Better quality score compression through sequence-based quality smoothing. - Yoshihiro Shibuya; Matteo Comin (BMC Bioinform., 2019)

Indexing k-mers in linear space for quality value compression. - Yoshihiro Shibuya; Matteo Comin (J. Bioinform. Comput. Biol., 2019)

Efficient Reconciliation of Genomic Datasets of High Similarity. - Yoshihiro Shibuya; Djamal Belazzougui; Gregory Kucherov (WABI, 2022)

Space-efficient representation of genomic k-mer count tables. - Yoshihiro Shibuya; Djamal Belazzougui; Gregory Kucherov (Algorithms Mol. Biol., 2022)

Locality-Preserving Minimal Perfect Hashing of k-mers. - Giulio Ermanno Pibiri; Yoshihiro Shibuya; Antoine Limasset (CoRR, 2022)

Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation. - Yoshihiro Shibuya; Djamal Belazzougui; Gregory Kucherov (J. Comput. Biol., 2022)

Sketching data structures for alignment-free analysis of genomic sequences. (Esquissage de structures de données pour l'analyse de séquences génomiques sans alignements). - Yoshihiro Shibuya (2022)

Locality-preserving minimal perfect hashing of k-mers. - Giulio Ermanno Pibiri; Yoshihiro Shibuya; Antoine Limasset (Bioinform., 2023)

Hyper-k-mers: Efficient Streaming k-mers Representation. - Igor Martayan; Lucas Robidou; Yoshihiro Shibuya; Antoine Limasset (RECOMB, 2025)

Processing-in-memory for genomics workloads. - William Andrew Simon; Leonid Yavits; Konstantina Koliogeorgi; Yann Falevoz; Yoshihiro Shibuya; Dominique Lavenier; Irem Boybat; Klea Zambaku; Berkan Sahin; Mohammad Sadrosadati; Onur Mutlu; Abu Sebastian; et al. (CoRR, 2025)