Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. - Hiroyuki Toh (Comput. Appl. Biosci., 1997)

A method for comparing circular genomes from gene locations: application to mitochondrial genomes. - Katsuhisa Horimoto; Mikita Suyama; Hiroyuki Toh; Kentaro Mori; Jinya Otsuka (Bioinform., 1998)

Statistical estimation of cluster boundaries in gene expression profile data. - Katsuhisa Horimoto; Hiroyuki Toh (Bioinform., 2001)

Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling. - Hiroyuki Toh; Katsuhisa Horimoto (Bioinform., 2002)

Deduction of a gene regulatory relationship framework from gene expression data by the application of graphical Gaussian modeling. - Sachiyo Aburatani; Satoru Kuhara; Hiroyuki Toh; Katsuhisa Horimoto (Signal Process., 2003)

ASIAN: a website for network inference. - Sachiyo Aburatani; Kousuke Goto; Shigeru Saito; Masaki Fumoto; Akira Imaizumi; Nobuyoshi Sugaya; Hiroo Murakami; Makihiko Sato; Hiroyuki Toh; Katsuhisa Horimoto (Bioinform., 2004)

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. - Tetsuya Sato 003; Yoshihiro Yamanishi; Minoru Kanehisa; Hiroyuki Toh (Bioinform., 2005)

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. - Daron M. Standley; Hiroyuki Toh; Haruki Nakamura (BMC Bioinform., 2005)

ASIAN: a web server for inferring a regulatory network framework from gene expression profiles. - Sachiyo Aburatani; Kousuke Goto; Shigeru Saito; Hiroyuki Toh; Katsuhisa Horimoto (Nucleic Acids Res., 2005)

Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. - Tetsuya Sato 003; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh (Bioinform., 2006)

Inference of Protein-Protein Interactions by Using Co-evolutionary Information. - Tetsuya Sato 003; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh (AB, 2007)

PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. - Kazutaka Katoh; Hiroyuki Toh (Bioinform., 2007)

ASH structure alignment package: Sensitivity and selectivity in domain classification. - Daron M. Standley; Hiroyuki Toh; Haruki Nakamura (BMC Bioinform., 2007)

Recent developments in the MAFFT multiple sequence alignment program. - Kazutaka Katoh; Hiroyuki Toh (Briefings Bioinform., 2008)

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. - Kazutaka Katoh; Hiroyuki Toh (BMC Bioinform., 2008)

Parallelization of the MAFFT multiple sequence alignment program. - Kazutaka Katoh; Hiroyuki Toh (Bioinform., 2010)

SeSAW: balancing sequence and structural information in protein functional mapping. - Daron M. Standley; Reiko Yamashita; Akira R. Kinjo; Hiroyuki Toh; Haruki Nakamura (Bioinform., 2010)

A comparative study of conservation and variation scores. - Fredrik Johansson; Hiroyuki Toh (BMC Bioinform., 2010)

Relative von Neumann Entropy for Evaluating amino acid conservation. - Fredrik Johansson; Hiroyuki Toh (J. Bioinform. Comput. Biol., 2010)

DROP: an SVM domain linker predictor trained with optimal features selected by random forest. - Teppei Ebina; Hiroyuki Toh; Yutaka Kuroda (Bioinform., 2011)

Profile comparison revealed deviation from structural constraint at the positively selected sites. - Hiroyuki Oda; Motonori Ota; Hiroyuki Toh (Biosyst., 2016)

Implementing LOD Surfer as a Search System for the Annotation of Multiple Protein Sequence Alignment. - Atsuko Yamaguchi; Hiroyuki Toh (JIST, 2018)

Phylogenetic Footprinting. - Hiroyuki Toh (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)