SHARP2: protein-protein interaction predictions using patch analysis. - Yoichi Murakami; Susan Jones (Bioinform., 2006)

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. - Kengo Kinoshita; Yoichi Murakami; Haruki Nakamura (Nucleic Acids Res., 2007)

Protein function annotation from sequence: prediction of residues interacting with RNA. - Ruth V. Spriggs; Yoichi Murakami; Haruki Nakamura; Susan Jones (Bioinform., 2009)

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. - Yoichi Murakami; Kenji Mizuguchi (Bioinform., 2010)

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. - Yoichi Murakami; Ruth V. Spriggs; Haruki Nakamura; Susan Jones (Nucleic Acids Res., 2010)

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. - Yoichi Murakami; Kenji Mizuguchi (BMC Bioinform., 2014)

Study of Characterization of Promiscuous Binding Sites in Protein-Small Molecule Complexes. - Yoichi Murakami (ICBRA, 2019)

Network-Based Analysis for Biological Discovery. - Lokesh P. Tripathi; Yi-An Chen; Kenji Mizuguchi; Yoichi Murakami (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

An Automated Vulnerability Assessment Approach for WebAPI that Considers Requests and Responses. - Toru Taya; Masaki Hanada; Yoichi Murakami; Atsushi Waseda; Yuki Ishida; Takao Mimura; Moo Wan Kim; Eiji Nunohiro (ICACT, 2022)

Web Game Development Tool for Learning Communication Functions for Beginners Networked Game Developers. - Yu Osuga; Yoshihiro Kawano; Yoichi Murakami; Dai Hanawa; Masaki Hanada; Eiji Nunohiro (NBiS, 2022)

QoE Metrics in Real-Time Web Games. - Kaoru Shiotsu; Yoshihiro Kawano; Yoichi Murakami; Dai Hanawa; Masaki Hanada; Eiji Nunohiro (NBiS, 2022)