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Boden, 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 176   3 Cited 3 times in Scopus3 0
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 18   Cited 0 times in Scopus0 0
Maetschke, S., Gallagher, M. and Boden, M. (2007). A comparison of sequence kernels for localization prediction of transmembrane proteins. In: D. Fogel, Computational Intelligence in Bioinformatics and Computational Biology 2007 (CIBCB 2007). IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2007 (CIBCB 2007), Honolulu, Hawaii, (367-372). 1-5 April 2007. 116   0 Cited 1 times in Scopus1
Ziemke, T., Carlsson, J. and Boden, M. (1999). An experimental comparison of weight evolution in neural control architectures for a 'Garbage-Collecting' Khepera robot. In: A. Loffler, F. Mondada and U. Ruckert, Proceedings of the 1st International Khepera Workshop. 1st International Khepera Workshop, Paderborn, Germany, (31-40). 10-11 December 1999. 40  
Mehdi, 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: 1239-1246. doi:10.1093/bioinformatics/btr121 50   8 Cited 8 times in Scopus8 0
Buske, Fabian A., Boden, Mikael, Bauer, Denis C. and Bailey, Timothy L. (2010) Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics, 26 7: 860-866. doi:10.1093/bioinformatics/btq049 55 2 23 Cited 24 times in Scopus24 0
Boden, 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 36   12 Cited 13 times in Scopus13 0
Maetschke, S. R., Towsey, M. and Boden, M. B. (2005). BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction. In: Y.P. Phoebe Chen and L. Wong, Proceedings of the 3rd Asia Pacific Bioinformatics Conference. 3rd Asia Pacific Bioinformatics Conference, Singapore, (141-150). 17-21 January 2005. 58  
Davis, L., Hawkins, J. C., Maetschke, S. R. and Boden, M B (2006). Comparing SVM sequence kernels: A protein subcellular localization theme. In: M. Boden and T. Bailey, Proceedings of the 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006). 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Tas, Australia, (39-47). 4 December, 2006. 59  
Kobe, 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 69 3 8 Cited 10 times in Scopus10 0
Zaugg, Julian, Gumulya, Yosephine, Gillam, Elizabeth M. J. and Bodén, Mikael (2014). Computational tools for directed evolution: a comparison of prospective and retrospective strategies. In Elizabeth M. J. Gillam, Janine N. Copp and David F. Ackerley (Ed.), Directed evolution library creation: methods and protocols 2nd ed. (pp. 315-333) New York, NY, United States: Humana Press. doi:10.1007/978-1-4939-1053-3_21 47   0 0
Suksawatchon, 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 46   Cited 2 times in Scopus2 0
Boden, MB and Niklasson, LF (1993) Connectionism. Artificial Intelligence Review, 7 5: 259-260. doi:10.1007/BF00849053 12   0 0
Niklasson, L. and Boden, M. B. (1999). Content, context and connectionist networks. In: Proceedings of the 21st Annual Meeting of the Cognitive Science Society. 21st Annual Meeting of the Cognitive Science Society, Vancouver, (474-479). August 1999. 43   2
Boden, Mikael and Wiles, Janet (2000) Context-free and context-sensitive dynamics in recurrent neural networks. Connection Science: journal of neural computing, artificial intelligence, and cognitive research, 12 3-4: 197-210. doi:10.1080/095400900750060122 88   23 Cited 31 times in Scopus31 0
Chang, 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 51   7 Cited 9 times in Scopus9 0
Buske, Fabian and Boden, Mikael (2007). Decoupling signal recognition from sequence models of protein secretion. In: Computational Models for Life Sciences - CMLS'07. Computational Models for Life Sciences - CMLS'07, Gold Coast, QLD, Australia, (147-156). 17 - 19 December 2007. doi:10.1063/1.2816618 59   0 Cited 0 times in Scopus0 0
Hawkins, John and Boden, Mikael (2006) Detecting and sorting targeting peptides wtih neural networks and support vector machines. Journal of Bioinformatics and Computational Biology, 4 1: 1-18. doi:10.1142/S0219720006001771 56   Cited 32 times in Scopus32 0
Boden, M. B. and Hawkins, J. C. (2005). Detecting residues in targeting peptides. In: Y. P. Chen and L. Wong, Proceedings of the 3rd Asia-Pacific Bioinformatics Conference. 3rd Asia-Pacific Bioinformatics Conference, Singapore, (131-140). 17-21 January, 2005. 34  
Arieshanti, 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. In: Proceedings of the 2009 IEEE Computational Intelligence for Bioinformatics and Computational Biology. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2009, Nashville, Tennessee, U.S.A., (46-52). 30 March - 2 April , 2009. doi:10.1109/CIBCB.2009.4925706 65   0 Cited 0 times in Scopus0 0
Boden, 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 23   4 Cited 5 times in Scopus5 0
Mazgut, 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 32   0 Cited 0 times in Scopus0 0
Chang, 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 34 5 4 Cited 5 times in Scopus5 1
Mehdi, 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 52 36 2 Cited 2 times in Scopus2 3
Roona, 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 21   0 Cited 1 times in Scopus1 2
Boden, M. B. and Hawkins, J. C. (2006). Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway. In: G.G Yen, 2006 IEEE Congress on Evolutionary Computation. 2006 IEEE Congress on Evolutionary Computation, Vancouver, BC, Canada, (2750-2755). 16-21 July, 2006. 58   0 Cited 0 times in Scopus0
Boden, Marie and Boden, Mikael (2007) Evolving spelling exercises to suit individual student needs. Applied Soft Computing, 7 1: 126-135. doi:10.1016/j.asoc.2005.03.001 132   2 Cited 3 times in Scopus3 0
Wakabayashi, M., Hawkins, J. C., Maetschke, S. R. and Boden, M. B. (2005). Exploiting sequence dependencies in the prediction of peroxisomal proteins. In: M. Gallagher, J. Hogan and F. Maire, Intelligent Data Engineering and Automated Learning - IDEAL2005. Intelligent Data Engineering and Automated Learning - IDEAL2005, Brisbane, Australia, (454-461). 6-8 July 2005. 69   3 Cited 3 times in Scopus3
Boden, M and Niklasson, L (1995). Features of distributed representations for tree-structures: A study of RAAM. In: Current Trends in Connectionism. Swedish Conference on Connectionism, Skovde Sweden, (121-139). Mar 02-03, 1995. 28   2
Boden, Mikael (2004) Generalization by symbolic abstraction in cascaded recurrent networks. Neurocomputing, 57 87-104. doi:10.1016/j.neucom.2004.01.006 47   5 Cited 6 times in Scopus6 0
Suksawatchon, J., Lursinsap, C. and Boden, M. B. (2005). Heuristic algorithm for computing reversal distance with multigene families via binary integer programming. In: G. B. Fogel, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005 (CIBCB '05). IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, U.S.A., (187-193). 14-15 November 2005. 65   0
Maetschke, S. R., Boden, M B and Gallagher, M R (2006). Higher order HMMs for localization prediction of transmembrance proteins. In: M. Boden and T. Bailey, Proceedings of the 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006). 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Australia, (49-53). 4 December, 2006. 55  
Hawkins, J., Mahony, D., Maetschke, S., Wakabayashi, M., Teasdale, R. D. and Boden, M. (2007) Identifying novel peroxisomal proteins. Proteins: Structure Function and Bioinformatics, 69 3: 606-616. doi:10.1002/prot.21420 70   11 Cited 12 times in Scopus12 6
Boden, M. and Bailey, T. L. (2006) Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinformatics, 22 15: 1809-1814. doi:10.1093/bioinformatics/btl198 41   12 Cited 12 times in Scopus12 0
Boden, Mikael and Hawkins, John (2005) Improved Access To Sequential Motifs: A Note On The Architectural Bias Of Recurrent Networks. IEEE Transactions on Neural Networks, 16 2: 491-494. doi:10.1109/TNN.2005.844086 166 225 2 Cited 4 times in Scopus4 0
Cao, 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: e16.1-e16.11. doi:10.1093/nar/gkt1313 52 2 4 Cited 3 times in Scopus3 4
Buske, 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 74   3 Cited 3 times in Scopus3 0
Buske, 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 59   0 Cited 0 times in Scopus0 0
Boden, M. and Blair, A. (2003) Learning the dynamics of embedded clauses. Applied Intelligence, 19 1-2: 51-63. doi:10.1023/A:1023816706954 61   10 Cited 9 times in Scopus9 3
Boden, M. B., Wiles, J. H., Tonkes, B. and Blair, A. D. (1999). Learning to predict a context-free language: Analysis of dynamics in recurrent hidden units. In: Proceedings of the Ninth International Conference on Artificial Neural Networks. ICANN'99, Edinburgh, UK, (359-364). 7-10 September, 1999. 52  
Boden, M, Wiles, J, Tonkes, B and Blair, A (1999). Learning to predict a context-free language: Analysis of dynamics in recurrent hidden units. In: Ninth International Conference On Artificial Neural Networks (icann99), Vols 1 and 2. 9th International Conference on Artificial Neural Networks (ICANN99), Edinburgh Scotland, (359-364). Sep 07-10, 1999. 25   1
Patrick, 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 60.1-60.15. doi:10.1186/1752-0509-6-60 78   2 Cited 2 times in Scopus2 3
Tino, P., Hammer, B. and Boden, M. (2007). Markovian bias of neural-based architectures with feedback connections. In Hammer, B. and Hitzler, P. (Ed.), Perspectives of Neural-Symbolic Integration (pp. 95-133) Heidelberg, Germany: Springer-Verlag. doi:10.1007/978-3-540-73954-8_5 46   Cited 0 times in Scopus0 0
Madala, 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 46   4 Cited 4 times in Scopus4 0
Bailey, 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 89 2 756 Cited 793 times in Scopus793 7
Marfori, 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 85   96 Cited 89 times in Scopus89 13
Mazgut, Jakub, Tino, Peter, Boden, Mikael and Yan, Hong (2010). Multilinear decomposition and topographic mapping of binary tensors. In: Konstantinos Diamantaras, Wlodek Duch and Lazaros S. Iliadis, Artificial Neural Networks – ICANN 2010: Proceedings of the 20th International Conference, Part I. 20th International Conference on Artificial Neural Networks (ICANN 2010), Thessaloniki, Greece, (317-326). 15-18 September 2010. doi:10.1007/978-3-642-15819-3_42 58   0 Cited 0 times in Scopus0 0
Hawkins, J. and Boden, M. (2006). Multi-stage redundancy reduction: effective utilisation of small protein data sets. In: Mikael Boden and Timothy L. Bailey, Proceedings of the A1 2006 Workshop on Intelligent Systems of Bioinformatics (WISB 2006). Intelligent Systems for Bioinformatics 2006, Hobart, Australia, (55-59). 4 December, 2006. 42  
Willadsen, 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 47 23 Cited 0 times in Scopus0 0
Boden, Mikael and Wiles, Janet (2002) On learning context-free and context-sensitive languages. IEEE Transactions on Neural Networks, 13 2: 491-493. doi:10.1109/72.991436 46   11 Cited 13 times in Scopus13 0

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