B. Schoelkopf and A. J. Smola, Learning with Kernels: Support Vector Machines, Regularization, Optimization , and Beyond, 2002.

B. Schoelkopf, K. Tsuda, and J. Vert, Kernel Methods in Computational Biology, 2004.

J. Vert and M. Kanehisa, Graph-driven features extraction from microarray data using diffusion kernels and kernel CCA, Advances in Neural Information Processing Systems 15, pp.1449-1456, 2003.

Y. Yamanishi, J. Vert, and M. Kanehisa, Protein network inference from multiple genomic data: a supervised approach, Bioinformatics, vol.20, issue.Suppl 1, pp.363-370, 2004.
DOI : 10.1093/bioinformatics/bth910
URL : https://hal.archives-ouvertes.fr/hal-00433586

T. Kim, T. Kato, and K. Tsuda, Protein classification via Kernel Matrix Completion, Kernel Methods in Computational Biology, pp.261-276, 2004.

F. Bach and M. Jordan, Kernel independent component analysis, 2003 IEEE International Conference on Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP '03)., pp.1-48, 2002.
DOI : 10.1109/ICASSP.2003.1202783

K. Tsuda, S. Akaho, and K. Asai, The em Algorithm for Kernel Matrix Completion with Auxiliary Data, Journal of Machine Learning Research, vol.4, pp.67-81, 2003.

R. I. Kondor and J. Lafferty, Diffusion Kernels on Graphs and Other Discrete Input, 2002.

K. Tsuda, T. Kim, and K. Asai, Marginalized kernels for biological sequences, Bioinformatics, vol.18, issue.Suppl 1, pp.268-275, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S268

T. Kawabata and K. Nishikawa, Protein structure comparison using the Markov transition model of evolution, Proteins: Structure, Function, and Genetics, vol.24, issue.1, pp.108-122, 2000.
DOI : 10.1002/1097-0134(20001001)41:1<108::AID-PROT130>3.0.CO;2-S