A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment. - Ryuichiro Nakato; Osamu Gotoh (APBC, 2008)

Cgaln: fast and space-efficient whole-genome alignment. - Ryuichiro Nakato; Osamu Gotoh (BMC Bioinform., 2010)

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. - Ryuichiro Nakato; Katsuhiko Shirahige (Briefings Bioinform., 2017)

Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile. - Ryuichiro Nakato; Katsuhiko Shirahige (Bioinform., 2018)

HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data. - Jiankang Wang; Ryuichiro Nakato (Briefings Bioinform., 2022)

CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells. - Jiankang Wang; Ryuichiro Nakato (Nucleic Acids Res., 2023)