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2010 Journal Article Using Gaussian process with test rejection to detect T-Cell epitopes in pathogen genomesYou, Liwen, Brusic, Vladimir, Gallagher, Marcus and Boden, Mikael (2010). Using Gaussian process with test rejection to detect T-Cell epitopes in pathogen genomes. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 7 (4) 4695825, 741-751. doi: 10.1109/TCBB.2008.131 |
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2010 Journal Article Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogasterBauer, Denis C., Buske, Fabian A., Bailey, Timothy L. and Boden, Mikael (2010). Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. Neurocomputing, 73 (13-15), 2300-2307. doi: 10.1016/j.neucom.2010.01.022 |
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2010 Journal Article The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expressionMohamad, Nurul and Bodén, Mikael (2010). The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression. BMC Systems Biology, 4 (44) 44, 1-12. doi: 10.1186/1752-0509-4-44 |
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2010 Journal Article The value of position-specific priors in motif discovery using MEMEBailey, Timothy L., Bodén, Mikael, Whitington, Tom and Machanick, Philip (2010). The value of position-specific priors in motif discovery using MEME. BMC Bioinformatics, 11 (179) 179, 1-14. doi: 10.1186/1471-2105-11-179 |
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2010 Journal Article A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodiesBoden, Mikael, Dellaire, Graham, Burrage, Kevin and Bailey, Timothy L. (2010). A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies. Journal of Computational Biology, 17 (4), 617-630. doi: 10.1089/cmb.2009.0140 |
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2010 Journal Article Assigning roles to DNA regulatory motifs using comparative genomicsBuske, Fabian A., Boden, Mikael, Bauer, Denis C. and Bailey, Timothy L. (2010). Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics, 26 (7) btq049, 860-866. doi: 10.1093/bioinformatics/btq049 |
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2010 Conference Publication Multilinear decomposition and topographic mapping of binary tensorsMazgut, Jakub, Tino, Peter, Boden, Mikael and Yan, Hong (2010). Multilinear decomposition and topographic mapping of binary tensors. 20th International Conference on Artificial Neural Networks (ICANN 2010), Thessaloniki, Greece, 15-18 September 2010. Heidelberg, Germany: Springer. doi: 10.1007/978-3-642-15819-3_42 |
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2009 Journal Article In silico characterization of protein chimeras: Relating sequence and function within the same foldBuske, Fabian A., Their, Ricarda, Gillam, Elizabeth M. J. and Boden, Mikael (2009). In silico characterization of protein chimeras: Relating sequence and function within the same fold. Proteins: Structure, Function, and Bioinformatics, 77 (1), 111-120. doi: 10.1002/prot.22422 |
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2009 Journal Article It's about time: Signal recognition in staged models of protein translocationBuske, Fabian A., Maetschke, Stefan and Boden, Mikael (2009). It's about time: Signal recognition in staged models of protein translocation. Pattern Recognition, 42 (4), 567-574. doi: 10.1016/j.patcog.2008.09.020 |
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2009 Journal Article MEME suite: Tools for motif discovery and searchingBailey, T. L., Boden, M. B., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J. Y., Li, W. W. and Noble, W. S. (2009). MEME suite: Tools for motif discovery and searching. Nucleic Acids Research, 37 (Suppl. 2), W202-W208. doi: 10.1093/nar/gkp335 |
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2009 Conference Publication Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymesArieshanti, I., Boden, M., Maetschke, S and Buske, F. A. (2009). Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2009, Nashville, Tennessee, U.S.A., 30 March - 2 April , 2009. United States of America: IEEE. doi: 10.1109/CIBCB.2009.4925706 |
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2008 Journal Article Determining nucleolar association from sequence by leveraging protein-protein interactionsBoden, M. and Teasdale, R. D. (2008). Determining nucleolar association from sequence by leveraging protein-protein interactions. Journal of Computational Biology, 15 (3), 291-304. doi: 10.1089/cmb.2007.0163 |
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2008 Journal Article Associating transcription factor-binding site motifs with target GO terms and target genesBoden, M. and Bailey, T. L. (2008). Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Research, 36 (12), 4108-4117. doi: 10.1093/nar/gkn374 |
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2008 Journal Article Network: Computation in Neural Systems: EditorialGoodhill, Geoff, Baker, Curtis, Balasubramanian, Vijay, Bazhenov, Maxim, Beck, Jeffrey, Becker, Sue, Bethge, Matthias, Boahen, Kwabena, Boden, Mikael, Bonin, Vincent, Bouret, Sebastien, Fairhall, Adrienne, Flash, Tamar, French, Robert, Gillies, Andrew, Gollisch, Tim, Gurney, Kevin, Gutkin, Boris, Hayhoe, Mary, Hunt, Jonathan, Ibbotson, Michael, Kepecs, Adam, Kingdom, Fred, Kropff, Emilio, Longden, Kit, Marder, Eve, Miikkulainen, Risto, Oliva, Aude, Olshausen, Bruno ... Zhaoping, Li (2008). Network: Computation in Neural Systems: Editorial. Network: Computation in Neural Systems, 19 (1), 1-2. doi: 10.1080/09548980801915409 |
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2008 Conference Publication Predicting SUMOylation sitesBauer, Denis C., Buske, Fabian A. and Boden, Mikael (2008). Predicting SUMOylation sites. 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, Melbourne, Australia, 15-17 October, 2008. Berlin, Germany: Springer-Verlag Berlin. doi: 10.1007/978-3-540-88436-1-3 |
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2007 Journal Article Computing the reversal distance between genomes in the presence of multi-gene families via binary integer programmingSuksawatchon, J., Lursinsap, C. and Boden, M. (2007). Computing the reversal distance between genomes in the presence of multi-gene families via binary integer programming. Journal of Bioinformatics and Computational Biology, 5 (1), 117-133. doi: 10.1142/S0219720007002552 |
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2007 Book Chapter Markovian bias of neural-based architectures with feedback connectionsTino, P., Hammer, B. and Boden, M. (2007). Markovian bias of neural-based architectures with feedback connections. Perspectives of Neural-Symbolic Integration. (pp. 95-133) edited by Hammer, B. and Hitzler, P.. Heidelberg, Germany: Springer-Verlag. doi: 10.1007/978-3-540-73954-8_5 |
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2007 Conference Publication Predicting nucleolar proteins using support-vector machinesBodén, Mikael (2007). Predicting nucleolar proteins using support-vector machines. 6th Asia-Pacific Bioinformatics Conference, Kyoto, Japan, 14-17 January, 2008. London, U.K.: Imperial College Press. doi: 10.1142/9781848161092_0005 |
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2007 Conference Publication A comparison of sequence kernels for localization prediction of transmembrane proteinsMaetschke, S., Gallagher, M. and Boden, M. (2007). A comparison of sequence kernels for localization prediction of transmembrane proteins. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2007 (CIBCB 2007), Honolulu, Hawaii, 1-5 April 2007. Piscataway, NJ, U.S.A.: IEEE - Institute of Electrical Electronics Engineers Inc.. doi: 10.1109/cibcb.2007.4221246 |
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2007 Conference Publication Understanding prediction systems for HLA-binding peptides and t-cell epitope identificationYou, L., Zhang, P., Boden, M. and Brusic, V. (2007). Understanding prediction systems for HLA-binding peptides and t-cell epitope identification. Pattern Recognition in Bioinformatics (PRIB 2007), Singapore, 1-2 October 2007. Heidelberg, Germany: Springer. doi: 10.1007/978-3-540-75286-8_32 |
