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2012 Journal Article NSort/DB: an intra-nuclear compartment protein databaseWilladsen, Kai, Mohamad, Nurul and Boden, Mikael (2012). NSort/DB: an intra-nuclear compartment protein database. Genomics, Proteomics & Bioinformatics, 10 (4), 226-229. doi: 10.1016/j.gpb.2012.07.001 |
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2012 Journal Article Computational modelling of linear motif-mediated protein interactionsKobe, Bostjan and Boden, Mikael (2012). Computational modelling of linear motif-mediated protein interactions. Current Topics in Medicinal Chemistry, 12 (14), 1553-1561. doi: 10.2174/156802612802652439 |
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2012 Journal Article Mapping the stabilome: a novel computational method for classifying metabolic protein stabilityPatrick, Ralph, Cao, Kim-Anh L., Davis, Melissa, Kobe, Bostjan and Bodén, Mikael (2012). Mapping the stabilome: a novel computational method for classifying metabolic protein stability. BMC Systems Biology, 6 (1) 60, 60.1-60.15. doi: 10.1186/1752-0509-6-60 |
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2012 Journal Article Matching cavities in G protein-coupled receptors to infer ligand-binding sitesMadala, Praveen K., Fairlie, David P. and Bodén, Mikael (2012). Matching cavities in G protein-coupled receptors to infer ligand-binding sites. Journal of Chemical Information and Modeling, 52 (5), 1401-1410. doi: 10.1021/ci2005498 |
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2011 Journal Article Molecular basis for specificity of nuclear import and prediction of nuclear localizationMarfori, Mary, Mynott, Andrew, Ellis, Jonathan J., Mehdi, Ahmed M., Saunders, Neil F. W., Curmi, Paul M., Forwood, Jade K., Bodén, Mikael and Kobe, Bostjan (2011). Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochimica et Biophysica Acta (BBA): Molecular Cell Research, 1813 (9), 1562-1577. doi: 10.1016/j.bbamcr.2010.10.013 |
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2011 Journal Article Sorting the nuclear proteomeBauer, Denis C., Willadsen, Kai, Buske, Fabian A., Lê Cao, Kim-Anh, Bailey, Timothy L., Dellaire, Graham and Bodén, Mikael (2011). Sorting the nuclear proteome. Bioinformatics, 27 (13) btr217, i7-i14. doi: 10.1093/bioinformatics/btr217 |
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2011 Journal Article A probabilistic model of nuclear import of proteinsMehdi, Ahmed M., Sehgal, Muhammad Shoaib B., Kobe, Bostjan, Bailey, Timothy L. and Boden, Mikael (2011). A probabilistic model of nuclear import of proteins. Bioinformatics, 27 (9) btr121, 1239-1246. doi: 10.1093/bioinformatics/btr121 |
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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 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 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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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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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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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 |
