Rakesh David

Rakesh David

School of Agriculture, Food and Wine

Faculty of Sciences, Engineering and Technology

Eligible to supervise Masters and PhD - email supervisor to discuss availability.

Research interests:

  • 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. A particular focus area is facilitating the ‘upskilling’ of biological data in accordance with the FAIR data principles, so it is analytics ready and can be used (and re-used) for answering multiple research questions.

Research projects:

  1. 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. 
  2. 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
  3. 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
  4. 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.

  • Appointments
    Date Position Institution name
    2016 - ongoing 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

  • Postgraduate Training
    Date Title Institution Country
    PhD The Australian National University Australia
    Masters of Biotechnology The University of Queensland Australia

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, Agriculture data sharing platform (18NCRIS RDP-62), Prof Mathew Gilliham, A/Prof Bettina Berger, Dr Rakesh David, $155k

2021 Co-investigator on Agrifood and Wine FAME grant, Optimising plant growth in simulated microgravity, led by Dr Philip Brewer and Prof Volker Hessel, $20k

 

  • 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

  • Memberships
    Date Role Membership Country
    2019 - ongoing Member RNA society United States
    2015 - ongoing Member Epigenetics Consortium of South Australia Australia
    2010 - ongoing Member Australian Society of Plant Scientists Australia
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