
Overview
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
Qualifications
- Bachelor of Science, Skövde University College
- Masters (Coursework) of Science, Skövde University College
- Doctor of Philosophy, University of Exeter
Research interests
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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
Works
Search Professor Mikael Boden’s works on UQ eSpace
2025
Journal Article
Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure
Shen, Sophie, Werner, Tessa, Lukowski, Samuel W., Andersen, Stacey, Sun, Yuliangzi, Shim, Woo Jun, Mizikovsky, Dalia, Kobayashi, Sakurako, Outhwaite, Jennifer, Chiu, Han Sheng, Chen, Xiaoli, Chapman, Gavin, Martin, Ella M. M. A., Xia, Di, Pham, Duy, Su, Zezhuo, Kim, Daniel, Yang, Pengyi, Tan, Men Chee, Sinniah, Enakshi, Zhao, Qiongyi, Negi, Sumedha, Redd, Meredith A., Powell, Joseph E., Dunwoodie, Sally L., Tam, Patrick P. L., Bodén, Mikael, Ho, Joshua W. K., Nguyen, Quan and Palpant, Nathan J. (2025). Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure. Nature Communications, 16 (1) 1356, 1356-1. doi: 10.1038/s41467-025-56533-2
2025
Journal Article
Do protein language models learn phylogeny?
Tule, Sanjana, Foley, Gabriel and Bodén, Mikael (2025). Do protein language models learn phylogeny?. Briefings in Bioinformatics, 26 (1) bbaf047. doi: 10.1093/bib/bbaf047
2025
Journal Article
TRIAGE: an R package for regulatory gene analysis
Zhao, Qiongyi, Shim, Woo Jun, Sun, Yuliangzi, Sinniah, Enakshi, Shen, Sophie, Boden, Mikael and Palpant, Nathan J. (2025). TRIAGE: an R package for regulatory gene analysis. Briefings in Bioinformatics, 26 (1) bbaf004, 1-13. doi: 10.1093/bib/bbaf004
2025
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 (2025). Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. Briefings in Functional Genomics, 24 elad055. doi: 10.1093/bfgp/elad055
2024
Journal Article
SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer
Mora, Ariane, Schmidt, Christina, Balderson, Brad, Frezza, Christian and Bodén, Mikael (2024). SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer. Genome Medicine, 16 (1) 144. doi: 10.1186/s13073-024-01415-3
2024
Journal Article
Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics
Joshi, Pallav, Krco, Stefan, Davis, Samuel J., Asser, Lachlan, Brück, Thomas, Soo, Rochelle M., Bodén, Mikael, Hugenholtz, Philip, Wilson, Liam A., Schenk, Gerhard and Morris, Marc T. (2024). Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. Applied Biosciences, 3 (4), 438-449. doi: 10.3390/applbiosci3040028
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 (s1), i277-i286. doi: 10.1093/bioinformatics/btae254
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
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) ycae067, ycae067. doi: 10.1093/ismeco/ycae067
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
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
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
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
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
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
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
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
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
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
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
Funding
Current funding
Past funding
Supervision
Availability
- Professor Mikael Boden is:
- Available for supervision
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Supervision history
Current supervision
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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
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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
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
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Doctor Philosophy
How SETD2 shapes cortical development
Associate Advisor
Other advisors: Professor Stefan Thor, Professor Michael Piper
Completed supervision
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2023
Doctor Philosophy
Cell Type Definition from Single Cell RNA-seq
Principal Advisor
Other advisors: Professor Michael Piper, Professor Jessica Mar, Professor Stefan Thor
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2023
Doctor Philosophy
Machine learning models of epigenetic dynamics driving cell fate
Principal Advisor
Other advisors: Professor Jessica Mar, Professor Stefan Thor
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2022
Doctor Philosophy
Methods for ancestral sequence reconstruction of large and complex protein families
Principal Advisor
Other advisors: Emeritus Professor Ross Barnard, Associate Professor Michael Landsberg, Professor Elizabeth Gillam
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2021
Doctor Philosophy
Identifying Genetic Regulators of Cell Fate Through Computational Analysis of Epigenetic Repression
Principal Advisor
Other advisors: Professor Nathan Palpant
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2020
Doctor Philosophy
Protein structural phylogeny, a missing chapter in molecular evolutionary biology
Principal Advisor
Other advisors: Professor Bostjan Kobe
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2020
Doctor Philosophy
A computational analysis of transcription factor interactions and binding guided by epigenetics
Principal Advisor
Other advisors: Professor Michael Piper, Professor Brandon Wainwright
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2019
Doctor Philosophy
Computational Modelling of Enzymes: Predicting and Understanding the Selectivity of an Epoxide Hydrolase
Principal Advisor
Other advisors: Dr Yosephine Gumulya
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2016
Doctor Philosophy
Molecular interaction motifs in a system-wide network context: Computationally charting transient kinase-substrate phosphorylation events
Principal Advisor
Other advisors: Professor Bostjan Kobe
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2015
Master Philosophy
A Human Factors Evaluation of Auditory Displays in Medical Electrical Equipment
Principal Advisor
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2013
Doctor Philosophy
Computational Models of Nucleo-Cytoplasmic Trafficking by Integrating Heterogeneous Data
Principal Advisor
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2011
Master Philosophy
The collection and data-driven analyses of proteins localized to nuclear compartments
Principal Advisor
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2010
Master Philosophy
Integrating sequence and structure for annotating proteins in the twilight zone: A machine learning approach
Principal Advisor
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2008
Doctor Philosophy
Machine architectures for biological sequence classification
Principal Advisor
Other advisors: Professor Janet Wiles, Associate Professor Rohan Teasdale
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2023
Doctor Philosophy
Statistical approaches to investigate cellular heterogeneity and stability in single-cell transcriptomic data
Associate Advisor
Other advisors: Professor Jessica Mar
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2023
Doctor Philosophy
Structure, function and inhibition of Fe-S cluster-dependent dehydratases from the ilvD/EDD family
Associate Advisor
Other advisors: Professor Luke Guddat, Professor Gary Schenk
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2022
Doctor Philosophy
Understanding How Antimicrobial Peptides Interact with Membranes
Associate Advisor
Other advisors: Professor Alan Mark
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2022
Doctor Philosophy
Understanding Cell Identity Through the Lens of Genome-Wide Epigenetic Repression
Associate Advisor
Other advisors: Professor Nathan Palpant
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2022
Doctor Philosophy
Ancestral reconstruction and characterisation of the CYP2U subfamily
Associate Advisor
Other advisors: Professor Elizabeth Gillam
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2020
Doctor Philosophy
Ancestral reconstruction of cytochrome P450 family 1, 4 and cytochrome P450 reductase: Insights into evolution and applications in biocatalysis
Associate Advisor
Other advisors: Professor Elizabeth Gillam
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2015
Master Philosophy
PreDiZ: a PDZ domain-peptide interaction prediction method
Associate Advisor
Other advisors: Professor Bostjan Kobe
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2015
Doctor Philosophy
Biometric Markers for Affective Disorders
Associate Advisor
Other advisors: Associate Professor Marcus Gallagher
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2012
Doctor Philosophy
Predicting tissue-specific transcription factor binding and gene expression in silico
Associate Advisor
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2010
Doctor Philosophy
Thermodynamic models for the analysis of quantitative transcriptional regulation
Associate Advisor
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2007
Doctor Philosophy
RULE-EXTRACTION FROM SUPPORT VECTOR MACHINES: MEDICAL DIAGNOSIS PREDICTION AND EXPLANATION
Associate Advisor
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2006
Master Philosophy
COMPUTATIOANL MODELLING OF THE LANGUAGE PRODUCTION SYSTEM: SEMANTIC MEMORY, CONFLICT MONITORING, AND COGNITIVE CONTROL PROCESSES
Associate Advisor
Other advisors: Professor Janet Wiles
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2006
Doctor Philosophy
ROBUSTNESS IN BOOLEAN MODELS OF GENETIC REGULATORY SYSTEMS
Associate Advisor
Other advisors: Professor Janet Wiles
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2006
Doctor Philosophy
FROM GENES TO PHENES AND BACK AGAIN: MODELING THE INTERACTION BETWEEN INDIVIDUAL BEHAVIOUR AND EVOLUTION
Associate Advisor
Other advisors: Dr Jim Hanan, Professor Janet Wiles
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Doctor Philosophy
TOPOLOGICAL MODELS OF TRANSMEMBRANE PROTEINS FOR SUBCELLULAR LOCALIZATION PREDICTION
Associate Advisor
Other advisors: Associate Professor Marcus Gallagher, Professor Geoffrey McLachlan
Media
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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