| [1] |
D. C. Anderson, W. Li, D. G. Payan, and W. S. Noble.
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. Journal of Proteome Research, 2(2):137-146, 2003. |
| [2] |
M. P. S. Brown, W. N. Grundy, D. Lin, N. Cristianini, C. Sugnet, T. S. Furey,
Jr. M. Ares, and D. Haussler.
Knowledge-based analysis of microarray gene expression data using support vector machines. Proceedings of the National Academy of Sciences of the United States of America, 97(1):262-267, 2000. |
| [3] |
M. Cuturi and J.-P. Vert.
A mutual information kernel for strings. In Proceedings of the International Joint Conference on Neural Networks, 2004. To appear. |
| [4] |
T. S. Furey, N. Cristianini, N. Duffy, D. W. Bednarski, M. Schummer, and
D. Haussler.
Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics, 16(10):906-914, 2001. |
| [5] |
S. M. Gomez, W. S. Noble, and A. Rzhetsky.
Learning to predict protein-protein interactions. Bioinformatics, 19:1875-1881, 2003. |
| [6] |
T. Gururaja, W. Li, W. S. Noble, D. G. Payan, and D. C. Anderson.
Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing. Journal of Proteome Research, 2003. To appear. |
| [7] |
C. Leslie, E. Eskin, and W. S. Noble.
The spectrum kernel: A string kernel for SVM protein classification. In R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, editors, Proceedings of the Pacific Symposium on Biocomputing, pages 564-575, New Jersey, 2002. World Scientific. |
| [8] |
C. Leslie, E. Eskin, J. Weston, and W. S. Noble.
Mismatch string kernels for discriminative protein classification. Submitted for publication, 2003. |
| [9] |
C. Leslie, E. Eskin, J. Weston, and W. S. Noble.
Mismatch string kernels for SVM protein classification. In Suzanna Becker, Sebastian Thrun, and Klaus Obermayer, editors, Advances in Neural Information Processing Systems, pages 1441-1448, Cambridge, MA, 2003. MIT Press. |
| [10] |
C. Leslie and R. Kuang.
Fast kernels for inexact string matching. In Conference on Learning Theory, 2003. To appear. |
| [11] |
L. Liao and W. S. Noble.
Combining pairwise sequence similarity and support vector machines for remote protein homology detection. In Proceedings of the Sixth Annual International Conference on Computational Molecular Biology, pages 225-232, Washington, DC, April 18-21 2002. |
| [12] |
L. Liao and W. S. Noble.
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. Journal of Computational Biology, 2003. To appear. |
| [13] |
P. Pavlidis, T. S. Furey, M. Liberto, D. Haussler, and W. N. Grundy.
Promoter region-based classification of genes. In R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, editors, Pacific Symposium on Biocomputing 2001, pages 151-163, Singapore, 2001. World Scientific. |
| [14] |
P. Pavlidis, J. Weston, J. Cai, and W. N. Grundy.
Gene functional classification from heterogeneous data. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, pages 242-248, 2001. |
| [15] |
P. Pavlidis, J. Weston, J. Cai, and W. S. Noble.
Learning gene functional classifications from multiple data types. Journal of Computational Biology, 9(2):401-411, 2002. |
| [16] |
W. T. Peng, M. D. Robinson, S. Mnaimneh, N. J. Krogan, G. Cagney, Q. Morris,
A. P. Davierwala, J. Grigull, X. Yang, W. Zhang, N. Mitsakakis, O. W. Ryan,
N. Datta, V. Jojic, C. Pal, V. Canadien, D. Richards, B. Beattie, L. F. Wu,
S. J. Altschuler, S. Roweis, B. J. Frey, A. Emili, J. F. Greenblatt, and
T. R. Hughes.
A panoramic view of yeast noncoding rna processing. Cell, 113:919-933, 2003. |
| [17] |
H. Saigo, J.-P. Vert, N. Ueda, and T. Akutsu.
Protein homology detection using string alignment kernels. Bioinformatics, 2004. To appear. |
| [18] |
N. H. Segal, P. Pavlidis, C. R. Antonescu, R. G. Maki, W. S. Noble, J. M.
Woodruff, J. J. Lewis, M. F. Brennan, A. N. Houghton, and C. Cordon-Cardo.
Classification and subtype prediction of soft tissue sarcoma by functional genomics and support vector machine analysis. American Journal of Pathology, 2003. To appear. |
| [19] |
N. H. Segal, P. Pavlidis, W. S. Noble, C. R. Antonescu, A. Viale, U. V. Wesley,
K. Busam, H. Gallardo, D. DeSantis, M. F. Brennan, C. Cordon-Cardo, J. D.
Wolchok, and A. N. Houghton.
Classification of clear cell sarcoma as melanoma of soft parts by genomic profiling. Journal of Clinical Oncology, 21:1775-1781, 2003. |
| [20] |
X. H-F. Zhang, K. A. Heller, I. Hefter, C. S. Leslie, and L. A. Chasin.
Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. Genome Research, 13(2637-2650), 2003. |