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projects [2021/09/20 07:30] – mikaelprojects [2021/09/20 17:03] (current) – mikael
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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, ancestor sequence reconstruction, protein engineering, bioeconomy === === Phylogenetics, ancestor sequence reconstruction, protein engineering, bioeconomy ===
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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's broader agenda, to be incorporated in a toolkit for ancestor reconstruction.   * Approach: Smart interrogation of experimental databases, visualisation of phylogeny juxtaposed with available data, and novel use of evolutionary models form part of our group's broader agenda, to be incorporated in a toolkit for ancestor reconstruction.
-  * Contacts: Gabe Foley g.foley@uq.edu.au, Sam Davis sam.davis@uq.edu.au+  * Contacts: Gabe Foley g.foley@uq.edu.au, Sam Davis sam.davis@uq.edu.au, m.boden@uq.edu.au
  
  
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   * 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   * 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, b.balderson@uq.edu.au+  * Contact: a.mora@uq.edu.au, b.balderson@uq.edu.au, m.boden@uq.edu.au
   * Collaborator: Thor   * Collaborator: Thor
  
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 == Problem: To what extent is epigenetic regulation conserved, and how can evolution help interpret and explain epigenetic regulation? == == 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.+ 
 +  * 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   * Contact: m.boden@uq.edu.au
   * Collaborator: Thor   * Collaborator: Thor
  
-== Problem: How can we leverage trends of epigenetic marks to highlight regulatory drivers in sparse single-cell and spatial transcriptominc data? == +== Problem: How can we leverage trends of epigenetic marks to highlight regulatory drivers in sparse single-cell and spatial transcriptomes? == 
-  * Approach: Evaluate how aggregates of key histone modifications (collected by ENCODE, say) act coordinately with gene expression.+ 
 +  * 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   * Contact: m.boden@uq.edu.au
  
 == Problem: What is the quantitative nature of DNA methylation and its role in cancer? == == 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.   * 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
  
  
  
  
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  • by mikael