ALEX: The Logic Programming Language with Explicit Control and without Cut-Operators. - Masaki Hoshida; Mario Tokoro (LP, 1988)

Folding Simulation using Temperature Parallel Simulated Annealing. - Makoto Hirosawa; Richard Feldmann; David Rawn; Masato Ishikawa; Masaki Hoshida; George Michaels (FGCS, 1992)

Protein Sequence Analysis by Parallel Inference Machine. - Masato Ishikawa; Masaki Hoshida; Makoto Hirosawa; Tomoyuki Toya; Kentaro Onizuka; Katsumi Nitta (FGCS, 1992)

MASCOT: multiple alignment system for protein sequences based on three- way dynamic programming. - Makoto Hirosawa; Masaki Hoshida; Masato Ishikawa; Tomoyuki Toya (Comput. Appl. Biosci., 1993)

Multiple sequence alignment by parallel simulated annealing. - Masato Ishikawa; Tomoyuki Toya; Masaki Hoshida; Katsumi Nitta; A. Ogiwara; Minoru Kanehisa (Comput. Appl. Biosci., 1993)

Comprehensive study on iterative algorithms of multiple sequence alignment. - Makoto Hirosawa; Yasushi Totoki; Masaki Hoshida; Masato Ishikawa (Comput. Appl. Biosci., 1995)