Professor Mikael Boden
Professor

Mikael Boden

Email: 
Phone: 
+61 7 336 51307

Background

Mikael Bodén has a PhD in Computer Science and statistical machine learning from the University of Exeter (UK) but has spent the last decade and a half in biological research environments, including the Institute for Molecular Bioscience/ARC Centre of Excellence in Bioinformatics and the School of Chemistry and Molecular Biosciences, where he is currently located. He is the director of UQ’s postgraduate program in bioinformatics. Mikael Bodén has supervised 7 postdocs from funding he received from both ARC and NHMRC; he has been the primary advisor for 11 PhD and 3 MPhil graduates; he is currently supervising another 6 PhD students in bioinformatics and computational biology. Mikael Bodén collaborates with researchers in neuroscience, developmental biology, protein engineering and bioeconomy to mention but a few, and contributes expertise in the processing, analysis and integration of biological data; this is exemplified by recent publications in Science, Nature Catalysis, Nature Communications, Cell Systems, Nucleic Acids Research and Bioinformatics.

Availability

Professor Mikael Boden is:
Available for supervision
Media expert

Fields of research

Bioinformatics and computational biology Biological Sciences Genetics Genomics Information and Computing Sciences Modelling and simulation Systems biology

Qualifications

  • Bachelor of Science, Skövde University College
  • Masters (Coursework) of Science, Skövde University College
  • Doctor of Philosophy, University of Exeter

Research interests

  • Bioinformatics

    Thanks to major advances in biotechnology and instrumentation, biology is becoming an information centred science. The field of bioinformatics draws on computer science, math and statistics to enable discoveries in biological data sets. Our research aims to develop, investigate and apply bioinformatics methodologies to understand and resolve a range of open problems in genomics, molecular and systems biology. Recent applications involve protein sorting, nuclear protein organisation, mechanisms of transcriptional regulation, sequence and structure determinants of protein function and modification, and protein engineering. Biological data are now available at scales that challenges our ability to process and analyse them. On the flip side, greater scale gives statistical power to distinguish biologically meaningful signals from mere noise or artefacts, i.e. to identify "drivers" and "determinants" of function and structure. Sometimes the number of features (that describe each observation) is so great that we must use (biological) expertise to constrain the search for signals. Broadly put, our research aims to 1. effectively manage the complexity of operations involved in analysing millions of sequence reads, thousands of genomes, and proteomes of thousands of dynamically regulated molecules, etc 2. enable the seamless aggregation (or integration) of uncertain and incomplete data, typical of the next wave of biotechnology, across genomics, proteomics, structural biology, etc, and of using biological expertise 3. empower the interpretation of "whole system" data, aimed at understanding of basis of disease and other scientifically relevant phenotypes, using statistics and machine learning

Search Professor Mikael Boden’s works on UQ eSpace

134 works between 1993 and 2025
All (134) Journal Article (97) Book Chapter (4) Conference Publication (32) Edited Outputs (1)

61 - 80 of 134 works

2013

Journal Article

PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

Oyarzun, 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

PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

2013

Journal Article

Repeat-encoded poly-Q tracts show statistical commonalities across species

Willadsen, 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

Repeat-encoded poly-Q tracts show statistical commonalities across species

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-α

Chang, 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

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

2013

Journal Article

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences

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

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences

2012

Journal Article

Crystal structure of rice importin-alpha and structural basis of its interaction with plant-specific nuclear localization signals

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

Crystal structure of rice importin-alpha and structural basis of its interaction with plant-specific nuclear localization signals

2012

Journal Article

NSort/DB: an intra-nuclear compartment protein database

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

NSort/DB: an intra-nuclear compartment protein database

2012

Journal Article

Computational modelling of linear motif-mediated protein interactions

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

Computational modelling of linear motif-mediated protein interactions

2012

Journal Article

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

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 (1) 60, 60.1-60.15. doi: 10.1186/1752-0509-6-60

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

2012

Journal Article

Matching cavities in G protein-coupled receptors to infer ligand-binding sites

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

Matching cavities in G protein-coupled receptors to infer ligand-binding sites

2011

Journal Article

Molecular basis for specificity of nuclear import and prediction of nuclear localization

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

Molecular basis for specificity of nuclear import and prediction of nuclear localization

2011

Journal Article

Sorting the nuclear proteome

Bauer, 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

Sorting the nuclear proteome

2011

Journal Article

A probabilistic model of nuclear import of proteins

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) btr121, 1239-1246. doi: 10.1093/bioinformatics/btr121

A probabilistic model of nuclear import of proteins

2010

Journal Article

Using Gaussian process with test rejection to detect T-Cell epitopes in pathogen genomes

You, 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

Using Gaussian process with test rejection to detect T-Cell epitopes in pathogen genomes

2010

Journal Article

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

Bauer, 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

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

2010

Journal Article

The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression

Mohamad, 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

The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression

2010

Journal Article

The value of position-specific priors in motif discovery using MEME

Bailey, 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

The value of position-specific priors in motif discovery using MEME

2010

Journal Article

A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies

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

A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies

2010

Journal Article

Assigning roles to DNA regulatory motifs using comparative genomics

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) btq049, 860-866. doi: 10.1093/bioinformatics/btq049

Assigning roles to DNA regulatory motifs using comparative genomics

2010

Conference Publication

Multilinear decomposition and topographic mapping of binary tensors

Mazgut, Jakub, Tino, Peter, Boden, Mikael and Yan, Hong (2010). Multilinear decomposition and topographic mapping of binary tensors. 20th International Conference on Artificial Neural Networks (ICANN 2010), Thessaloniki, Greece, 15-18 September 2010. Heidelberg, Germany: Springer. doi: 10.1007/978-3-642-15819-3_42

Multilinear decomposition and topographic mapping of binary tensors

2009

Journal Article

In silico characterization of protein chimeras: Relating sequence and function within the same fold

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

In silico characterization of protein chimeras: Relating sequence and function within the same fold

Current funding

  • 2025 - 2028
    Learning from the past to design drugs for the future
    NHMRC IDEAS Grants
    Open grant
  • 2023 - 2026
    What drives the Anterior Expansion of the Central Nervous System?
    ARC Discovery Projects
    Open grant
  • 2023 - 2025
    What is the common factor driving brain overgrowth in ASD? Investigating the relationship between epigenetic marks neural stem cell proliferation.
    Simons Foundation Autism Research Initiative - Pilot Award
    Open grant
  • 2022 - 2026
    TRIAGE: A disease agnostic computational and modelling platform to accelerate variant classification
    NHMRC MRFF Genomics Health Futures Mission
    Open grant
  • 2022 - 2025
    Dual-function ribonucleases: unexpected agents of antibiotic resistance
    NHMRC IDEAS Grants
    Open grant

Past funding

  • 2021 - 2024
    EnzOnomy - an enzyme-based production pipeline for the bioeconomy
    ARC Discovery Projects
    Open grant
  • 2016 - 2019
    Reconstructing proteins to explain and engineer biological diversity
    ARC Discovery Projects
    Open grant
  • 2012 - 2015
    Tracing nature's template: Using statistical machine learning to evolve biocatalysts
    ARC Discovery Projects
    Open grant
  • 2011
    A systems biology approach to elucidate common principles and mechanisms underlying triplet repeat expansion associated genetic defects
    NHMRC Project Grant
    Open grant
  • 2005
    Mining Long-range Dependencies and Interactions in Amino Acid Sequences
    UQ Early Career Researcher
    Open grant
  • 2003 - 2005
    Recurrent neural networks for biological sequence analysis
    UQ New Staff Research Start-Up Fund
    Open grant

Availability

Professor Mikael Boden is:
Available for supervision

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Supervision history

Current supervision

  • Doctor Philosophy

    Using Statistical Models to Integrate Epigenetic Information by Distinguishing Sources of Variability

    Principal Advisor

    Other advisors: Professor Michael Piper

  • Doctor Philosophy

    Bioinformatics of epigenetics at multiple scales: from evolution of epigenetic factors to tracing their marks in organellar development

    Principal Advisor

    Other advisors: Professor Stefan Thor

  • Doctor Philosophy

    Grounding the computational design of enzymes in their relative diversity

    Principal Advisor

    Other advisors: Professor Gary Schenk

  • Doctor Philosophy

    Do cell types exist in a continuum? Single-cell bioinformatics across species, over time and space

    Principal Advisor

    Other advisors: Professor Stefan Thor

  • Doctor Philosophy

    Finding meaningful variation in biological data by deep learning

    Principal Advisor

    Other advisors: Professor Nathan Palpant

  • Doctor Philosophy

    Merger of natural and engineered biological sequence space

    Principal Advisor

    Other advisors: Dr Michael Forbes

  • Doctor Philosophy

    Dual-function ribonucleases: unexpected agents of antibiotic resistance

    Principal Advisor

    Other advisors: Professor Phil Hugenholtz

  • Doctor Philosophy

    Bioinformatics of epigenetics at multiple scales: from evolution of epigenetic factors to tracing their marks in organellar development

    Principal Advisor

    Other advisors: Professor Stefan Thor

  • Doctor Philosophy

    Changing the prokaryotic classification status quo with a global genome-based taxonomy

    Associate Advisor

    Other advisors: Professor Phil Hugenholtz

  • Doctor Philosophy

    Changing the prokaryotic classification status quo with a global genome-based taxonomy

    Associate Advisor

    Other advisors: Professor Phil Hugenholtz

  • Doctor Philosophy

    Decoding the genetic pathways governing cell diversity in the mammalian hypothalamus

    Associate Advisor

    Other advisors: Professor Michael Piper, Professor Stefan Thor

  • Doctor Philosophy

    How SETD2 shapes cortical development

    Associate Advisor

    Other advisors: Professor Stefan Thor, Professor Michael Piper

Completed supervision

Enquiries

Contact Professor Mikael Boden directly for media enquiries about:

  • Artificial Intelligence (AI)
  • Bioinformatics
  • Biology and computers
  • Computational biology
  • Computer learning
  • DNA sequencing
  • Machine learning
  • Systems biology

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