Dr Scott Berry
Senior Lecturer

Dr Scott Berry

  • 2016 Ph.D. Plant Science and Microbiology. John Innes Centre, Norwich, U.K.
  • 2010 B.Sc. (Hons.) Theoretical Physics, The University of Western Australia.
  • 2007 B.Sc. Theoretical Physics and Biochemistry, The University of Adelaide.
Medicine & Health
School of Medical Sciences

I lead a research group investigating quantitative control of gene expression at the single-cell level – ranging from epigenetic memory and cellular decision-making to global RNA metabolism in the context of cellular physiology.

Proper control of gene expression underpins the normal development of organisms, and is dysregulated in diseases such as cancer. We seek to better understand which components of a cell are involved in this control, and how they work together. Our fundamental discoveries regarding the normal operation of cells underpin the identification of new disease mechanisms and possible therapeutic targets. We also contribute to the development of new research methodologies and analysis methods for use in drug discovery and diagnostics applications.

We make extensive use of high-throughput microscopy, including highly multiplexed immunofluorescence and RNA fluorescence in situ hybridisation, as well as live-cell imaging and automated image analysis. Together, these approaches enable detailed measurement of quantitative cellular phenotypes (for example, the abundance and localisations of specific proteins or RNAs) across large cell populations. We analyse resulting datasets using data science methods and interpret and explore hypotheses through the development of minimal mathematical models. We complement these image-based experimental approaches with functional genomics experiments (based on next-generation sequencing) and we use perturbation experiments including genome and epigenome-editing to test specific hypotheses.

 

Phone
+61-2-9385 0790
Location
Single Molecule Science - EMBL Australia Lowy Cancer Research Centre - Level 3
  • Journal articles | 2022
    Berry S; Müller M; Rai A; Pelkmans L, 2022, 'Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells', Cell Systems, vol. 13, pp. 454 - 470.e15, http://dx.doi.org/10.1016/j.cels.2022.04.005
    Journal articles | 2022
    Berry S; Pelkmans L, 2022, 'Mechanisms of cellular mRNA transcript homeostasis', Trends in Cell Biology, vol. 32, pp. 655 - 668, http://dx.doi.org/10.1016/j.tcb.2022.05.003
    Journal articles | 2021
    Müller M; Avar M; Heinzer D; Emmenegger M; Aguzzi A; Pelkmans L; Berry S, 2021, 'Author Correction: High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production (Scientific Data, (2021), 8, 1, (162), 10.1038/s41597-021-00944-5)', Scientific Data, vol. 8, pp. 313, http://dx.doi.org/10.1038/s41597-021-01096-2
    Journal articles | 2021
    Müller M; Pelkmans L; Berry S, 2021, 'High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production', Scientific Data, vol. 8, http://dx.doi.org/10.1038/s41597-021-00944-5
    Journal articles | 2017
    Berry S; Dean C; Howard M, 2017, 'Slow Chromatin Dynamics Allow Polycomb Target Genes to Filter Fluctuations in Transcription Factor Activity', Cell Systems, vol. 4, pp. 445 - 457.e8, http://dx.doi.org/10.1016/j.cels.2017.02.013
    Journal articles | 2017
    Berry S; Rosa S; Howard M; Bühler M; Dean C, 2017, 'Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression', Genes and Development, vol. 31, pp. 2115 - 2120, http://dx.doi.org/10.1101/gad.305227.117
    Journal articles | 2017
    Yang H; Berry S; Olsson TSG; Hartley M; Howard M; Dean C, 2017, 'Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis', Science, vol. 357, pp. 1142 - 1145, http://dx.doi.org/10.1126/science.aan1121
    Journal articles | 2015
    Berry S; Dean C, 2015, 'Environmental perception and epigenetic memory: Mechanistic insight through FLC', Plant Journal, vol. 83, pp. 133 - 148, http://dx.doi.org/10.1111/tpj.12869
    Journal articles | 2015
    Berry S; Hartley M; Olsson TSG; Dean C; Howard M, 2015, 'Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance', eLife, vol. 4, http://dx.doi.org/10.7554/eLife.07205
    Journal articles | 2014
    King JD; Berry S; Clarke BR; Morris RJ; Whitfield C, 2014, 'Lipopolysaccharide O antigen size distribution is determined by a chain extension complex of variable stoichiometry in Escherichia coli O9a', Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. 6407 - 6412, http://dx.doi.org/10.1073/pnas.1400814111
    Journal articles | 2012
    Richards D; Berry S; HOward M, 2012, 'Illustrations of mathematical modeling in biology: Epigenetics, meiosis, and an outlook', Cold Spring Harbor Symposia on Quantitative Biology, vol. 77, pp. 175 - 181, http://dx.doi.org/10.1101/sqb.2013.77.015941
    Journal articles | 2011
    Berry SD; Bourke P; Wang JB, 2011, 'QwViz: Visualisation of quantum walks on graphs', Computer Physics Communications, vol. 182, pp. 2295 - 2302, http://dx.doi.org/10.1016/j.cpc.2011.06.002
    Journal articles | 2011
    Berry SD; Wang JB, 2011, 'Two-particle quantum walks: Entanglement and graph isomorphism testing', Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, http://dx.doi.org/10.1103/PhysRevA.83.042317
    Journal articles | 2010
    Berry SD; Wang JB, 2010, 'Quantum-walk-based search and centrality', Physical Review A - Atomic, Molecular, and Optical Physics, vol. 82, http://dx.doi.org/10.1103/PhysRevA.82.042333
  • Software / Code | 2022
    Spitzer H; Berry S, 2022, CAMPA, GitHub, Published: 09 May 2022, Software / Code, https://github.com/theislab/campa
    Preprints | 2021
    Berry S; Müller M; Pelkmans L, 2021, Nuclear RNA concentration coordinates RNA production with cell size in human cells, http://dx.doi.org/10.1101/2021.05.17.444432
    Preprints | 2022
    Spitzer H; Berry S; Donoghoe M; Pelkmans L; Theis F, 2022, Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps, http://dx.doi.org/10.1101/2022.05.07.490900
    Preprints |
    Yin J-A; Frick L; Scheidmann MC; Trevisan C; Dhingra A; Spinelli A; Wu Y; Yao L; Vena DL; De Cecco E; Ging K; Liu T; Täger J; Rodriguez S; Guo J; Berry S; Losa M; Hornemann S; Kampmann M; Pelkmans L; Hoepfner D; Heutink P; Aguzzi A, Robust and Versatile Arrayed Libraries for Human Genome-Wide CRISPR Activation, Deletion and Silencing, http://dx.doi.org/10.1101/2022.05.25.493370

  • 2019 Early-career researcher award (Lorne genome conference, Australia)
  • 2017-2021 HFSP Long Term Fellowship (University of Zurich, Switzerland)
  • 2017-2019 EMBO Long Term Fellowship (University of Zurich, Switzerland)
  • 2016 John Innes Foundation prize for excellence in scientific research – annual Ph.D. thesis prize (Norwich, U.K.)
  • 2014 EMBO Short Term Fellowship (FMI, Basel, Switzerland)
  • 2011-2015 John Innes Foundation Rotation PhD Scholarship
  • 2010 Maslen Physics Prize (University of Western Australia)
  • 2010 John and Patricia Farrant Scholarship
  • 2007 Silver Bragg Medal (Australian Institute of Physics)
  • 2007 R.K. Morton Scholarship (University of Adelaide – Biochemistry)
  • 2007 Angus Hurst Prize (University of Adelaide – Physics)

Quantitative regulation of gene expression in single cells

We are interested in the mechanisms used by cells to regulate gene-specific and global RNA abundance – ranging from epigenetic memory and cellular decision-making to global RNA metabolism in the context of cellular physiology. We seek to generate a quantitative understanding of these processes.

Our research methodology is a combination of ‘top-down’ (data-driven) and ‘bottom-up’ (hypothesis-driven) approaches. We make extensive use of high-throughput microscopy and automated image analysis, which enables detailed measurement of quantitative cellular phenotypes (for example, the abundance and localisations of specific proteins or RNAs) across large cell populations. Resulting datasets are then analysed using a variety of methods from data science. We complement these image-based approaches with functional genomics experiments, based on next-generation sequencing – providing exquisite genomic resolution, and use perturbation experiments including genome and epigenome-editing to test specific hypotheses.

  • Human Frontiers Science Programme (HFSP): Long-term Fellowship 2017-2021
  • European Molecular Biology Organisation (EMBO): Long-term Fellowship 2017-2019

 

  • 2022-current: Co-Chair - UNSW RNA special interest group
  • 2022-current: Conference Organisation Committee - Australian Epigenetics (AusEpi22)
  • 2022-current: Scientific Program Committee - 26th Congress of the International Union of Biochemistry and Molecular Biology (IUBMB).