Rapid Whole-Genome Identification of High Quality CRISPR Guide RNAs with the Crackling Method Permalink
CV
Education
- PhD
- School of Computer Science, Queensland University of Technology
- QUT Centre for Data Science
- Transformational Bioinformatics, CSIRO
- Primary supervisor: Associate Professor Dimitri Perrin
- Bachelor of Engineering (Computer and Software Systems - Honours Class I) (completed 2017)
- School of Electrical Engineering and Computer Science, Queensland University of Technology
Honours, Awards and Scholarships
- Three Minute Thesis (3MT) - QUT Faculty of Science Runner-up (August 2021)
- 3MT is a global competition that asks research students to present their thesis in three minutes
- QUT Science and Engineering Faculty High Achiever Award (December 2020)
- SEF’s HDR High Achieve Awards recognise students who demonstrate sustained levels of high achievement as evidenced by the quality of their research outputs and other esteem measures.
- International Society Molecular Biology Fellowship Award (June 2020)
- To cover the registration to ISMB 2020
- CSIRO Post-graduate Top-up Scholarship (February 2020 – ongoing)
- To engage in a collaborative project utilising serverless cloud computing
- Predicting CRISPR-Cas9 activity using cloud computing
- Operating budget $10,000 p.a.
- Stipend top-up $10,000 p.a.
- GitHub Arctic Code Vault Contributor (February 2020)
- Contributed the open-source bioinformatic pipeline, Crackling
- International Conference on Computational Biology Travel Fellowship (August 2019)
- To offset travel and conference expenses. USD 200
- Australian Bioinformatics and Computational Biology Society Travel Grant (October 2018)
- To offset travel expenses. $300
- QUT Research Training Program Scholarship February (2018 – ongoing)
- To support students undertaking a research doctorate
- Approximately $28,000 per annum
- QUT Dean’s List for Excellent Academic Performance (September 2016)
- To acknowledge students who have achieved a semester Grade Point Average (GPA) of 6.50 or above
Publications
Talks
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Poster at International HPC Summer School 2023, Online
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Ultra-fast off-target scoring for large and complex genomes
Poster at Cold Spring Harbor Meetings - Genome Engineering: CRISPR Frontiers, Online
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Allele-specific CRISPR targeting maps produced using the faster and better Crackling method
Poster at Joint Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB), Online
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Fast design of efficient guide RNAs across entire genomes
Talk at CRISPR Conference, Online
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Optimal CRISPR guide RNA design for gene editing in corals
Talk at Pacific Symposium on Biocomputing (PSB), Online
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Optimal CRISPR guide RNA design for gene editing in corals
Poster at Pacific Symposium on Biocomputing (PSB), Online
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CRISPR, faster, better - The Crackling method for whole-genome target detection
Talk at Annual Conference of the Australian Bioinformatics and Computational Biology Society (ABACBS), Australian National University (Online), Australian National Territory
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CRISPR, faster, better - The Crackling method for whole-genome target detection
Talk at International Conference on Intelligent Systems for Molecular Biology (ISMB), Online
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Improving CRISPR guide design with consensus approaches
Talk at International Conference on Bioinformatics (InCoB), Universitas Yarsi, Jakarta, Indonesia
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Consensus approaches for CRISPR guide design
Poster at International Conference on Intelligent Systems for Molecular Biology (ISMB) & European Conference on Computational Biology (ECCB), Basel, Switzerland
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Improving CRISPR guide design with consensus approaches
Poster at CRISPR Conference, Québec City Convention Centre, Canada
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A performance review of computational tools for CRISPR-Cas9 guide design
Talk at Annual Conference of the Australian Bioinformatics and Computational Biology Society (ABACBS), University of Melbourne, Australia
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A performance review of computational tools for CRISPR-Cas9 guide design
Poster at Annual Conference of the Australian Bioinformatics and Computational Biology Society (ABACBS), University of Melbourne, Australia
Teaching
Referees
Available upon request