13 05:24:38
MEM-based pangenome indexing for k-mer queries
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead
Published
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Research Articleposted 2023-12-01 09:44:53
SparseRNAFolD: Optimized Sparse RNA Pseudoknot-Free Folding with Dangle Consideration
Mateo Gray, Sebastian Will, Hosna Jabbari
Published
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Research Articleposted 2023-11-17 19:31:45
Unifying Duplication Episode Clustering andGene-Species Mapping Inference
Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka, Jarosław Paszek
Published
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Research Articleposted 2023-11-08 16:58:50
Fractional Hitting Sets for Efficient Multiset Sketching
Timoth ́e Rouz ́e, Igor Martayan, Camille Marchet, Antoine Limasset
Published
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Research Articleposted 2023-10-30 02:15:38
PFP-FM: An Accelerated FM-index
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
Published
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Research Articleposted 2023-09-27 03:47:35
Infrared: a declarative tree decomposition-powered framework for bioinformatics
Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, Sebastian Will
Published
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Research Articleposted 2023-04-07 13:03:35
Salt corrections for RNA secondary structures in the ViennaRNA package
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Published
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