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

129 works between 1993 and 2024
All (129) Journal Article (93) Book Chapter (4) Conference Publication (31) Edited Outputs (1)

1 - 20 of 129 works

2024

Journal Article

Optimal phylogenetic reconstruction of insertion and deletion events

Tule, Sanjana, Foley, Gabriel, Zhao, Chongting, Forbes, Michael and Bodén, Mikael (2024). Optimal phylogenetic reconstruction of insertion and deletion events. Bioinformatics, 40 (Supplement_1), i277-i286. doi: 10.1093/bioinformatics/btae254

Optimal phylogenetic reconstruction of insertion and deletion events

2024

Journal Article

Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary

Prabhu, Apoorva, Tule, Sanjana, Chuvochina, Maria, Bodén, Mikael, McIlroy, Simon J, Zaugg, Julian and Rinke, Christian (2024). Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary. ISME Communications, 4 (1) ARTN ycae067. doi: 10.1093/ismeco/ycae067

Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary

2024

Journal Article

Development of a highly selective NAD+‐dependent glyceraldehyde dehydrogenase and its application in minimal cell‐free enzyme cascades

Teshima, Mariko, Sutiono, Samuel, Döring, Manuel, Beer, Barbara, Boden, Mikael, Schenk, Gerhard and Sieber, Volker (2024). Development of a highly selective NAD+‐dependent glyceraldehyde dehydrogenase and its application in minimal cell‐free enzyme cascades. ChemSusChem, 17 (4) e202301132, 1-13. doi: 10.1002/cssc.202301132

Development of a highly selective NAD+‐dependent glyceraldehyde dehydrogenase and its application in minimal cell‐free enzyme cascades

2024

Journal Article

Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity

Balderson, Brad, Fane, Mitchell, Harvey, Tracey J, Piper, Michael, Smith, Aaron and Bodén, Mikael (2024). Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. Briefings in Functional Genomics. doi: 10.1093/bfgp/elad055

Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity

2023

Journal Article

Cytocipher determines significantly different populations of cells in single cell RNA-seq data

Balderson, Brad, Piper, Michael, Thor, Stefan and Boden, Mikael (2023). Cytocipher determines significantly different populations of cells in single cell RNA-seq data. Bioinformatics, 39 (7) btad435. doi: 10.1093/bioinformatics/btad435

Cytocipher determines significantly different populations of cells in single cell RNA-seq data

2023

Journal Article

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

Sun, Yuliangzi, Shim, Woo Jun, Shen, Sophie, Sinniah, Enakshi, Pham, Duy, Su, Zezhuo, Mizikovsky, Dalia, White, Melanie D., Ho, Joshua W. K., Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J (2023). Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Research, 51 (11), e62-e62. doi: 10.1093/nar/gkad307

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

2023

Journal Article

Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle

Afonso, Juliana, Shim, Woo Jun, Boden, Mikael, Salinas Fortes, Marina Rufino, da Silva Diniz, Wellison Jarles, de Lima, Andressa Oliveira, Rocha, Marina Ibelli Pereira, Cardoso, Tainã Figueiredo, Bruscadin, Jennifer Jessica, Gromboni, Caio Fernando, Nogueira, Ana Rita Araujo, Mourão, Gerson Barreto, Zerlotini, Adhemar, Coutinho, Luiz Lehmann and de Almeida Regitano, Luciana Correia (2023). Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochemistry and Biophysics Reports, 33 101420, 1-9. doi: 10.1016/j.bbrep.2023.101420

Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle

2023

Journal Article

Structural and functional insight into the mechanism of the Fe‐S cluster‐dependent dehydratase from Paralcaligenes ureilyticus

Bayaraa, Tenuun, Lonhienne, Thierry, Sutiono, Samuel, Melse, Okke, Brück, Thomas B., Marcellin, Esteban, Bernhardt, Paul V., Boden, Mikael, Harmer, Jeffrey R., Sieber, Volker, Guddat, Luke W. and Schenk, Gerhard (2023). Structural and functional insight into the mechanism of the Fe‐S cluster‐dependent dehydratase from Paralcaligenes ureilyticus. Chemistry: A European Journal, 29 (9) e202203140, 1-13. doi: 10.1002/chem.202203140

Structural and functional insight into the mechanism of the Fe‐S cluster‐dependent dehydratase from Paralcaligenes ureilyticus

2022

Conference Publication

H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle

Afonso, J., Shim, W.J., Boden, M., Palpant, N., Fortes, M.R.S., Diniz, W.J.S., Lima, A.O., Rocha, M.I.P., Cardoso, T.F., Bruscadin, J.J., Gromboni, C.F., Nogueira, A.R.A., Mourão, G.B., Zerlotini, A., Coutinho, L.L. and Regitano, L.C.A. (2022). H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_553

H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle

2022

Journal Article

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys, Thomson, Raine E. S., Kobe, Bostjan, Barnard, Ross T., Guddat, Luke, Schenk, Gerhard, Carsten, Jörg, Gumulya, Yosephine, Rost, Burkhard, Haltrich, Dietmar, Sieber, Volker, Gillam, Elizabeth M. J. and Bodén, Mikael (2022). Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PL o S Computational Biology, 18 (10) e1010633, e1010633. doi: 10.1371/journal.pcbi.1010633

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

2022

Journal Article

Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals

Lv, You, Zheng, Shan, Goldenzweig, Adi, Liu, Fengjiang, Gao, Yan, Yang, Xiuna, Kandale, Ajit, McGeary, Ross P., Williams, Simon, Kobe, Bostjan, Schembri, Mark A., Landsberg, Michael J., Wu, Bin, Brück, Thomas B., Sieber, Volker, Boden, Mikael, Rao, Zihe, Fleishman, Sarel J., Schenk, Gerhard and Guddat, Luke W. (2022). Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals. Applied Biosciences, 1 (2), 163-178. doi: 10.3390/applbiosci1020011

Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals

2022

Journal Article

Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates

Harris, Kurt L., Thomson, Raine E.S., Gumulya, Yosephine, Foley, Gabriel, Carrera-Pacheco, Saskya E., Syed, Parnayan, Janosik, Tomasz, Sandinge, Ann-Sofie, Andersson, Shalini, Jurva, Ulrik, Bodén, Mikael and Gillam, Elizabeth M.J. (2022). Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. Molecular Biology and Evolution, 39 (6) msac116. doi: 10.1093/molbev/msac116

Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates

2022

Journal Article

Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes

Yaghmaeian Salmani, Behzad, Balderson, Brad, Bauer, Susanne, Ekman, Helen, Starkenberg, Annika, Perlmann, Thomas, Piper, Michael, Bodén, Mikael and Thor, Stefan (2022). Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes. Development, 149 (5) dev200076. doi: 10.1242/dev.200076

Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes

2022

Journal Article

Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2

Mora, Ariane, Rakar, Jonathan, Cobeta, Ignacio Monedero, Salmani, Behzad Yaghmaeian, Starkenberg, Annika, Thor, Stefan and Bodén, Mikael (2022). Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2. Nucleic Acids Research, 50 (3), 1280-1296. doi: 10.1093/nar/gkac006

Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2

2022

Book Chapter

Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Ross, Connie M., Foley, Gabriel, Boden, Mikael and Gillam, Elizabeth M. J. (2022). Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP). Enzyme engineering. (pp. 85-110) edited by Francesca Magnani, Chiara Marabelli and Francesca Paradisi. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-1826-4_6

Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP)

2021

Journal Article

Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid

Wilson, Liam A., Knaven, Esmée G., Morris, Marc T., Monteiro Pedroso, Marcelo, Schofield, Christopher J., Brück, Thomas, Boden, Mikael, Waite, David W., Hugenholtz, Philip, Guddat, Luke and Schenk, Gerhard (2021). Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid. Antimicrobial Agents and Chemotherapy, 65 (10) e00936-21, e0093621. doi: 10.1128/aac.00936-21

Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid

2021

Journal Article

ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

Newell, Rhys, Pienaar, Richard, Balderson, Brad, Piper, Michael, Essebier, Alexandra and Bodén, Mikael (2021). ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates. Genomics, 113 (4), 1855-1866. doi: 10.1016/j.ygeno.2021.04.026

ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

2021

Journal Article

Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype

Kojic, Marija, Gawda, Tomasz, Gaik, Monika, Begg, Alexander, Salerno-Kochan, Anna, Kurniawan, Nyoman D., Jones, Alun, Drożdżyk, Katarzyna, Kościelniak, Anna, Chramiec-Głąbik, Andrzej, Hediyeh-Zadeh, Soroor, Kasherman, Maria, Shim, Woo Jun, Sinniah, Enakshi, Genovesi, Laura A., Abrahamsen, Rannvá K., Fenger, Christina D., Madsen, Camilla G., Cohen, Julie S., Fatemi, Ali, Stark, Zornitza, Lunke, Sebastian, Lee, Joy, Hansen, Jonas K., Boxill, Martin F., Keren, Boris, Marey, Isabelle, Saenz, Margarita S., Brown, Kathleen ... Wainwright, Brandon J. (2021). Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nature Communications, 12 (1) 2678, 2678. doi: 10.1038/s41467-021-22888-5

Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype

2020

Journal Article

Conserved epigenetic regulatory logic infers genes governing cell identity

Shim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001

Conserved epigenetic regulatory logic infers genes governing cell identity

2020

Journal Article

Evolutionary model of protein secondary structure capable of revealing new biological relationships

Lai, Jhih‐Siang, Rost, Burkhard, Kobe, Bostjan and Bodén, Mikael (2020). Evolutionary model of protein secondary structure capable of revealing new biological relationships. Proteins: Structure, Function, and Bioinformatics, 88 (9) prot.25898, 1251-1259. doi: 10.1002/prot.25898

Evolutionary model of protein secondary structure capable of revealing new biological relationships

Current funding

  • 2023 - 2026
    What drives the Anterior Expansion of the Central Nervous System?
    ARC Discovery Projects
    Open grant
  • 2023 - 2024
    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 - 2024
    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

    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: Dr Gabriel Foley

  • 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, Dr Gabriel Foley

  • Doctor Philosophy

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

    Principal Advisor

    Other advisors: Professor Michael Piper, Dr Gabriel Foley

  • 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

    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

Need help?

For help with finding experts, story ideas and media enquiries, contact our Media team:

communications@uq.edu.au