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2016 Journal Article ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein librariesHuang, Weiliang, Johnston, Wayne A., Boden, Mikael and Gillam, Elizabeth M.J. (2016). ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries. BioTechniques, 60 (2), 91-94. doi: 10.2144/000114381 |
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2016 Journal Article Cell-type-specific expression of NFIX in the developing and adult cerebellumFraser, James, Essebier, Alexandra, Gronostajski, Richard M., Boden, Mikael, Wainwright, Brandon J., Harvey, Tracey J. and Piper, Michael (2016). Cell-type-specific expression of NFIX in the developing and adult cerebellum. Brain Structure and Function, 222 (5), 1-20. doi: 10.1007/s00429-016-1340-8 |
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2015 Journal Article Sequencing technologies and tools for short tandem repeat variation detectionCao, Minh Duc, Balasubramanian, Sureshkumar and Boden, Mikael (2015). Sequencing technologies and tools for short tandem repeat variation detection. Briefings in Bioinformatics, 16 (2) bbu001, 193-204. doi: 10.1093/bib/bbu001 |
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2015 Journal Article A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases.Oyarzun, Patricio, Ellis, Jonathan J., Gonzalez-Galarza, Faviel F., Jones, Andrew R, Middleton, Derek, Boden, Mikael and Kobe, Bostjan (2015). A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases.. Vaccine, 33 (10), 1267-1273. doi: 10.1016/j.vaccine.2015.01.040 |
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2014 Journal Article Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylationRoona, Gergely, Borsos, Mate, Ellis, Jonathan J., Mehdi, Ahmed M., Christie, Mary, Koornyei, Zsuzsanna, Neubrandt, Mate, Tooth, Judit, Bozooky, Zoltan, Buday, Laszlo, Madaraasz, Emilia, Bodaen, Mikael, Kobe, Bostjan and Veertessy, Beata G. (2014). Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle, 13 (22), 3551-3564. doi: 10.4161/15384101.2014.960740 |
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2014 Journal Article PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation eventsPatrick, Ralph, Lê Cao, Kim-Anh, Kobe, Bostjan and Bodén, Mikael (2014). PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. Bioinformatics, 31 (3), 382-389. doi: 10.1093/bioinformatics/btu663 |
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2014 Journal Article Importin alpha and nonclassical nuclear localization signalChang, Chiung-Wen, Couñago, Rafael, Williams, Simon, Bodén, Mikael and Kobe, Boštjan (2014). Importin alpha and nonclassical nuclear localization signal. Acta Crystallographica Section A Foundations and Advances, 70 (a1), C1634-C1634. doi: 10.1107/s205327331408365x |
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2014 Journal Article Dimensionality reduction and topographic mapping of binary tensorsMazgut, Jakub, Tino, Peter, Boden, Mikael and Yan, Hong (2014). Dimensionality reduction and topographic mapping of binary tensors. Pattern Analysis and Applications, 17 (3), 497-515. doi: 10.1007/s10044-013-0317-y |
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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 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) ARTN 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 |
