Mikael Boden

Summary

Affiliation: University of Queensland
Country: Australia

Publications

  1. ncbi request reprint Prediction of subcellular localization using sequence-biased recurrent networks
    Mikael Boden
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
    Bioinformatics 21:2279-86. 2005
  2. pmc Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures
    Mikael Boden
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, St Lucia, Australia
    BMC Bioinformatics 7:68. 2006
  3. ncbi request reprint Identifying sequence regions undergoing conformational change via predicted continuum secondary structure
    Mikael Boden
    School of Information Technology and Electrical Engineering, QLD 4072, The University of Queensland Australia
    Bioinformatics 22:1809-14. 2006
  4. pmc Sorting the nuclear proteome
    Denis C Bauer
    Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia
    Bioinformatics 27:i7-14. 2011
  5. ncbi request reprint Identifying novel peroxisomal proteins
    John Hawkins
    ARC Centre for Complex Systems, The University of Queensland, St Lucia, Queensland 4072, Australia
    Proteins 69:606-16. 2007
  6. doi request reprint DLocalMotif: a discriminative approach for discovering local motifs in protein sequences
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Australia
    Bioinformatics 29:39-46. 2013
  7. ncbi request reprint Computational modelling of linear motif-mediated protein interactions
    Bostjan Kobe
    Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Curr Top Med Chem 12:1553-61. 2012
  8. pmc Assigning roles to DNA regulatory motifs using comparative genomics
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
    Bioinformatics 26:860-6. 2010
  9. pmc Inferring short tandem repeat variation from paired-end short reads
    Minh Duc Cao
    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia QLD 4072, Australia, Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia, School of Biological Sciences, Monash University, Melbourne, Australia and Advanced Water Management Centre, The University of Queensland, Queensland, Australia
    Nucleic Acids Res 42:e16. 2014
  10. doi request reprint A probabilistic model of nuclear import of proteins
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
    Bioinformatics 27:1239-46. 2011

Detail Information

Publications31

  1. ncbi request reprint Prediction of subcellular localization using sequence-biased recurrent networks
    Mikael Boden
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
    Bioinformatics 21:2279-86. 2005
    ..However, due to the low similarity of such sequences and the dynamical nature of the sorting process, the computational prediction of subcellular localization of proteins is challenging...
  2. pmc Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures
    Mikael Boden
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, St Lucia, Australia
    BMC Bioinformatics 7:68. 2006
    ..e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models...
  3. ncbi request reprint Identifying sequence regions undergoing conformational change via predicted continuum secondary structure
    Mikael Boden
    School of Information Technology and Electrical Engineering, QLD 4072, The University of Queensland Australia
    Bioinformatics 22:1809-14. 2006
    ....
  4. pmc Sorting the nuclear proteome
    Denis C Bauer
    Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia
    Bioinformatics 27:i7-14. 2011
    ..Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed...
  5. ncbi request reprint Identifying novel peroxisomal proteins
    John Hawkins
    ARC Centre for Complex Systems, The University of Queensland, St Lucia, Queensland 4072, Australia
    Proteins 69:606-16. 2007
    ..We use the predictor to screen several additional eukaryotic genomes to revise previously estimated numbers of peroxisomal proteins. Available at http://pprowler.itee.uq.edu.au...
  6. doi request reprint DLocalMotif: a discriminative approach for discovering local motifs in protein sequences
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Australia
    Bioinformatics 29:39-46. 2013
    ..Using negatives, i.e. sequences known to not contain a local motif, can further increase the specificity of their discovery...
  7. ncbi request reprint Computational modelling of linear motif-mediated protein interactions
    Bostjan Kobe
    Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Curr Top Med Chem 12:1553-61. 2012
    ..Computational approaches will play an increasing role in the future, allowing new relationships and system-wide understanding to be unearthed from the large datasets becoming available through high-throughput studies...
  8. pmc Assigning roles to DNA regulatory motifs using comparative genomics
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
    Bioinformatics 26:860-6. 2010
    ..Their functional roles are defined by the genes they regulate. Uncovering these roles not only sheds light on the TF at hand but puts it into the context of the complete regulatory network...
  9. pmc Inferring short tandem repeat variation from paired-end short reads
    Minh Duc Cao
    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia QLD 4072, Australia, Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia, School of Biological Sciences, Monash University, Melbourne, Australia and Advanced Water Management Centre, The University of Queensland, Queensland, Australia
    Nucleic Acids Res 42:e16. 2014
    ..In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats. ..
  10. doi request reprint A probabilistic model of nuclear import of proteins
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
    Bioinformatics 27:1239-46. 2011
    ..Despite progress on experimentally characterizing a number of nuclear localization signals, their presence alone remains an unreliable indicator of actual translocation...
  11. ncbi request reprint The applicability of recurrent neural networks for biological sequence analysis
    John Hawkins
    School of Information Technology and Electrical Engineering, University of Queensland, QLD 4072, Australia
    IEEE/ACM Trans Comput Biol Bioinform 2:243-53. 2005
    ..Furthermore, as the patterns within the sequence become more ambiguous, the choice of specific recurrent architecture becomes more critical...
  12. pmc The value of position-specific priors in motif discovery using MEME
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    BMC Bioinformatics 11:179. 2010
    ....
  13. pmc Repeat-encoded poly-Q tracts show statistical commonalities across species
    Kai Willadsen
    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072, Australia
    BMC Genomics 14:76. 2013
    ....
  14. pmc NSort/DB: an intranuclear compartment protein database
    Kai Willadsen
    School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
    Genomics Proteomics Bioinformatics 10:226-9. 2012
    ..nsort.org/db/. Availability of this data set will enable systematic analyses of the protein complements of nuclear compartments, improving our understanding of the diverse functional repertoire of these structures...
  15. pmc STAR: predicting recombination sites from amino acid sequence
    Denis C Bauer
    Institute for Molecular Bioscience, The University of Queensland, QLD 4072, Australia
    BMC Bioinformatics 7:437. 2006
    ..The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone...
  16. doi request reprint A Bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies
    Mikael Boden
    Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
    J Comput Biol 17:617-30. 2010
    ..Supplementary Material is available online at www.liebertonline.com...
  17. ncbi request reprint Detecting and sorting targeting peptides with neural networks and support vector machines
    John Hawkins
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
    J Bioinform Comput Biol 4:1-18. 2006
    ..873 for non-plant and 0.849 for plant proteins. The model improves upon the accuracy of our previous subcellular localization predictor (PProwler v1.1) by 2% for plant data (which represents 7.5% improvement upon TargetP)...
  18. ncbi request reprint Predicting nuclear localization
    John Hawkins
    ARC Centre for Complex Systems, School of Information Technology and Electrical Engineering, University of Queensland, QLD 4072, Australia
    J Proteome Res 6:1402-9. 2007
    ..The final predictor NUCLEO operates with a realistic success rate of 0.70 and a correlation coefficient of 0.38, as established on the independent test set. (NUCLEO is available at: http://pprowler.itee.uq.edu.au.)...
  19. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net...
  20. doi request reprint PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events
    Ralph Patrick
    School of Chemistry and Molecular Biosciences and Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia 4072, Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, St Lucia 4102, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, 4072, Australia
    Bioinformatics 31:382-9. 2015
    ..Lack of specificity in many kinase substrate binding motifs means that sequence methods for predicting kinase binding sites are susceptible to high false-positive rates...
  21. pmc Predicting the dynamics of protein abundance
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
    Mol Cell Proteomics 13:1330-40. 2014
    ..The software and data used in this research are available at http://bioinf.scmb.uq.edu.au/proteinabundance/. ..
  22. ncbi request reprint Predicting the solvent accessibility of transmembrane residues from protein sequence
    Zheng Yuan
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, 4072, Australia
    J Proteome Res 5:1063-70. 2006
    ..This approach can be used to annotate the membrane proteins in proteomes to provide extra structural and functional information...
  23. pmc Associating transcription factor-binding site motifs with target GO terms and target genes
    Mikael Boden
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Nucleic Acids Res 36:4108-17. 2008
    ..Results on human reference sets are similarly encouraging. Validation of our target gene prediction method shows that its accuracy exceeds that of simple motif scanning...
  24. pmc PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity
    Patricio OyarzĂșn
    School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 14:52. 2013
    ..The ability to predict what epitopes are most likely to dominate an immune response remains a challenge...
  25. pmc Mapping the stabilome: a novel computational method for classifying metabolic protein stability
    Ralph Patrick
    School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
    BMC Syst Biol 6:60. 2012
    ....
  26. doi request reprint Matching cavities in g protein-coupled receptors to infer ligand-binding sites
    Praveen K Madala
    Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    J Chem Inf Model 52:1401-10. 2012
    ..The method enables qualitative prediction of ligand binding for all nonredundant human G protein-coupled receptors...
  27. doi request reprint Determining nucleolar association from sequence by leveraging protein-protein interactions
    Mikael Boden
    ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
    J Comput Biol 15:291-304. 2008
    ..For supplementary material, see www.itee.uq.edu.au/~ pprowler/nucleoli...
  28. doi request reprint In silico characterization of protein chimeras: relating sequence and function within the same fold
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Australia
    Proteins 77:111-20. 2009
    ..Specifically, the model is used to assess the structural viability of P450 chimeras deriving from proteins with only 18% sequence similarity to those used for model tuning...
  29. doi request reprint Robust Estimation of Evolutionary Distances with Information Theory
    Minh Duc Cao
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia Clayton School of Information Technology, Monash University, Clayton, Vic, Australia
    Mol Biol Evol 33:1349-57. 2016
    ....
  30. ncbi request reprint CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data
    Timothy O'Connor
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Nucleic Acids Res . 2016
    ..Unlike distance-based methods, CisMapper can predict which transcription start site of a gene is regulated by a particular binding site of the TF...
  31. doi request reprint Computational tools for directed evolution: a comparison of prospective and retrospective strategies
    Julian Zaugg
    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
    Methods Mol Biol 1179:315-33. 2014
    ..From our evaluation, we suggest that each tool can play a role in the design process; however this is largely dictated by the data available and the desired experimental strategy for the project. ..