The Machine learning and Bioinformatics group

Prediction servers

Selected recent publications

Hawkins, J., Mahony, D., Maetschke, S., Wakabayashi, M., Teasdale, R.D., and Bodén, M., Identifying Novel Peroxisomal Proteins. Proteins: Structure, Function and Bioinformatics. Accepted. 2007.
Hawkins, J., Davis, L., and Bodén, M., Predicting Nuclear Localization, Journal of Proteome Research. Accepted. 2007.
Maetschke, S., Gallagher, M. and Bodén, M. A Comparison of Sequence Kernels for Localization Prediction of Transmembrane Proteins. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. Accepted. 2007.
Suksawatchon, J., Lursinsap, C. and Bodén, M., Computing the Reversal Distance Between Genomes in the Presence of Multi-Gene Families via Binary Integer Programming. Journal of Bioinformatics and Computational Biology. Accepted. 2007.
Bauer, D., Bodén, M., Thier, R. and Gillam, E. M. STAR: Predicting recombination sites from amino acid sequence. BMC Bioinformatics, 7:437, 2006. doi:10.1186/1471-2105-7-437.
Bodén, M. and Bailey, T. L. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure, Bioinformatics. 22(15):1809-1814. 2006.
Bodén, M., Yuan, Z. and Bailey, T. L. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. BMC Bioinformatics. 7:68, 2006.
Bodén, M. and Hawkins, J. Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway, IEEE Congress on Evolutionary Computation, 2006.
Yuan, Z., Zhang, F., Davis, M. J., Bodén, M. and Teasdale, R. D. Predicting the solvent accessibility of transmembrane residues from protein sequence. Journal of Proteome Research. 5(5), pp. 1063-1070, 2006.	DOI
Bodén, M., Yuan, Z. and Bailey, T. L. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. BMC Bioinformatics. In press.
Hawkins, J. and Bodén, M. Detecting and sorting targeting peptides with recurrent networks and support vector machines. Journal of Bioinformatics and Computational Biology, 4(1), 2006.
Bauer, D., Bodén, M., Thier, R. and Yuan, Z. Predicting structural disruption of proteins caused by crossover. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 514-520. San Diego, 2005.
Hawkins, J. and Bodén, M. Predicting Peroxisomal proteins. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 469-474. San Diego, 2005.
Suksawatchon, J., Lursinsap, C. and Bodén, M., Heuristic Algorithm for Computing Reversal Distance with MultiGene Families via Binary Integer Programming. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 187-193. San Diego, 2005.
Bodén, M. and Hawkins, J. Prediction of subcellular localisation using sequence-biased recurrent networks. Bioinformatics. 21(10), pp. 2279-2286, 2005.
Wakabayashi, M., Hawkins, J., Maetschke, S. and Bodén, M., Exploiting sequence dependencies in the prediction of peroxisomal proteins. In Intelligent Data Engineering and Automated Learning - IDEAL 2005, pp. 454-461, 2005.
Bodén, M. and Bodén, M. Evolving spelling exercises to suit individual student needs. Applied Soft Computing. In press.
Hawkins, J. and Bodén, M. The Applicability of Recurrent Neural Networks for Biological Sequence Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2(3), pp. 243-253, 2005.
Bodén, M. and Hawkins, J. Improved access to sequential motifs: A note on the architectural bias of recurrent networks. IEEE Transactions on Neural Networks. 16(2), 491-494, 2005.
Bodén, M. and Hawkins, J. Detecting residues in targeting peptides. In Proceedings of the Asia-Pacific Bioinformatics Conference, pp. 131-140. Imperial College Press. Singapore. 2005.
Maetschke, S., Towsey, M. and Bodén, M. BLOMAP: An encoding of amino acids which improves signal peptide cleavage prediction. In Proceedings of the Asia-Pacific Bioinformatics Conference, pp. 141-150. Imperial College Press. Singapore. 2005.
Hawkins, J. and Bodén, M. Detecting and sorting targeting peptides with recurrent networks and support vector machines. Journal of Bioinformatics and Computational Biology, 4(1), 2006.
Bauer, D., Bodén, M., Thier, R. and Yuan, Z. Predicting structural disruption of proteins caused by crossover. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, 2005. Accepted.
Hawkins, J. and Bodén, M. Predicting Peroxisomal proteins. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, 2005. Accepted.
Bodén, M. and Hawkins, J. Prediction of subcellular localisation using sequence-biased recurrent networks. Bioinformatics. 21(10), pp. 2279-2286, 2005.
Wakabayashi, M., Hawkins, J., Maetschke, S. and Bodén, M., Exploiting sequence dependencies in the prediction of peroxisomal proteins. In Intelligent Data Engineering and Automated Learning - IDEAL 2005, pp. 454-461, 2005.
Maetschke, S., Towsey, M. and Bodén, M. BLOMAP: An encoding of amino acids which improves signal peptide cleavage prediction. In Proceedings of the Asia-Pacific Bioinformatics Conference. Singapore. 2005.
Hawkins, J. and Bodén, M. The Applicability of Recurrent Neural Networks for Biological Sequence Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2(2), 2005.
Bodén, M. and Hawkins, J. Improved access to sequential motifs: A note on the architectural bias of recurrent networks. IEEE Transactions on Neural Networks. 16(2), 491-494, 2005.
Bodén, M. and Hawkins, J. Detecting residues in targeting peptides. In Proceedings of the Asia-Pacific Bioinformatics Conference. Singapore. 2005.

Resources

International Society for Computational Biology (ISCB)
IEEE Explore
Association for Computing Machinery (the Digital Library Portal)
UCI Machine learning repository
scholar.Google.com (web-based citation search engine)

Online-Books

Databases

Journals

Conferences

Pacific Symposium on Biocomputing
Intelligent Systems and Molecular Biology (ISMB) 2006 (Brazil)
- Acceptance rate 13% in 2005
European Conference on Computational Biology (ECCB) 2005 (Madrid), 2006 (Eilat)
- Acceptance rate 14% in 2004, co-organised with ISMB 2004
Research in Computational Molecular Biology (RECOMB) 2006 (Venice)
- Acceptance rate around 30%, 30-40 accepted of 130
- Deadline 23 September 2005
Asia-Pacific Bioinformatics Conference (APBC) 2006 (Taiwan)
- Acceptance rate 30% in 2005
- Deadline 15 July 2005
IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2005
Neural Information Processing Systems
International Conference on Machine Learning (ICML) 2005
International Joint Conference on Neural Networks (IJCNN) 2005
International Conference on Artificial Neural Networks (ICANN) 2005
IEEE World Congress on Computational Intelligence (WCCI) 2006
Parallel Problem Solving from Nature (PPSN) 2006 (Reykjavik)
European Conference on Machine Learning (ECML) 2005