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projects [2021/08/25 12:10] – mikael | projects [2021/09/20 17:03] (current) – mikael | ||
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==== Research projects with the Boden group ==== | ==== Research projects with the Boden group ==== | ||
+ | |||
+ | Informal collection of project ideas, at different levels and duration. | ||
=== Phylogenetics, | === Phylogenetics, | ||
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== 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? == | == 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' | * 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, | + | * Contacts: Gabe Foley g.foley@uq.edu.au, |
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== Problem: Assessing reproducibility of ChIP-seq does not address intra-experimental bias == | == Problem: Assessing reproducibility of ChIP-seq does not address intra-experimental bias == | ||
- | * Approach: The group previously developed ChIP-R to evaluate reproducibility of ChIP-seq replicates, by adapting the rank-product test, applied to each site independently; | + | * Approach: The group previously developed ChIP-R to evaluate reproducibility of ChIP-seq replicates, by adapting the rank-product test, applied to each site independently; |
* Contact: m.boden@uq.edu.au | * Contact: m.boden@uq.edu.au | ||
- | == Problem: | + | == Problem: |
- | * Approach: | + | * Approach: |
* Contact: m.boden@uq.edu.au | * Contact: m.boden@uq.edu.au | ||
+ | |||
+ | == Problem: how can we link cell states identified in one single-cell RNA-seq experiment to another? == | ||
+ | |||
+ | * Approach: identify a universal representation of cell states that recapitulate statistical properties in gene expression, say by data matrix decomposition or similar with machine learning | ||
+ | * Contact: a.mora@uq.edu.au, | ||
+ | * Collaborator: | ||
+ | |||
+ | == Problem: Interrogation of single-cell ATAC-seq and integration with single-cell RNA-seq == | ||
+ | |||
+ | * 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: | * Collaborator: | ||
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Increasingly genome technologies uncover spatial and temporal specificity of observations, | Increasingly genome technologies uncover spatial and temporal specificity of observations, | ||
- | == What is the nature of DNA methylation and its role in cancer? == | + | == Problem: To what extent is epigenetic regulation conserved, and how can evolution help interpret and explain epigenetic regulation? == |
+ | |||
+ | * Approach: The conservation of histone-modifying enzymes is broadly appreciated to exist in many higher species, and is especially relevant to the development of organs. The plan is to probe and model variance //within// species, trace conservation and model evolution //across// species via (on the one hand) positioning of epigenetic marks (at key developmental stages) and sequence and expression of epigenetic components. | ||
+ | * Contact: m.boden@uq.edu.au | ||
+ | * Collaborator: | ||
+ | |||
+ | == Problem: How can we leverage trends of epigenetic marks to highlight regulatory drivers in sparse single-cell and spatial transcriptomes? | ||
+ | |||
+ | * Approach: Evaluate how key histone modifications (collected by ENCODE, say) act coordinately with gene expression; model such coordination with view of predicting epigenetic regulation | ||
+ | * Contact: m.boden@uq.edu.au | ||
+ | |||
+ | == Problem: | ||
* Approach: Data aggregation and careful integration of massive public data sets give rise to new hypotheses. | * Approach: Data aggregation and careful integration of massive public data sets give rise to new hypotheses. | ||
- | * Contact: Ariane Mora a.mora@uq.edu.au | + | * Contact: Ariane Mora a.mora@uq.edu.au, m.boden@uq.edu.au |