Author

Yoshihiro Shibuya

Institut PasteurORCID 0000-0002-3137-1504Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Research Focus:benchmarking· 2 Assay:DNA methylation· 1 Research Focus:software / tool· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Djamal BelazzouguiiD· 2 shared Grégory KucheroviD· 2 shared Antoine LimassetiD· 1 shared Bertrand Le GaliD· 1 shared Giulio Ermanno PibiriiD· 1 shared Igor MartayaniD· 1 shared Lucas RobidouiD· 1 shared Pierre PeterlongoiD· 1 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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2 shared papersBioinformatics

Djamal BelazzouguiORCID

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4 papers

Recent·Most cited

Kaminari: a resource-frugal index for approximate colored k-mer queries

Victor Levallois, Yoshihiro Shibuya, Bertrand Le Gal, Yoann Dufresne, Rob Patro, Pierre Peterlongo, Giulio Ermanno Pibiri

Kaminari improves approximate k-mer query performance by using k-mer minimizers and integer compression, outperforming Bloom filters in memory and speed with minimal false positive impact.

Bioinformatics Advances · Jan 1, 2026Peer-reviewedBioinformatics

Hyper-k-mers: efficient streaming k-mers representation

Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset

The paper introduces hyper-k-mers, a more efficient k-mer representation, and presents KFC, a tool that significantly reduces memory usage and improves speed for k-mer counting.

bioRxiv · Nov 6, 2024 · PreprintBioinformatics

Efficient reconciliation of genomic datasets of high similarity

Yoshihiro Shibuya, Djamal Belazzougui, Grégory Kucherov

The paper introduces a method using IBLTs and syncmers to efficiently estimate Jaccard similarity and identify differing k-mers between genomic datasets.

bioRxiv · Jun 7, 2022 · PreprintBioinformatics

Set-Min sketch: a probabilistic map for power-law distributions with application to k-mer annotation

Yoshihiro Shibuya, Djamal Belazzougui, Grégory Kucherov

The paper introduces Set-Min sketch, a probabilistic data structure for representing k-mer count tables with improved accuracy over existing methods.

Journal of Computational Biology · Jan 20, 2022Peer-reviewedBioinformatics