School of Agriculture, Food and Wine
Faculty of Sciences
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
- My Research
- Grants and Funding
- Professional Activities
- Plant Epigenetics
- Accelerating biological discovery though Machine Learning-based methods
My research is focussed on non-coding RNA-mediated gene regulatory mechanisms and how this contributes towards physiological adaption. I use a wide variety of approaches that include in planta experiments, deep sequencing and bioinformatic tools to identify novel epigenetic components and to understand biological significance. See details below for epigenetic related projects that I lead or am involved in.
A parallel research focus of mine is the use of Machine Learning models to analyse complex biological data to reveal new hidden layers of information. Key to success in this area is the upskilling of biological data so it is Machine Learning ready and can be used (and re-used) for answering multiple research questions in accordance with the FAIR data principles. See details below for Machine Learning-based projects that I lead or am involved in.
- Epitranscriptome modifications (In association with A/Prof. Iain Searle, School of Biological Sciences, UA): Molecular functions of post-transcriptional RNA modifications, 5-methylcytosine (m5C) in regulating gene expression and responses to the environment.
- RNA transport and signalling: Investigate the role of cell-to-cell and systemic transport of RNA transcripts in response to developmental and environmental cues using grafting techniques in combination with high-throughput RNA sequencing. Identifying molecular signatures of mobile RNA transcripts in plants using bioinformatic approaches. GitHub repository: https://github.com/CharlotteSai/DiRT
- Machine Learning based Text Analytics: Natural Language Processing and Machine Learning models for automatic extraction of protein features from unstructured biomedical text. GitHub repository: https://github.com/RhysMenezes/find-a-protein
- Understanding the drivers of crop yield variability: Yields of major crops in Australia are often below their water-limited potential. Genotype x Environment x Management complexity results in crop growth with spatial and temporal variability. The GRDC funded project will use Machine Learning-based methods to discover underlying relationships between climate, crop and soil variables that cause variable crop growth and yields to inform paddock management decisions.
Date Position Institution name 2016 Postdoctoral Research Fellow University of Adelaide, Adelaide 2013 - 2015 Postdoctoral Research Fellow University of Adelaide, Adelaide 2012 - 2013 Postdoctoral Research Fellow The Australian National University
Date Title Institution Country — PhD The Australian National University Australia — Masters of Biotechnology The University of Queensland Australia
Year Citation 2021 Li, J., Wu, X., Do, T., Nguyen, V., Zhao, J., Ng, P. Q., . . . Searle, I. (2021). Quantitative and Single-Nucleotide Resolution Profiling of RNA 5-Methylcytosine. In Methods in Molecular Biology (Vol. 2298, pp. 135-151). Springer US.
Year Citation 2017 Burgess, A., David, R., Sibbritt, T., Jones, A., Preiss, T., Searle, I. R., & David, R. (2017). RNA 5-methylcytosine is required for oxidative stress tolerance in Arabidopsis thaliana. Poster session presented at the meeting of COMBIO. 2015 David, R., Lim, H. M., & Searle, I. R. (2015). Identification of pla/ubp14, an Arabidopsis mutant that displays lengthened plastochron and larger organs. Poster session presented at the meeting of Annual Genetics Society of Australasia conference. — David, R. (n.d.). CropTiPS database information poster presented at ComBio2017 (Adelaide). Poster session presented at the meeting of Unknown Conference.
Year Citation — Adelaide, T. U. O., David, R., Tyerman, S., Gilliham, M., Hooper, C., & Castleden, I. (n.d.). Knowledgebase of Crop Transport information, Physiology and Signalling (CropTiPS) version 1.0.
Year Citation — Sai, N., Rodriguez Lopez, C. M., Bogias, K., Pederson, S., Burgess, A., Breen, J., . . . David, R. (n.d.). DiRT: Dicistronic RNA Transcripts - A bioinformatic pipeline to detect di-cistronic tRNA-mRNA transcripts from short-read RNA-sequencing data [Computer Software]. — David, R., Hooper, C. M., Castleden, I. R., Gilliham, M., & Tyerman, S. (n.d.). CropTiPS database (Crop Transport information, Physiology and Signalling) - www.croptips.org [Computer Software].
2018 Co-investigator on Interdisciplinary Research Fund, University of Adelaide, Accelerating biological discovery through Artificial Intelligence, Prof Mathew Gilliham and Dr Rakesh David. $90k
2019 Co-investigator on NCRIS funded Agriculture data sharing platform, $155k, Agriculture data sharing platform (18NCRIS RDP-62), Prof Mathew Gilliham, A/Prof Bettina Berger, Dr Rakesh David, $155k
- 2018-2019: Invited Guest Lecture for 'Research Skills for Applied Biology II' (APP BIOL 2500WT), Lecture title: Plants as Vaccine Biofactories, Undergraduate, Year 2, University of Adelaide
- 2015: Design and implementation of practical component for GENETICS3211 – Plant Transgene Expression and RNA Modifications, Undergraduate, Year 3, University of Adelaide.
- 2004-2005: Practical demonstrating experience: BOTN3006 - Plant Molecular Biology and Biotechnology. Undergraduate, Year 3, University of Queensland. BIOT7011 - DNA and Protein Technology, Postgraduate, University of Queensland. BIOC7009 – Emerging Biotechnologies II, Postgraduate, University of Queensland.
Past Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2018 - 2020 Co-Supervisor A Multiple 'Omics' Approach to Study the Interaction between the Vitis Vinifera Transcriptome and Epigenome and the Barossa Valley Terroir Doctor of Philosophy Doctorate Full Time Mr Pastor Jullian Fabres 2015 - 2018 Co-Supervisor Identification and Functional Characterization of Long Noncoding RNAs Involved in Endosperm Development of Arabidopsis thaliana Doctor of Philosophy Doctorate Full Time Mr Quang Trung Do 2014 - 2016 Co-Supervisor Conservation and Function of RNA 5-methylcytosine in Plants Doctor of Philosophy Doctorate Full Time Miss Alice Louise Burgess
Other Supervision Activities
Date Role Research Topic Location Program Supervision Type Student Load Student Name 2018 - 2018 Principal Supervisor tRNA:mRNA dicistronic transcripts are a conserved feature in flowering plants transcriptomes The University of Adelaide, School of Agriculture, Food & Wine Master of Biotechnology (Plant Biotechnology) Master Full Time Fei Zheng
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