• The University of Western Australia (M316), 35 Stirling Highway,

    6009 Perth

    Australia

  • 548 Citations
  • 11 h-Index
20072019

Research output per year

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Personal profile

Biography

I am a Research Fellow in computational biology at the ARC Centre of Excellence in Plant Energy Biology.

I studied process engineering and medical biotechnology (MBt, 2005) at the University of Technology in Berlin, Germany. I completed my PhD (2011) in molecular biology at the University of Western Australia researching underlying genetic mechanisms of childhood brain cancers. I have been working as a Research Fellow in plant computational biology at UWA since 2012.

Google Scholar, Scopus

TweetMe, Twitter PEB, Facebook PEB

Current projects

  • Genome-scale model of Arabidopsis energy metabolism
  • Subcellular location conservation and diversity of protein across crops

Online Resources

The compendium of crop proteins with annotated locations (cropPAL)

The subcellular location database for Arabidopsis proteins   (SUBA)

The prototype of a searchable linked genotype-phenotype platform (AgriConnect)

Research

Genome-scale modelling of Arabidopsis tissues

My research focusses on complex metabolic dependencies in plant tissues and their role in the energy efficiency of plants. My work and input from researchers at PEB contribute to ongoing refinements and insights into the spatial separation of metabolic processes across Arabidopsis tissues, cell types and subcellular spaces. Together with mathematical modelling approaches, these strategies are being used to pinpoint biochemical limitations within plants that can be addressed to increase crop growth, resilience and yield quality.

Subcellulome conservation and divergence in crops

My network of contributors and myself are also working on advancing our knowledge in the subcellular protein distributions within plant cells that allows the extrapolation of protein functions. The majority of genes in plant genomes are not well known in terms of their function, location and role within the metabolic network. In our data resources cropPAL and SUBA are continuously collating globally-generated experimental evidence of protein subcellular locations as well as computational predictions. We are currently housing >3500 data sets from scientists around the world on 12 crop species and Arabidopsis. Analysis pipelines and software are being developed to analyse these data in order to pinpoint important events of conservation versus diversification that lead to species-specific plant behaviour.

Techniques and Expertise

Molecular, Cell and Organism Biology

  • Protein immunolabelling, isolation, purification and quantitation by FACS, MACS, electrophoresis
  • Expression profiling, cloning & transgene tracking
  • Microscopy: 4 channel Fluorescence microscopy, Quantitative Confocal microscopy, 3D imaging, Electron microscopy
  • Cancer cell, stem cell tissue culture technologies
  • Cell and tissue behaviours: cell migration, necrosis-apoptosis, permeability and diffusion, in situ receptor activation
  • Organisms: Animal cancer trials, Human research and preclinical trials

Bioinformatics

  • Large-scale data integration
  • Network building and topology analysis (co-expression, metabolic networks)
  • Machine learning
  • Prediction modelling and optimisation

Research expertise keywords

  • Molecular biology and gene expression
  • Cell biology
  • Protein structure and function
  • Computational biology and genomics for sustainable agriculture
  • Genetic manipulation
  • Bioinformatics
  • Metabolic flux analysis
  • Metabolism
  • Network Analysis
  • Network simulation

Industry keywords

  • Biotechnology
  • Bioinformatics

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Research Output

  • 548 Citations
  • 11 h-Index
  • 14 Article
  • 2 Conference paper
  • 1 Chapter
  • 1 Doctoral Thesis

Going to market with DeweyFish: the journey from partnership to commercialisation

Black, K., Hooper, C., Castleden, I., Aryamanesh, N. & Millar, H., 14 Aug 2019, Proceedings of the IATUL Conferences. USA: Purdue University Press, 4

Research output: Chapter in Book/Conference paperConference paper

Open Access
  • cropPAL2: Creating Ongoing, Mutually Beneficial Collaboration Between Biological Scientists and Librarians

    Black, K., Hooper, C., Gedeon, A. K., Toufexis, K., Albatis, M., Nicholls, S. & Millar, A., 2017, eResearch Australasia 2017, Brisbane, Australia.

    Research output: Chapter in Book/Conference paperConference paper

    Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples

    Hooper, C. M., Stevens, T. J., Saukkonen, A., Castleden, I. R., Singh, P., Mann, G. W., Fabre, B., Ito, J., Deery, M. J., Lilley, K. S., Petzold, C. J., Millar, A. H., Heazlewood, J. L. & Parsons, H. T., 1 Dec 2017, In : Plant Journal. 92, 6, p. 1202-1217 16 p.

    Research output: Contribution to journalArticle

    Open Access
  • 6 Citations (Scopus)

    SUBA4: The interactive data analysis centre for Arabidopsis subcellular protein locations

    Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanesh, N. & Millar, A. H., 4 Jan 2017, In : Nucleic Acids Research. 45, D1, p. D1064-D1074

    Research output: Contribution to journalArticle

    Open Access
  • 81 Citations (Scopus)

    Finding The Subcellular Location Of Barley, Wheat, Rice And Maize Proteins: The Compendium Of Crop Proteins With Annotated Locations (cropPAL)

    Hooper, C., Castleden, I., Aryamanesh, N., Jacoby, R. & Millar, H., 1 Jan 2016, In : Plant & Cell Physiology. 57, 1, p. 1-9

    Research output: Contribution to journalArticle

    Open Access
    File
  • 16 Citations (Scopus)
    563 Downloads (Pure)

    Datasets

    Subcellular Localisation database for Arabidopsis proteins version 4

    Hooper, C. (Creator), Castleden, I. (Creator), The University of Western Australia, 26 Oct 2016

    Dataset

    File

    The compendium of crop Proteins with Annotated Locations (cropPAL) version 1

    Hooper, C. (Creator), Castleden, I. (Creator), Aryamanesh, N. (Creator), Jacoby, R. (Creator), Millar, H. (Creator), The University of Western Australia, 2 Jun 2015

    Dataset

    File

    Subcellular Localisation database for Arabidopsis proteins version 3

    Tanz, S. (Creator), Hooper, C. (Creator), The University of Western Australia, 13 Dec 2016

    Dataset

    File

    The compendium of crop Proteins with Annotated Locations (cropPAL) version 2

    Hooper, C. (Creator), Millar, H. (Creator), Castleden, I. (Creator), The University of Western Australia, 1 Jun 2017

    Dataset

    File

    Projects