research:gabe

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research:gabe [2021/08/26 11:17] – gaberesearch:gabe [2022/10/13 15:30] (current) – gabe
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 LinkedIn: [[https://www.linkedin.com/in/gabrielfoley|gabrielfoley]]\\ LinkedIn: [[https://www.linkedin.com/in/gabrielfoley|gabrielfoley]]\\
 Twitter: [[https://twitter.com/gabefoley|@gabefoley]]\\ Twitter: [[https://twitter.com/gabefoley|@gabefoley]]\\
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 +==== Research  ====
  
 My research is focussed on ancestral sequence reconstruction (ASR) and how it can be used to understand the large scale evolutionary histories of protein families. In short, we take huge sets of related modern day proteins and predict what the ancestors of these proteins looked like. From here, we can take these predictions into a lab and synthesise them, essentially 'resurrecting' the ancestors from millions of years ago. These ancestral proteins are useful in understanding how evolution has shaped the functional properties of the proteins in question and are also a fantastic starting point to engineer novel properties within proteins for industrial applications. My research is focussed on ancestral sequence reconstruction (ASR) and how it can be used to understand the large scale evolutionary histories of protein families. In short, we take huge sets of related modern day proteins and predict what the ancestors of these proteins looked like. From here, we can take these predictions into a lab and synthesise them, essentially 'resurrecting' the ancestors from millions of years ago. These ancestral proteins are useful in understanding how evolution has shaped the functional properties of the proteins in question and are also a fantastic starting point to engineer novel properties within proteins for industrial applications.
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 +My current role is within the EnzOnomy project, an ARC Discovery Project focussed on sustainable protein engineering methods to convert renewable resources into industry-relevant chemicals. We use ASR to engineer and optimise the enzymes that allow these chemicals to be produced.
  
 In my PhD I was involved with the development of a novel ASR tool, Graphical Representation of Ancestral Sequence Predictions (GRASP) that allows ancestral prediction at scales of data previously unavailable - tens of thousands of sequences can now be used to improve the fidelity of our predictions. An important key finding from my work was that insertions and deletions of sequence content that confound analysis at this scale can be effectively managed and actually used to suggest novel 'hybrid ancestors' made of blocks of content not previously explored by nature. In my PhD I was involved with the development of a novel ASR tool, Graphical Representation of Ancestral Sequence Predictions (GRASP) that allows ancestral prediction at scales of data previously unavailable - tens of thousands of sequences can now be used to improve the fidelity of our predictions. An important key finding from my work was that insertions and deletions of sequence content that confound analysis at this scale can be effectively managed and actually used to suggest novel 'hybrid ancestors' made of blocks of content not previously explored by nature.
  
-{{:research:fig1_overview01.png?400|}} 
  
-//**Figure 1**: Overview of ASR within GRASP. **a)** The amino acids in modern day sequences are used to predict the sequences of ancestral proteins. **b)** A joint reconstruction that determines the most likely assignment for all ancestral position. **c)** A marginal reconstruction that determines the probability distributions for a specific ancestral position.// 
  
 +{{ :research:fig1_overview01.png?400 | }}
  
-My current role is within the EnzOnomy project, an ARC Discovery Project focussed on sustainable protein engineering methods to convert renewable resources into industry-relevant chemicals. We use ASR to engineer and optimise the enzymes that allow these chemicals to be produced.+**Figure 1**: Overview of ASR within GRASP. **a)** The amino acids in modern day sequences are used to predict the sequences of ancestral proteins. **b)** A joint reconstruction that determines the most likely assignment for all ancestral position. **c)** A marginal reconstruction that determines the probability distributions for a specific ancestral position. 
 + 
 +==== Education  ====
  
-I am currently completing my PhD, //Methods for ancestral sequence reconstruction of large and complex protein families// at UQ under the primary supervision of Mikael Boden and I previously completed a Bachelor of Biotechnology (Honours Class I) majoring in Bioinformatics and Innovation Management at UQ.+I completed my PhD, //Methods for ancestral sequence reconstruction of large and complex protein families// at UQ under the primary supervision of Mikael Bodén and I previously completed a Bachelor of Biotechnology (Honours Class I) majoring in Bioinformatics and Innovation Management at UQ.
  
 ==== Publications  ==== ==== Publications  ====
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 ==== Awards  ==== ==== Awards  ====
 +2022 Best Poster – Life Sciences Queensland Bioeconomy Forum
 2019 / 2017 Top ranked tutor in the School of Chemistry and Molecular Biosciences \\ 2019 / 2017 Top ranked tutor in the School of Chemistry and Molecular Biosciences \\
 2019 Best Speaker (Early Career Researcher) International Conference on Cytochrome P450 \\ 2019 Best Speaker (Early Career Researcher) International Conference on Cytochrome P450 \\
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