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)

41 - 60 of 134 works

2017

Journal Article

Bioinformatics approaches to predict target genes from transcription factor binding data

Essebier, Alexandra, Lamprecht, Marnie, Piper, Michael and Bodén, Mikael (2017). Bioinformatics approaches to predict target genes from transcription factor binding data. Methods (San Diego, Calif.), 131, 111-119. doi: 10.1016/j.ymeth.2017.09.001

Bioinformatics approaches to predict target genes from transcription factor binding data

2017

Journal Article

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

Patrick, Ralph, Kobe, Bostjan, Lê Cao, Kim-Anh and Bodén, Mikael (2017). PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. Bioinformatics, 33 (12), 1773-1781. doi: 10.1093/bioinformatics/btx072

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

2016

Journal Article

Structure and function of the TIR domain from the grape NLR protein RPV1

Williams, Simon J., Yin, Ling, Foley, Gabriel, Casey, Lachlan W., Outram, Megan A., Ericsson, Daniel J., Lu, Jiang, Boden, Mikael, Dry, Ian B. and Kobe, Bostjan (2016). Structure and function of the TIR domain from the grape NLR protein RPV1. Frontiers in Plant Science, 7 (DECEMBER2016) 1850, 1850. doi: 10.3389/fpls.2016.01850

Structure and function of the TIR domain from the grape NLR protein RPV1

2016

Journal Article

Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

Patrick, Ralph, Horin, Coralie, Kobe, Bostjan, Cao, Kim-Anh Le and Bodén, Mikael (2016). Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence. Biochimica et Biophysica Acta, 1864 (11), 1599-1608. doi: 10.1016/j.bbapap.2016.08.001

Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

2016

Journal Article

CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data

O'Connor, Timothy, Boden, Mikael and Bailey, Timothy L. (2016). CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data. Nucleic Acids Research, 45 (4), e19. doi: 10.1093/nar/gkw956

CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data

2016

Journal Article

Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-alpha (vol 14, pg 1144, 2013)

Chang, Chiung-Wen, Counago, Rafael Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2016). Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-alpha (vol 14, pg 1144, 2013). Traffic, 17 (6), 704-704. doi: 10.1111/tra.12395

Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-alpha (vol 14, pg 1144, 2013)

2016

Journal Article

Statistical enrichment of epigenetic states around triplet repeats that can undergo expansions

Essebier, Alexandra, Wolf, Patricia Vera, Cao, Minh Duc, Carroll, Bernard J., Balasubramanian, Sureshkumar and Boden, Mikael (2016). Statistical enrichment of epigenetic states around triplet repeats that can undergo expansions. Frontiers in Neuroscience, 10 (MAR) 92, 92.1-92.12. doi: 10.3389/fnins.2016.00092

Statistical enrichment of epigenetic states around triplet repeats that can undergo expansions

2016

Journal Article

Robust estimation of evolutionary distances with information theory

Cao, Minh Duc, Allison, Lloyd, Dix, Trevor I. and Boden, Mikael (2016). Robust estimation of evolutionary distances with information theory. Molecular Biology and Evolution, 33 (5), 1349-1357. doi: 10.1093/molbev/msw019

Robust estimation of evolutionary distances with information theory

2016

Journal Article

ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries

Huang, 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

ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries

2016

Journal Article

Cell-type-specific expression of NFIX in the developing and adult cerebellum

Fraser, 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

Cell-type-specific expression of NFIX in the developing and adult cerebellum

2015

Journal Article

Sequencing technologies and tools for short tandem repeat variation detection

Cao, 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

Sequencing technologies and tools for short tandem repeat variation detection

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

A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases.

2014

Journal Article

Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation

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

Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation

2014

Journal Article

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

Patrick, 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

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

2014

Conference Publication

Importin alpha and nonclassical nuclear localization signal

Chang, Chiung-Wen, Couñago, Rafael, Williams, Simon, Bodén, Mikael and Kobe, Boštjan (2014). Importin alpha and nonclassical nuclear localization signal. XXIII IUCr Congress, Montreal, Canada, 5-12 August 2014. Hoboken, NJ United States: Wiley-Blackwell. doi: 10.1107/s205327331408365x

Importin alpha and nonclassical nuclear localization signal

2014

Journal Article

Dimensionality reduction and topographic mapping of binary tensors

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

Dimensionality reduction and topographic mapping of binary tensors

2014

Journal Article

Predicting the dynamics of protein abundance

Mehdi, 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

Predicting the dynamics of protein abundance

2014

Book Chapter

Computational tools for directed evolution: a comparison of prospective and retrospective strategies

Zaugg, 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

Computational tools for directed evolution: a comparison of prospective and retrospective strategies

2014

Journal Article

Inferring short tandem repeat variation from paired-end short reads

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, e16.1-e16.11. doi: 10.1093/nar/gkt1313

Inferring short tandem repeat variation from paired-end short reads

2013

Journal Article

Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α

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

Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α

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

Before you email them, read our advice on how to contact a supervisor.

Supervision history

Current supervision

  • 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

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

    Principal Advisor

    Other advisors: Professor Michael Piper

  • Doctor Philosophy

    How SETD2 shapes cortical development

    Associate Advisor

    Other advisors: Professor Stefan Thor, Professor Michael Piper

  • 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

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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