HUNT: launch of a full-length cDNA database from the Helix Research Institute. - Henrik T. Yudate; Makiko Suwa; Ryotaro Irie; Hiroshi Matsui; Tetsuo Nishikawa; Yoshitaka Nakamura; Daisuke Yamaguchi; Zhang Zhi Peng; Tomoyuki Yamamoto; Keiichi Nagai; Koji Hayashi; Tetsuji Otsuki; et al. (Nucleic Acids Res., 2001)

GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures. - Yukimitsu Yabuki; Yuri Mukai; Mark B. Swindells; Makiko Suwa (Bioinform., 2004)

Neural network-based prediction of transmembrane -strand segments in outer membrane proteins. - M. Michael Gromiha; Shandar Ahmad; Makiko Suwa (J. Comput. Chem., 2004)

A simple statistical method for discriminating outer membrane proteins with better accuracy. - M. Michael Gromiha; Makiko Suwa (Bioinform., 2005)

Discrimination of outer membrane proteins using support vector machines. - Keun-Joon Park; M. Michael Gromiha; Paul Horton; Makiko Suwa (Bioinform., 2005)

Application of residue distribution along the sequence for discriminating outer membrane proteins. - M. Michael Gromiha; Shandar Ahmad; Makiko Suwa (Comput. Biol. Chem., 2005)

TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins. - M. Michael Gromiha; Shandar Ahmad; Makiko Suwa (Nucleic Acids Res., 2005)

GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model. - Yukimitsu Yabuki; Takahiko Muramatsu; Takatsugu Hirokawa; Hidehito Mukai; Makiko Suwa (Nucleic Acids Res., 2005)

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. - Hideki Nagasaki; Masanori Arita; Tatsuya Nishizawa; Makiko Suwa; Osamu Gotoh (Bioinform., 2006)

TMB Finding Pipeline: Novel Approach for Detecting β-Barrel Membrane Proteins in Genomic Sequences. - M. Michael Gromiha; Yukimitsu Yabuki; Makiko Suwa (J. Chem. Inf. Model., 2007)

TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences. - M. Michael Gromiha; Yukimitsu Yabuki; Srinesh Kundu; Sivasundaram Suharnan; Makiko Suwa (Nucleic Acids Res., 2007)

Neural network based prediction of protein structure and Function: Comparison with other machine learning methods. - M. Michael Gromiha; Shandar Ahmad; Makiko Suwa (IJCNN, 2008)

TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. - Yu-Yen Ou; M. Michael Gromiha; Shu-An Chen; Makiko Suwa (Comput. Biol. Chem., 2008)

TMFunction: database for functional residues in membrane proteins. - M. Michael Gromiha; Yukimitsu Yabuki; M. Xavier Suresh; A. Mary Thangakani; Makiko Suwa; Kazuhiko Fukui (Nucleic Acids Res., 2009)

Development of a Machine Learning Method to Predict Membrane Protein-Ligand Binding Residues Using Basic Sequence Information. - M. Xavier Suresh; M. Michael Gromiha; Makiko Suwa (Adv. Bioinformatics, 2015)