GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. - Kazuharu Arakawa; Yohei Yamada; Kosaku Shinoda; Yoichi Nakayama; Masaru Tomita (BMC Bioinform., 2006)

HybGFS: a hybrid method for genome-fingerprint scanning. - Kosaku Shinoda; Nozomu Yachie; Takeshi Masuda; Naoyuki Sugiyama; Masahiro Sugimoto; Tomoyoshi Soga; Masaru Tomita (BMC Bioinform., 2006)

Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. - Kosaku Shinoda; Masaru Tomita; Yasushi Ishihama (Bioinform., 2008)

emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. - Kosaku Shinoda; Masaru Tomita; Yasushi Ishihama (Bioinform., 2010)