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2014 Journal Article Predicting the dynamics of protein abundanceMehdi, Ahmed M., Patrick, Ralph, Bailey, Timothy L. and Boden, Mikael (2014). Predicting the dynamics of protein abundance. Molecular and Cellular Proteomics, 13 (5), 1330-1340. doi: 10.1074/mcp.M113.033076 |
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2014 Book Chapter Computational tools for directed evolution: a comparison of prospective and retrospective strategiesZaugg, Julian, Gumulya, Yosephine, Gillam, Elizabeth M. J. and Bodén, Mikael (2014). Computational tools for directed evolution: a comparison of prospective and retrospective strategies. Directed evolution library creation: methods and protocols. (pp. 315-333) edited by Elizabeth M. J. Gillam, Janine N. Copp and David F. Ackerley. New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-1053-3_21 |
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2014 Journal Article Inferring short tandem repeat variation from paired-end short readsCao, Minh Duc, Tasker, Edward, Willadsen, Kai, Imelfort, Michael, Vishwanathan, Sailaja, Sureshkumar, Sridevi, Balasubramanian, Sureshkumar and Bodén, Mikael (2014). Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Research, 42 (3) e16, e16.1-e16.11. doi: 10.1093/nar/gkt1313 |
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2013 Journal Article Distinctive conformation of minor site-specific nuclear localization signals bound to importin-αChang, Chiung-Wen, Counago, Rafael Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2013). Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α. Traffic, 14 (11), 1144-1154. doi: 10.1111/tra.12098 |
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2013 Journal Article PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversityOyarzun, Patricio, Ellis, Jonathan J., Boden, Mikael and Kobe, Bostjan (2013). PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. BMC Bioinformatics, 14 (1) 52, 52. doi: 10.1186/1471-2105-14-52 |
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2013 Journal Article Repeat-encoded poly-Q tracts show statistical commonalities across speciesWilladsen, Kai, Minh Duc Cao, Wiles, Janet, Balasubramanian, Sureshkumar and Boden, Mikael (2013). Repeat-encoded poly-Q tracts show statistical commonalities across species. Bmc Genomics, 14 (1) 76, 76.1-76.10. doi: 10.1186/1471-2164-14-76 |
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2013 Journal Article DLocalMotif: a discriminative approach for discovering local motifs in protein sequencesMehdi, Ahmed M., Sehgal, Muhammad Shoaib B., Kobe, Bostjan, Bailey, Timothy L. and Boden, Mikael (2013). DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. Bioinformatics, 29 (1), 39-46. doi: 10.1093/bioinformatics/bts654 |
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2013 Journal Article The distribution of different classes of nuclear localization signals (NLSs) in diverse organisms and the utilization of the minor NLS-binding site in plant nuclear import factor importin-αChang, Chiung-Wen, Counago, Rafael Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2013). The distribution of different classes of nuclear localization signals (NLSs) in diverse organisms and the utilization of the minor NLS-binding site in plant nuclear import factor importin-α. Plant Signaling and Behavior, 8 (10), e25976.1-e25976.6. doi: 10.4161/psb.25976 |
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2012 Journal Article Crystal structure of rice importin-alpha and structural basis of its interaction with plant-specific nuclear localization signalsChang, Chiung-Wen, Counago, Rafael Lemos Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2012). Crystal structure of rice importin-alpha and structural basis of its interaction with plant-specific nuclear localization signals. Plant Cell, 24 (12), 5074-5088. doi: 10.1105/tpc.112.104422 |
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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 |
