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
My research interests is in plant epigenetics with a focus on understanding non-coding RNA-mediated mechanisms to fine-tune gene expression and maintain genome stability and how these ultimately contribute towards physiological adaption. I use a combination of next-generation sequencing, bioinformatics and molecular tools to dissect these pathways and elucidate the biological significance of epigenetic machinery.
- Epitranscriptome modifications: 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 mobile RNA transcripts in response to stress 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
- 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
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 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].
Interdisciplinary Research Funding Scheme - University of Adelaide (2018)
- Design and implementation of practical component for GENETICS3211 – Plant Transgene Expression and RNA Modifications (Undergraduate, Year 3, University of Adelaide, 2015)
- Practical demonstrating experience: BOTN3006 - Plant Molecular Biology and Biotechnology (Undergraduate, Year 3 – University of Queensland, 2004), BIOT7011 - DNA and Protein Technology (Postgraduate, University of Queensland, 2005), BIOC7009 – Emerging Biotechnologies II (Postgraduate, University of Queensland, 2005)
- Guest Lecture (2018, 2019): Research Skills for Applied Biology II (APP BIOL 2500WT)
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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