Yamanishi, Y.,
"Chemogenomic approaches to infer drug-target interaction networks",
Data Mining for Systems Biology, Methods in Molecular Biology Series (DeLisi, C., Kanehisa, M. and Mamitsuka, H., eds.), Springer, 2011. (To Appear)
Lodhi, H. and Yamanishi, Y.,
Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques, IGI Global, 2010.
[link to publisher][link to amazon]
Yamanishi, Y. and Kashima, H.
"Prediction of compound-protein interactions with machine learning methods",
Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques (Lodhi, H. and Yamanishi, Y., eds.), pp.304-317, 2010.
[link to publisher][link to amazon]
Sato T., Yamanishi Y., Kanehisa M., Horimoto K. and Toh H.,
"Improvement of the mirrortree method by extracting evolutionary information",
Sequence and Genome Analysis: Methods and Applications (Zhao, Z., eds.), pp.-, iConcept Press, 2010.
[link to publisher][link to amazon]
Yamanishi, Y.,
"Supervised inference of metabolic networks from the integration of genomic data and chemical information",
Elements of Computational Systems Biology (Lodhi, H. and S. Muggleton, S., eds.), pp.189-212, Wiley, 2010.
[link to publisher][link to amazon]
Yamanishi Y., Vert, J.-P., and Kanehisa, M.,
"Heterogeneous data comparison and gene selection with kernel canonical correlation analysis",
Kernel Methods in Computational Biology (Schoelkopf, B. and Tsuda, K. and Vert, J.-P., eds.), pp.209-230, MIT Press, 2004.
[pdf]
Journal articles and peer-reviewed proceedings
Pauwels, E., Stoven, V., and Yamanishi, Y.,
"Predicting drug side-effect profiles: a chemical fragment-based approach",
BMC Bioinformatics, 12:169, 2011.
[pdf][web supplements][pubmed]
Yamanishi, Y., Pauwels, E., Saigo, H. and Stoven, V.,
"Extracting sets of chemical substructures and protein domains governing drug-target interactions",
Journal of Chemical Information and Modeling, Vol.51(5), pp.1183-1194, 2011.
[pdf][web supplements][pubmed]
Kashima, H., Oyama, S., Yamanishi, Y., and Tsuda, K.
"Cartesian Kernel: An Efficient Alternative to the Pairwise Kernel",
IEICE Transaction on Information and Systems, Vol. E93-D, No. 10, pp.2672-2679, 2010.
Tamura, T., Yamanishi, Y., Tanabe, M., Goto, S., Kanehisa, M., Horimoto, K., and Akutsu, T.,
"Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer",
Genome Informatics, Vol.24, pp.193-203, 2010.
(Proceedings of IBSB2010)
Yamanishi, Y., Kotera, M., Kanehisa, M., and Goto, S.,
"Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework",
Bioinformatics, Vol.26, pp.i246-i254, 2010.
[pdf][web supplements][pubmed]
(Proceedings of ISMB2010: 46 accepted papers out of 240 submissions = 19 %)
Kashima, H., Yamanishi, Y., Kato, T., Sugiyama, M., and Tsuda, K.,
"Simultaneous Inference of Biological Networks of Multiple Species from Genome-wide Data and Evolutionary Information: A Semi-supervised Approach",
Bioinformatics, Vol.25, pp.2962-2968, 2009.
[pdf][web supplements][pubmed]
Bleakley, K. and Yamanishi, Y.,
"Supervised prediction of drug-target interactions using bipartite local models",
Bioinformatics, Vol.25, pp.2397-2403, 2009.
[pdf][web supplements][pubmed]
Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.,
"E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs",
Bioinformatics, Vol.25, pp.i79-i86, 2009.
[pdf][online software][pubmed]
(Proceedings of ISMB/ECCB2009: 46 accepted papers out of 242 submissions = 18 %)
Kashima, H., Oyama, S., Yamanishi, Y., and Tsuda, K.
"On Pairwise Kernels: An Efficient Alternative and Generalization Analysis",
Proceedings of the 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Lecture Notes in Artificial Intelligence, Vol.5476, pp.1030-1037, 2009.
Kashima, H., Kato, T., Yamanishi, Y., Sugiyama, M., and Tsuda, K.
"Link Propagation: A Fast-semi Supervised Learning Algorithm for Link Prediction",
Proceedings of the 9th SIAM Conference on Data Mining (SDM), pp.1099-1110, 2009.
Yamanishi, Y.,
"Supervised Bipartite Graph Inference",
Advances in Neural Information Processing Systems 21 (Koller, D., Schuurmans, D., Bengio, Y. and Bottou, L. eds.), pp.1841-1848, MIT Press, Cambridge, MA, 2009.
[pdf]
(Proceedings of NIPS2008: 123 oral presentations and 250 accepted papers out of 1022 submissions = 12 %)
Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., and Kanehisa, M.,
"Prediction of drug-target interaction networks from the integration of chemical and genomic spaces",
Bioinformatics, Vol.24, pp.i232-i240, 2008.
[pdf][web supplements][pubmed]
(Proceedings of ISMB2008: 49 accepted papers out of 287 submissions = 17 %)
Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.,
"KEGG for linking genomes to life and the environment",
Nucleic Acids Res., Vol.36, pp.D480-D484, 2008.
[pdf][pubmed]
Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.,
"An improved scoring scheme for predicting glycan structures from gene expressison data",
Genome Informatics, Vol.18(1), pp.237-246, 2007.
[pdf][pubmed]
(Proceedings of IBSB2007)
Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., and Toh, H.,
"Inference of Protein-Protein Interactions by Using Co-evolutionary Information",
Proceedings of the 2nd international conference on Algebraic Biology (Anai, H., Horimoto, K. and Kutsia, T. eds.), Lecture Notes in Computer Science 4545, p.322-333, Springer, Heidelberg, 2007.
Yamanishi, Y. and Vert, J.-P.,
"Kernel matrix regression",
Proceedings of the 12th International Conference on Applied Stochastic Models and Data Analysis (ASMDA 2007), 2007.
The longer version is found in Technical Report HAL-00133355, 2007.
[html]
Yamanishi, Y., Bach, F., and Vert, J.-P.,
"Glycan Classification with Tree Kernels",
Bioinformatics, Vol.23(10), pp.1211-1216, 2007.
[pdf][web supplements][pubmed]
Yamanishi, Y., Mihara, H., Osaki, M., Muramatsu, H., Esaki, N., Sato, T., Hizukuri, Y., Goto, S., and Kanehisa, M.,
"Prediction of missing enzyme genes in a bacterial metabolic network: Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa",
FEBS Journal, Vol.274, pp.2262-2273, 2007.
[pdf][pubmed]
Okamoto, S., Yamanishi, Y., Ehira, S., Kawashima, S., Tonomura, K., and Kanehisa, M.,
"Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis",
Proteomics, Vol.7(6), pp.900-909, 2007.
[pdf][pubmed]
Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., and Toh, H.,
"Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions",
Bioinformatics, Vol.22(20), pp.2488-2492, 2006.
[pdf][web supplements][pubmed]
Yamanishi, Y. and Tanaka, Y.,
"Sensitivity Analysis in Kernel Principal Component Analysis",
Compstat 2006: Proceedings in Computational Statistics, Rizzi, A. and Vichi, M. (Eds.), pp.787-794, Physica-Verlag/Springer, 2006.
[pdf]
Yamanishi, Y. and Vert, J.-P.,
"Estimating Protein Network from Multiple Genomic Data by Kernel Methods",
Proceedings of the Institute of Statistical Mathematics, Vol.54-2, pp.357-373, 2006. (in Japanese)
[pdf]
Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., and Kanehisa, M.,
"Extraction of leukemia specific glycan motifs by computational comparative glycomics",
Carbohydrate Research, Vol.340-14, pp.2270-2278, 2005.
[pdf][pubmed]
Sato, T., Yamanishi, Y., Kanehisa, M., and Toh, H.,
"The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding phylogenetic relationships",
Bioinformatics, Vol.21-17, pp.3482-3489, 2005.
[pdf][web supplements][pubmed]
Yamanishi, Y., Vert, J.-P. and Kanehisa, M.,
"Supervised Enzyme Network Inference from the Integration of Genomic Data and Chemical Information",
Bioinformatics, Vol.21, pp.i468-i477, 2005.
[ps][pdf][web supplements][pubmed]
(Proceedings of ISMB2005: 56 accepted papers out of 428 submissions = 13 %)
Tamori, A., Yamanishi, Y., Kawashima, S., Kanehisa, M., Enomoto, M., Tanaka, H., Kubo, S., Shiomi, S., and Nishiguchi, S.,
"Alteration of Gene Expression in Hepatitis B Virus DNA integrated human hepatocellular carcinoma",
Clinical Cancer Research, Vol.11-16, pp.5821-5826, 2005.
[pubmed]
Vert, J.-P. and Yamanishi, Y.,
"Supervised graph inference",
Advances in Neural Information Processing Systems 17, Lawrence K. Saul and Yair Weiss and Leon Bottou (Eds.), pp.1433-1440, 2005.
[pdf]
(Proceedings of NIPS2004: Oral presentation, 24 accepted papers as oral out of 882 = 3%)
Yamanishi, Y. and Tanaka, Y.,
"Sensitivity Analysis in Functional Principal Component Analysis",
Computational Statistics, Vol.20-2, pp.313-329, 2005.
[ps][pdf]
Yamanishi, Y., Vert, J.-P. and Kanehisa, M.,
"Protein Network Inference from Multiple Genomic Data: A Supervised Approach",
Bioinformatics, Vol.20, pp.i363-i370, 2004.
[ps][pdf][web supplements][pubmed]
(Proceedings of ISMB2004: 50 accepted papers out of 492 submissions = 10 %)
Hizukuri, Y., Yamanishi, Y., Hashimoto, K. and Kanehisa, M.,
"Extraction of Species-specific Glycan Substructures",
Genome Informatics, Vol.15, pp.69-81, 2004. (Proceedings of IBSB2004)
[ps][pdf][pubmed]
Yamanishi, Y., Vert, J.-P., Nakaya, A. and Kanehisa, M.,
"Extraction of Correlated Gene Clusters from Multiple Genomic Data by Generalized Kernel Canonical Correlation Analysis",
Bioinformatics, Vol.19, pp.i323-i330, 2003.
[ps][pdf][pubmed]
(Proceedings of ISMB2003: 35 accepted papers out of 242 submissions = 14 %)
Yamanishi, Y. and Tanaka, Y.,
"Geographically Weighted Functional Multiple Regression Analysis: A Numerical Investigation",
Journal of Japanese Society of Computational Statistics, Vol.15(2), pp.307-317, 2003.
[ps][pdf]
Yamanishi, Y., Itoh, M. and Kanehisa, M.,
"Extraction of Organism Groups from Phylogenetic Profiles Using Independent Component Analysis",
Genome Informatics, Vol.13, pp.61-70, 2002.
[ps][pdf][pubmed]
(Proceedings of GIW2002)
Yamanishi, Y., Tanaka, Y.,
"Principal Component Analysis for Functional Data",
Journal of Faculty of Environmental Science and Technology, Okayama University, Vol.6, pp.25-34, 2001.
Thesis
Yamanishi, Y., Development of methods for analyzing the correlation between heterogeneous genomic data and their application to inferring protein network,
Doctoral Thesis, Graduate School of Science, Kyoto University, March, 2005.
Yamanishi, Y., Studies on Principal Component and Regression Analyses for Functional Data,
Master Thesis, Graduate School of Natural Science and Technology, Okayama University, February, 2001.
Yamanishi, Y., Pauwels, E., Saigo, H. and Stoven, V.,
"Identification of chemogenomic features from drug-target interaction networks by sparse canonical correspondence analysis",
The 5th International Workshop on Machine Learning in Systems Biology (MLSB2011): A satellite of the 19th International Conference on Intelligent Systems for Molecular Biology (ISMB2011), Wienna, Austria, Jul.20-Jul.21, 2011.
Tamura, T., Yamanishi, Y., Tanabe, M., Goto, S., Kanehisa, M., Horimoto, K., and Akutsu, T.,
"Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer",
The 10th International Workshop on Bioinformatics & Systems Biology (IBSB2010), Uji, Japan, Jul.25-Jul.28, 2010.
Yamanishi, Y., Kotera, M., Kanehisa, M., and Goto, S.,
"Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework",
The 18th International Conference on Intelligent Systems for Molecular Biology (ISMB2010), Bonston, USA, Jul.8-Jul.13, 2010.
Yamanishi, Y.,
"Prediction of drug-target interactions from the integration of chemical, genomic and pharmacological data",
Workshop on Bioinformatics for Medical and Pharmaceutical Research (website), Paris, France, Nov.16-Nov.17, 2009.
Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.,
"E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs",
The 17th International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology (ISMB/ECCB2009), Stockholm, Sweden, Jun.27-Jul.2, 2009.
Yamanishi, Y.,
"Supervised bipartite graph inference",
The 22nd Annual Conference on Neural Information Processing Systems (NIPS2008), Vancouver and Whistler, British Columbia, Canada, Dec.8-Dec.11, 2008.
Yamanishi, Y.,
"Supervised bipartite graph inference: applications to predicting drug-target interactions",
The workshop on Statistic Mathematic and Applications, Frejus (La Villa Clythia), France, Sep.01-05, 2008.
Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., and Kanehisa, M.,
"Prediction of drug-target interaction networks from the integration of chemical and genomic spaces",
The 16th International Conference on Intelligent Systems for Molecular Biology (ISMB2008), Toronto, Canada, Jun.20-Jun.23, 2008.
Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.,
"An improved scoring scheme for predicting glycan structures from gene expressison data",
The 7th International Workshop on Bioinformatics & Systems Biology (IBSB2007), Tokyo, Japan, Jul.31-Aug.2, 2007.
Yamanishi, Y. and Vert, J.-P.,
"Kernel matrix regression",
The 12th International Conference on Applied Stochastic Models and Data Analysis (ASMDA2007), the special session "Supervised Prediction with Neural Networks and SVMs", Chania, Crete, Greece, May.29-Jun.1, 2007.
Tanaka, Y. and Yamanishi, Y.,
"On Some Measures of Influence in Sensitivity Analysis in Kernel Principal Component Analysis",
The 8th Workshop of the ERCIM Working Group on Matrix Computations and Statistics (website) (a sattelite of COMPSTAT2006), Salerno, Italy, Sep.2-Sep.3, 2006.
Yamanishi, Y. and Tanaka, Y.,
"Sensitivity Analysis in Kernel Principal Component Analysis",
The 17th International Conference on Computational Statistics (COMPSTAT2006), the 17th Conference of IASC-ERS (COMPSTAT2006), Rome, Italy, Aug.28-Sep.1, 2006.
Yamanishi, Y.,
"Metabolic Network Inference from Multiple Types of Genomic Data",
INRA Workshop on System Biology (INRA), Paris, France, Feb.2, 2006.
Yamanishi, Y., Vert, J.-P. and Kanehisa, M.,
"Supervised Enzyme Network Inference from the Integration of Genomic Data and Chemical Information",
The 13th International Conference on Intelligent Systems for Molecular Biology (ISMB2005), Detroit, USA, Jun.26-Jun.29, 2005.
Vert, J.-P. and Yamanishi, Y.,
"Supervised graph inference",
The 18th Annual Conference on Neural Information Processing Systems (NIPS2004), pp.1433-1440, Vancouver and Whistler, British Columbia, Canada, Dec.14-Dec.16, 2004.
Yamanishi, Y., Vert, J.-P. and Kanehisa, M.,
"Protein Network Inference from Multiple Genomic Data: A Supervised Approach",
The 12th International Conference on Intelligent Systems for Molecular Biology (ISMB2004), Glasgow, Scotland, Jul.31-Aug.4, 2004.
Hizukuri, Y., Yamanishi, Y., Hashimoto, K. and Kanehisa, M.,
"Extraction of Species-specific Glycan Substructures",
The 4th International Workshop on Bioinformatics & Systems Biology (IBSB2004), Kyoto, Japan, May 31-Jun.3, 2004.
Yamanishi, Y., Vert, J.-P. and Kanehisa, M.,
"Detecting Correlations between Multiple Types of Genomic Data",
The 3rd International Workshop on Bioinformatics & Systems Biology (IBSB2003), Dresden, Germany, Aug.16-19, 2003.
Yamanishi, Y., Vert, J.-P., Nakaya, A. and Kanehisa, M.,
"Extraction of Correlated Gene Clusters from Multiple Genomic Data by Generalized Kernel Canonical Correlation Analysis",
The 11th International Conference on Intelligent Systems for Molecular Biology (ISMB2003), Brisbane, Australia, Jun.29-Jul.3, 2003.
Yamanishi, Y., Vert, J.-P. and Kanehisa, M.,
"Generalized Kernel Canonical Correlation Analysis for Multiple Genomic Data",
Workshop on Kernel Methods in Computational Biology (a satellite of RECOMB2003), Berlin, Germany, Apr.14, 2003.
Yamanishi, Y., Itoh, M. and Kanehisa, M.,
"Extraction of Organism Groups from Phylogenetic Profiles Using Independent Component Analysis",
The 13th International Conference on Genome Informatics (GIW2002), pp.61-70, Tokyo, Japan, Dec.16-18, 2002.
Oide, N., Yamanishi, Y. and Tanaka, Y.,
"Sensitivity Analysis in Functional Principal Component Analysis",
The 4th Conference of Asian Regional Section of the International Association for Statistical Computing, Proceedings pp.205-208, Pusan, Korea, Dec.5-7, 2002.
[ps][pdf]
Yamanishi, Y.,
"Modeling spatial non-stationarity in functional regression",
Research Conference on High-dimensional Nonlinear Statistical Modeling, Proceedings pp.4, Wulkow, Germany, Sep.15-19, 2001.
Yamanishi, Y. and Tanaka, Y.,
"Geographically Weighted Functional Multiple Regression Analysis: A Numerical Investigation",
International Conference on New Trends in Computational Statistics with Biomedical Applications (ICNCB), Proceedings pp.287-294, Osaka, Japan, Aug.30-Sep.1, 2001.
[ps][pdf]
Yamanishi, Y. and Tanaka, Y.,
"Geographically Weighted Functional Regression Analysis",
The 53rd Session of the International Statistical Institute (ISI2001), Contributed Papers, Vol3, pp.149-150, Seoul, Korea, Aug.22-Aug.29, 2001.
[ps][pdf]
Yamanishi, Y. and Tanaka, Y.,
"Sensitivity Analysis in Functional Principal Component Analysis",
The 7th Japan-China Symposium on Statistics, Proceeding pp.37-40, Tokyo, Japan, Oct.29-31, 2000.
[ps][pdf]
Tanaka, Y., Watadani, S. and Yamanishi, Y.,
"On multiple-case diagnostics in multivariate method",
International Conference on Measurement and Multivariate Analysis (ICMMA), Proceedings pp.143-146, Banff, Canada, May11-14, 2000.
[ps][pdf]
Yamanishi, Y, Tanaka, Y.,
"Principal Component Analysis for Functional Data",
Joint Conference on Recent Developments in Statistics, Proceedings pp.31-35, Sockcho, Korea, Jan.7-9, 2000.
Seminar (not updated)
Yoshihiro Yamanishi, Protein network inference from multiple genomic data and identification of missing enzymes, Centre de Geostatistique, Ecole des Mines de Paris, Fontainebleau, France, Nov.23, 2004.
Yoshihiro Yamanishi, Protein Network Inference from Multiple Genomic Data: A Supervised Approach, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, Aug.9, 2004.