Augustine Chen, Genomics team, Otago Genomics Facility

Nanopore sequencing specialist

Tel +64 3 479 5123
email augustine.chen@otago.ac.nz
Location: OGF Lab, Room G20, Biochemistry Department

Biographical information

Augustine was awarded a PhD in Biochemistry from the University of Otago, Dunedin. His PhD and postdoctoral research with Associate Professor Chris Brown included elucidating unique translational control mechanisms used by the human hepatitis B virus and exploring the therapeutic potential of miRNA.

In 2010, he joined Professor Parry Guilford’s group as a Research Fellow to develop a test for a company to detect high-risk strains of Human Papilloma Virus linked to cervical cancer. From 2012–2020, he was involved in an ongoing HRC funded study which elucidated vulnerabilities associated with E-cadherin deficient cancer cells through synthetic lethal approach utilising genome-wide siRNA knockdown, followed by targeting using FDA approved drugs and novel compounds.

He is currently a senior research fellow (0.5 FTE) with his own research funding to co-develop an NGS-based test (utilising Oxford Nanopore Technologies platform) for applications in early cancer detection as well as environmental monitoring. Since 2021, he has a part-time (0.5 FTE) appointment as a nanopore sequencing specialist in the Otago Genomics Facility.

Publications

Gardner, P., Coray, D. S., Sibaeva, N., McGimpsey, S., Smith, L., Chen, A., & Fineran, P. (2023). The mutational robustness of RNA and protein. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference Conference Contribution - Published proceedings: Abstract

Clarke, R. M., Hess, A., Caulton, A., Brauning, R., McRae, K. M., Chen, A., … Clarke, S. M. (2023, August). Structural variation in NZ sheep: Identification and implementation. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand. Conference Contribution - Verbal presentation and other Conference outputs

Chen, A. (2023, November). Flow cell loading. Workshop presentation at the Genetics Otago (GO) Annual Symposium & Workshops, Dunedin, New Zealand. Conference Contribution - Verbal presentation and other Conference outputs

Hannah, S. J., Chen, A., Day, R. C., & Black, M. A. (2022). Improvising read accuracy for ctDNA diagnostics. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go Conference Contribution - Published proceedings: Abstract

Clarke, R. M., Hess, A., Caulton, A., Brauning, R., McRae, K., Chen, A., & Clarke, S. (2022, August). Simultaneous investigation of genomic regions of interest: The use of adaptive sampling. Poster session presented at the Applied Genetics/Genomics in Breeding Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand. Conference Contribution - Poster Presentation (not in published proceedings)

2023

Conference Contribution - Published proceedings: Abstract

Conference Contribution - Verbal presentation and other Conference outputs

Chen, A. (2023, November). Flow cell loading. Workshop presentation at the Genetics Otago (GO) Annual Symposium & Workshops, Dunedin, New Zealand.

2022

Conference Contribution - Published proceedings: Abstract

Conference Contribution - Poster Presentation (not in published proceedings)

2021

Journal - Research Article

Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461

2019

Journal - Research Article

Bougen-Zhukov, N., Nouri, Y., Godwin, T., Taylor, M., Hakkaart, C., Single, A., Brew, T., Permina, E., Chen, A., Black, M. A., & Guilford, P. (2019). Allosteric AKT inhibitors target synthetic lethal vulnerabilities in E-cadherin-deficient cells. Cancers, 11(9), 1359. doi: 10.3390/cancers11091359

Beetham, H., Chen, A., Telford, B. J., Single, A., Jarman, K. E., Lackovic, K., … Guilford, P. (2019). A high-throughput screen to identify novel synthetic lethal compounds for the treatment of E-cadherin-deficient cells. Scientific Reports, 9, 12511. doi: 10.1038/s41598-019-48929-0

Godwin, T. D., Kelly, S. T., Brew, T. P., Bougen-Zhukov, N. M., Single, A. B., Chen, A., Stylianou, C. E., … Currie, S. K., Telford, B. J., Beetham, H. G., … Black, M. A., & Guilford, P. J. (2019). E-cadherin-deficient cells have synthetic lethal vulnerabilities in plasma membrane organisation, dynamics and function. Gastric Cancer, 22(2), 273-286. doi: 10.1007/s10120-018-0859-1

2017

Conference Contribution - Published proceedings: Abstract

Single, A., Chen, A., Telford, B., Beetham, H., & Guilford, P. (2017). Statins show synthetic lethality in E-cadherin-deficient cells and are synergistic with SRC and HDAC inhibitors. Clinical Cancer Research, 23(1, Suppl. ), B41. doi: 10.1158/1557-3265.PMCCAVULN16-B41

Guilford, P. J., Chen, A., Telford, B., Single, A., Beetham, H., & Godwin, T. (2017). Synthetic lethal targeting of E-cadherin-deficient cancers. Clinical Cancer Research, 23(1, Suppl.), B04. doi: 10.1158/1557-3265.PMCCAVULN16-B04

Conference Contribution - Verbal presentation and other Conference outputs

Kelly, S. T., Stylianou, C., Chen, A., Guilford, P. J., & Black, M. A. (2017, September). In silico detection of candidate synthetic lethal gene pairs using cancer genomics data. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2016

Conference Contribution - Published proceedings: Abstract

Chen, A., Telford, B. J., Single, A., Beetham, H., Simpson, K. J., & Guilford, P. J. (2016). Synthetic lethal approaches targeting E-cadherin-deficient cancers. Cancer Research, 76(14, Suppl.), 3814. doi: 10.1158/1538-7445.AM2016-3814

Conference Contribution - Verbal presentation and other Conference outputs

Guilford, P., Chen, A., Single, A., Beetham, H., Telford, B., Hakkaart, C., & Godwin, T. (2016, August-September). Hereditary diffuse gastric cancer: Battling the curse. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Nelson, New Zealand.

2015

Journal - Research Article

Single, A., Beetham, H., Telford, B. J., Guilford, P., & Chen, A. (2015). A comparison of real-time and endpoint cell viability assays for improved synthetic lethal drug validation. Journal of Biomolecular Screening, 20(10), 1286-1293. doi: 10.1177/1087057115605765

Telford, B. J., Chen, A., Beetham, H., Frick, J., Brew, T. P., Gould, C. M., Single, A., Godwin, T., … Guilford, P. (2015). Synthetic lethal screens identify vulnerabilities in GPCR signalling and cytoskeletal organization in E-cadherin-deficient cells. Molecular Cancer Therapeutics, 14(5), 1213-1223. doi: 10.1158/1535-7163.mct-14-1092

Conference Contribution - Published proceedings: Abstract

Beetham, H., Chen, A., Jarman, K. E., Falk, H., & Guilford, P. J. (2015). The discovery of novel synthetic lethal compounds for the treatment of E-cadherin deficient tumours. Proceedings of the Diagnostic Drug Device Discovery (D4) Conference. Retrieved from https://www.regonline.com.au/builder/site/Default.aspx?EventID=1758070

Conference Contribution - Poster Presentation (not in published proceedings)

Beetham, H., Chen, A., Single, A., Telford, B. J., & Guilford, P. J. (2015, August-September). The discovery of novel synthetic lethal compounds for the treatment of E-cadherin deficient tumours. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Single, A., Chen, A., & Guilford, P. (2015, October). A synergistic synthetic lethal drug combination for the treatment of E-cadherin-deficient tumours. Poster session presented at the Otago Spotlight Series: Cancer Research, Wellington, New Zealand.

Beetham, H., Chen, A., Single, A., Telford, B., & Guilford, P. (2015, October). The discovery of novel synthetic lethal compounds for the treatment of E-cadherin deficient tumours. Poster session presented at the Otago Spotlight Series: Cancer Research, Wellington, New Zealand.

2014

Journal - Research Article

Chen, A., Beetham, H., Black, M. A., Priya, R., Telford, B. J., Guest, J., Wiggins, G. A. R., Godwin, T. D., … Guilford, P. J. (2014). E-cadherin loss alters cytoskeletal organization and adhesion in non-malignant breast cells but is insufficient to induce an epithelial-mesenchymal transition. BMC Cancer, 14, 552. doi: 10.1186/1471-2407-14-552

Chen, A., T-Thienprasert, N. P., & Brown, C. M. (2014). Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus. World Journal of Gastroenterology, 20(25), 7993-8004. doi: 10.3748/wjg.v20.i25.7993

Waugh, E., Chen, A., Baird, M. A., Brown, C. M., & Ward, V. K. (2014). Characterization of the chemokine response of RAW264.7 cells to infection by murine norovirus. Virus Research, 181, 27-34. doi: 10.1016/j.virusres.2013.12.025

Conference Contribution - Poster Presentation (not in published proceedings)

Beetham, H., Chen, A., Telford, B. J., & Guilford, P. J. (2014, August). A cell based high throughput screen to find novel synthetic lethal lead-like compounds for the treatment of E-cadherin deficient tumours. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Guilford, P., Telford, B., Chen, A., Beetham, H., Single, A., Frick, J., Brew, T., & Godwin, T. (2014, November). Synthetic lethal targeting of E-cadherin-deficient cancers. Verbal presentation at the Frontiers of Biology Satellite Meeting: From Protein Structure and Function to Drugs, Wellington, New Zealand.

2013

Conference Contribution - Published proceedings: Abstract

Chen, A., Telford, B., Beetham, H., Single, A., Godwin, T., & Guilford, P. (2013). Synthetic lethal interactions with the tumour suppressor protein E-cadherin. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/conference_2013

Single, A., Chen, A., Telford, B., & Guilford, P. (2013). Synthetic lethal interactions for the treatment of E-cadherin negative tumours. New Zealand Medical Journal, 126(1374). Retrieved from http://www.nzma.org.nz/journal

Conference Contribution - Verbal presentation and other Conference outputs

Garama, D., Stevens, S., Chen, X., Biswas, A., Sarman, A., Chen, A., & Brown, C. (2013, February). Translational control of gene expression by mRNA elements. Verbal presentation at the 38th Lorne Conference on Protein Structure and Function, Lorne, Australia.

2012

Journal - Research Article

Chen, A., & Brown, C. (2012). Distinct families of cis-acting RNA replication epsilon elements from hepatitis B viruses. RNA Biology, 9(2), 130-136. doi: 10.4161/rna.18649

Conference Contribution - Verbal presentation and other Conference outputs

Guilford, P., Telford, B., Black, M., & Chen, A. (2012, August). Synthetic lethal targeting of the tumour suppressor gene CDH1 in common cancers. Invited presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2011

Conference Contribution - Poster Presentation (not in published proceedings)

Chen, A., Sarman, A., Riad, S., Stevens, S., & Brown, C. (2011, September). Changes in gene expression in a breast cancer cell line using RNA-Seq. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Stevens, S. G., Biswas, A., Gagnon, J., Wilkinson, T., Chen, A., Chen, S., & Brown, C. M. (2011, August). Bioinformatic approaches to the identification of localisation elements. Verbal presentation at the European Molecular Biology Organization (EMBO) Conference on Intracellular RNA Localization & Localized Translation, Tuscany, Italy.

Brown, C. M., Das, A., Stevens, S., Biswas, A., Gagnon, J., McKinney, C., Chen, A., & Chen, S. (2011, September). Bioinformatic approaches to discover post-transcriptional regulatory elements in human mRNAs. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

2009

Journal - Research Article

Jacobs, G. H., Chen, A., Stevens, S. G., Stockwell, P. A., Black, M. A., Tate, W. P., & Brown, C. M. (2009). Transterm: A database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Research, 37(Database issue), D72-D76. doi: 10.1093/nar/gkn763

Conference Contribution - Published proceedings: Abstract

Brown, C. M., Wilkinson, T., Panjaworayan, N., Firth, A. E., Chen, A., Stevens, S. G., Wong, A., Black, M., … Roessner, S. K. (2009). Analysis of virus and human genome sequences for RNA regulatory elements. Proceedings of the Webster Centre for Infectious Diseases Symposium. WCID. Retrieved from http://www.webstercentre.otago.ac.nz/WCIDSymposiumProgramme.pdf

2008

Conference Contribution - Verbal presentation and other Conference outputs

Brown, C., Chen, A., Ballantine, S., Black, M., Jacobs, G., & Stevens, S. (2008, November-December). Identification of post-transcriptional regulatory elements in mRNA sequences. Verbal presentation at the New Zealand Institute of Chemistry, New Zealand Society for Biochemistry and Molecular Biology and the New Zealand Society of Plant Biologists Combined Conference, Dunedin, New Zealand.

2007

Awarded Doctoral Degree

Chen, A. (2007). Translational control mechanisms used by the human Hepatitis B virus: An upstream open reading frame modulates expression of the pregenomic RNA (PhD). University of Otago, Dunedin, New Zealand. 155p.

2005

Journal - Research Article

Chen, A., Kao, Y. F., & Brown, C. M. (2005). Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons. Nucleic Acids Research, 33(4), 1169-1181.

Conference Contribution - Published proceedings: Abstract

Panjaworayan, N., Rackham, O., Chen, A., Kao, A. Y.-F., & Brown, C. M. (2005). Post-transcriptional regulation of gene expression in hepatitis B virus. Proceedings of the Meeting on the Molecular Biology of Hepatitis B Viruses. (pp. 30). Heidelberg, Germany. [Abstract]

1997

Journal - Research Article

Chen, A., Grigor, M. R., Thompson, C. M., & Harris, E. L. (1997). Kallikrein binding protein (KBP) maps to rat Chromosome 6 but does not cosegregate with blood pressure in a GH x BN cross. Mammalian Genome, 8(9), 701-703.