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Dr Simone Cree

Simone MacmilResearch Fellow

MSc(Baroda), PhD(Oklahoma)

Email simone.macmil@otago.ac.nz 
Tel +64 3 364 1222

Research Interests

  • G-quadruplex DNA, Next Generation DNA Sequencing, analysis and annotation
  • Whole Genome Sequencing
  • Whole Exome sequencing
  • Targeted Re-sequencing
  • Transcriptomes- EST profiling
  • De Novo Assembly
  • Microbial genomics
  • Protocol optimization and automation
  • Protein purification
  • Enzyme assays and kinetics
  • Tissue culture

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Publications

Cree, S. L., & Kennedy, M. A. (2014). Relevance of G-quadruplex structures to pharmacogenetics. Frontiers in Pharmacology, 5, 160. doi: 10.3389/fphar.2014.00160

Cree, S. L., Fredericks, R., Miller, A., Pearce, F. G., Filichev, V., Fee, C., & Kennedy, M. A. (2016). DNA G-quadruplexes show strong interaction with DNA methyltransferases in vitro. FEBS Letters, 590(17), 2870-2883. doi: 10.1002/1873-3468.12331

Cree, S., Maggo, S., Slow, S., Ton, K., de Jong, L., Anderson, T., Pearson, J., Miller, A., Walker, L., Murdoch, D., & Kennedy, M. (2017). Long read nanopore sequencing in the laboratory. Proceedings of the MapNet Conference. Retrieved from http://scienceevents.co.nz/mapnet/

Cree, S. L., Miller, A. L., Chua, E. W., Maggo, S., & Kennedy, M. A. (2015, August). Long-read nanopore Sequencing for the detection of genetic polymorphisms in the CYP2D6 gene. Verbal presentation at the 7th Annual New Zealand Next Generation Sequencing (NGS) Conference, Palmerston North, New Zealand.

Chua, E. W., Cree, S., Barclay, M. L., Doudney, K., Lehnert, K., Aitchison, A., & Kennedy, M. A. (2015). Exome sequencing and array-based comparative genomic hybridisation analysis of preferential 6-methylmercaptopurine producers. Pharmacogenomics Journal, 15, 414-421. doi: 10.1038/tpj.2015.9

Journal - Research Article

Maggo, S. D. S., Chua, E. W., Chin, P., Cree, S., Pearson, J., Doogue, M., & Kennedy, M. A. (2017). A New Zealand platform to enable genetic investigation of adverse drug reactions. New Zealand Medical Journal, 130(1466), 62-69. Retrieved from http://www.nzma.org.nz/journal

de Jong, L. C., Cree, S., Lattimore, V., Wiggins, G. A. R., Spurdle, A. B., kConFab Investigators, Miller, A., Kennedy, M. A., & Walker, L. C. (2017). Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events. Breast Cancer Research, 19, 127. doi: 10.1186/s13058-017-0919-1

Chua, E. W., Cree, S. L., Ton, K. N. T., Lehnert, K., Shepherd, P., Helsby, N., & Kennedy, M. A. (2016). Cross-comparison of exome analysis, next-generation sequencing of amplicons, and the iPLEX® ADME PGx Panel for pharmacogenomic profiling. Frontiers in Pharmacology, 7, 1. doi: 10.3389/fphar.2016.00001

Cree, S. L., Fredericks, R., Miller, A., Pearce, F. G., Filichev, V., Fee, C., & Kennedy, M. A. (2016). DNA G-quadruplexes show strong interaction with DNA methyltransferases in vitro. FEBS Letters, 590(17), 2870-2883. doi: 10.1002/1873-3468.12331

Chua, E. W., Cree, S., Barclay, M. L., Doudney, K., Lehnert, K., Aitchison, A., & Kennedy, M. A. (2015). Exome sequencing and array-based comparative genomic hybridisation analysis of preferential 6-methylmercaptopurine producers. Pharmacogenomics Journal, 15, 414-421. doi: 10.1038/tpj.2015.9

Cree, S. L., & Kennedy, M. A. (2014). Relevance of G-quadruplex structures to pharmacogenetics. Frontiers in Pharmacology, 5, 160. doi: 10.3389/fphar.2014.00160

Stevens, A. J., Stuffrein-Roberts, S., Cree, S. L., Gibb, A., Miller, A. L., Doudney, K., Aitchison, A., Eccles, M. R., Joyce, P. R., … Kennedy, M. A. (2014). G-quadruplex structures and CpG methylation cause drop-out of the maternal allele in polymerase chain reaction amplification of the imprinted MEST gene promoter. PLoS ONE, 9(12), e113955. doi: 10.1371/journal.pone.0113955

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Conference Contribution - Published proceedings: Abstract

Cree, S., Maggo, S., Slow, S., Ton, K., de Jong, L., Anderson, T., Pearson, J., Miller, A., Walker, L., Murdoch, D., & Kennedy, M. (2017). Long read nanopore sequencing in the laboratory. Proceedings of the MapNet Conference. Retrieved from http://scienceevents.co.nz/mapnet/

Kennedy, M. A., Maggo, S. D. S., Foulds, J., Luty, S., Chua, E. W., Cree, S., Ton, K., Liau, Y., Miller, A. L., Chin, P., … Doogue, M. (2017). DNA banking and genetic analysis of adverse drug reactions in the New Zealand healthcare setting. Proceedings of the American Society of Human Genetics (ASHG) Annual Meeting. 2123. Retrieved from http://www.ashg.org/2017meeting/

Stevens, A. J., Stuffrein-Roberts, S., Macmil, S., Gibb, A., Doudney, K., Miller, A. L., Bagshaw, A., Aitchison, A., Eccles, M. R., Joyce, P. R., … Kennedy, M. A. (2013). Allelic-dropout during PCR of the imprinted MEST promoter caused by interaction between G-quadruplex structures and DNA methylation. Proceedings of the 4th International Meeting on G-quadruplex Nucleic Acids: From Structure to Chemistry and Biology. 83. Retrieved from http://www.g4meeting2013.com/

Macmil, S. L., Fredericks, R., Miller, A., Fee, C., Filichev, V. V., & Kennedy, M. A. (2013). Structure based function: Investigating the role of G-quadruplex structures in de novo DNA methylation. Proceedings of the 4th International Meeting on G-quadruplex Nucleic Acids: From Structure to Chemistry and Biology. 79. Retrieved from http://www.g4meeting2013.com/

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Conference Contribution - Poster Presentation (not in published proceedings)

Jodczyk, S., Cree, S., & Kennedy, M. A. (2015, August-September). Trialling the MinION™ nanopore DNA sequencer for direct measurement of human telomere length. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Ton, K. N. T., Macmil, S., Rand, C., Stanton, J.-A., & Kennedy, M. A. (2015, August-September). A next generation sequencing PGx panel for predicting adverse drug reaction and unusual response. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

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Conference Contribution - Verbal presentation and other Conference outputs

Cree, S. L., Miller, A. L., Chua, E. W., Maggo, S., & Kennedy, M. A. (2015, August). Long-read nanopore Sequencing for the detection of genetic polymorphisms in the CYP2D6 gene. Verbal presentation at the 7th Annual New Zealand Next Generation Sequencing (NGS) Conference, Palmerston North, New Zealand.

Cree, S. (2014, November). Initial experiences with the Oxford nanopore MinION DNA sequencing device. Verbal presentation at the 10th Annual Carney Pharmacogenomics Symposium, Christchurch, New Zealand.

Kennedy, M. A., Chua, E. W., Macmil, S., Foulds, J., Barclay, M., Savage, R., … Miller, A. (2013, August). Genomic medicine and adverse drug reactions. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.

Chua, E. W., Macmil, S., Foulds, J., Barclay, M., Savage, R., Helsby, N. A., Miller, A., & Kennedy, M. A. (2013, August). Understanding adverse Drug Reactions or responses Using Genomic Sequencing (UDRUGS). Verbal presentation at the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists New Zealand Section (ASCEPT-NZ) Annual Scientific Meeting, Queenstown, New Zealand.

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