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==== Research projects with the Boden group ==== | ==== Research projects with the Boden group ==== | ||
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+ | Informal collection of project ideas, at different levels and duration. | ||
=== Phylogenetics, | === Phylogenetics, | ||
All biological components that are genetically encoded are subject to evolution—selective pressures in their ecological niche. With biochemists and protein engineers, we develop (phylogenetic) tools for detecting what specific changes explain the make-up of a gene or protein; this leads to a fundamental appreciation of genetic determinants of success, but can also be used to design novel, reconstruct ancient variants or even re-run evolution artificially to generate products that perform in conditions for medical, industrial and agricultural applications in the emerging bioeconomy. | All biological components that are genetically encoded are subject to evolution—selective pressures in their ecological niche. With biochemists and protein engineers, we develop (phylogenetic) tools for detecting what specific changes explain the make-up of a gene or protein; this leads to a fundamental appreciation of genetic determinants of success, but can also be used to design novel, reconstruct ancient variants or even re-run evolution artificially to generate products that perform in conditions for medical, industrial and agricultural applications in the emerging bioeconomy. | ||
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- | - Inferring sequence and traits of ancestral genes and proteins | ||
- | - Phylogenetic prospecting of proteins and their variants for protein engineering | ||
== Problem: What are the evolutionary drivers of metallo beta-lactamases? | == Problem: What are the evolutionary drivers of metallo beta-lactamases? | ||
- | * Approach: Reconstruction of the enzyme super-family incorporating MBLs and analysis of evolutionary determinants relevant to their antibiotic | + | * Approach: Reconstruction of the enzyme super-family incorporating MBLs and analysis of evolutionary determinants relevant to establishing |
* Contacts: m.boden@uq.edu.au | * Contacts: m.boden@uq.edu.au | ||
* Collaborators: | * Collaborators: | ||
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+ | == Problem: What ancestors in a phylogeny recapitulate a given mix of experimental properties? == | ||
+ | * Approach: Smart interrogation of experimental databases, visualisation of phylogeny juxtaposed with available data, and novel use of evolutionary models form part of our group' | ||
+ | * Contacts: Gabe Foley g.foley@uq.edu.au, | ||
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+ | ---- | ||
=== Analytical tools for sequencing data, omics data integration methods, machine learning === | === Analytical tools for sequencing data, omics data integration methods, machine learning === | ||
- | == What are the genetic drivers | + | New (sequencing) technologies bring new opportunities and challenges, including long- and short read technologies at single-cell or bulk resolution, and with spatial specificity. We develop tools for leveraging |
- | Bioinformatics methods for understanding transcriptional and epigenetic regulation during mammalian development and in disease is a significant focus. We are relying on technologies such as single-cell RNA-seq and ChIP-seq, in collaboration with developmental, | + | == Problem: Assessing reproducibility of ChIP-seq does not address intra-experimental bias == |
- | - Data integration | + | |
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- | == Problem: | + | == Problem: |
- | * Approach: | + | |
- | | + | * Approach: |
- | * Contacts: | + | |
- | * Collaborators: | + | |
+ | == Problem: how can we link cell states identified in one single-cell RNA-seq experiment to another? == | ||
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+ | * Approach: identify a universal representation | ||
+ | * Contact: a.mora@uq.edu.au, | ||
+ | * Collaborator: | ||
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+ | == Problem: Interrogation of single-cell ATAC-seq and integration with single-cell RNA-seq == | ||
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+ | * Approach: Regulatory markers are present but look different in ATAC- and RNA-seq. We expect the mapping of representative cells in each data type could be based on regulatory footprints; this needs to be explored via the use of appropriate models that accommodate the uncertainty of inter-set labelling. | ||
+ | * Contact: m.boden@uq.edu.au, | ||
+ | * Collaborator: Palpant | ||
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+ | ---- | ||
=== Models of development and disease across time and space === | === Models of development and disease across time and space === | ||
- | | + | Increasingly genome technologies uncover spatial and temporal specificity of observations, |
- | * Approach: | + | |
- | * Contacts: | + | == Problem: To what extent is epigenetic regulation conserved, and how can evolution help interpret and explain epigenetic regulation? == |
- | * Collaborators: | + | |
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+ | * Contact: m.boden@uq.edu.au | ||
+ | * Collaborator: | ||
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+ | == Problem: | ||
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+ | * Approach: | ||
+ | * Contact: m.boden@uq.edu.au | ||
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+ | == Problem: What is the quantitative nature of DNA methylation and its role in cancer? == | ||
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+ | * Approach: Data aggregation and careful integration of massive public data sets give rise to new hypotheses. | ||
+ | * Contact: Ariane Mora a.mora@uq.edu.au, | ||
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