| 2008 | APBC | KEGG for Medical and Pharmaceutical Applications. | Minoru Kanehisa |
| 2008 | ECCB | Mining significant tree patterns in carbohydrate sugar chains. | Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, Hiroshi Mamitsuka |
| 2008 | ISMB | Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. | Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa |
| 2006 | ISAAC | A 6-Approximation Algorithm for Computing Smallest Common AoN-Supertree with Application to the Reconstruction of Glycan Trees. | Kiyoko F. Aoki-Kinoshita, Minoru Kanehisa, Ming-Yang Kao, Xiang-Yang Li, Weizhao Wang |
| 2006 | ISMB | ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. | Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa |
| 2006 | ISMB | Identification of metabolic units induced by environmental signals. | Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu |
| 2006 | KDD | A new efficient probabilistic model for mining labeled ordered trees. | Kosuke Hashimoto, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka |
| 2005 | ECCB | A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. | Jean-Marc Schwartz, Minoru Kanehisa |
| 2005 | ISMB | Supervised enzyme network inference from the integration of genomic data and chemical information. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2004 | ISMB | Application of a new probabilistic model for recognizing complex patterns in glycans. | Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka |
| 2004 | ISMB | Protein network inference from multiple genomic data: a supervised approach. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2003 | ECCB | Extracting active pathways from gene expression data. | Jean-Philippe Vert, Minoru Kanehisa |
| 2003 | ISMB | Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. | Yoshihiro Yamanishi, Jean-Philippe Vert, Akihiro Nakaya, Minoru Kanehisa |
| 2000 | RECOMB | Sequence comparison to graph comparison--a new generation of algorithms for network analysis of interacting molecules (abstract only). | Minoru Kanehisa |