Dr Rob Day
| Position | Research Fellow |
|---|---|
| Department | Department of Biochemistry |
| Qualifications | PhD |
| Research summary | Agricultural science, developmental biology, cancer biology, genomics and technology development |
| Memberships | Executive Committee Australasian Genomics Technology Association (AGTA) |
Research
My main research interest is the development and application of new genetic/genomics based technologies in areas of agricultural biology, developmental biology and medicine. I am best known for adapting genomics technologies for use with minute amounts of starting material to discover key imprinted genes controlling seed development in plants.
I currently use the Illumina MiSeq sequencing platform in the Centre for Translational Cancer Research and am developing new methods for sequence-based diagnostics from single cells and circulating tumor DNA. I am eager to promote and facilitate the use of genomics technology in all areas of biology and currently collaborate with several groups. Also, as way of promoting the field I have convened and/or helped organize several genomics meetings and serve on the executive committee of the Australasian Genomic Technologies Association the principal body for the promotion of genomics research in Australasia.
Additional details
I also helped manage the Otago Genomics Facility during a colleagues maternity leave. During this time we focused on developing standard operating procedures for sample processing and project management. This greatly enhanced my knowledge of genomics and bioinformatics. I have also served on the Project Advisory Committee for New Zealand Genomics Ltd.
Publications
Begemann, A., Sticht, H., Begtrup, A., Vitobello, A., Faivre, L., Siddharth, B., … Day, R., … Sadleir, L. G., … Rauch, A. (2020). New insights into the clinical and molecular spectrum of the novel CYFIP2-related neurodevelopmental disorder and impairment of the WRC-mediated actin dynamics. Genetics in Medicine. Advance online publication. doi: 10.1038/s41436-020-01011-x
Marsman, J., Gimenez, G., Day, R. C., Horsfield, J. A., & Jones, G. T. (2020). A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. Human Molecular Genetics, 29(4), 554-565. doi: 10.1093/hmg/ddz256
Zou, D., Day, R., Cocadiz, J. A., Parackal, S., Mitchell, W., Black, M. A., … Jackson, C., & Guilford, P. (2020). Circulating tumor DNA is a sensitive marker for routine monitoring of treatment response in advanced colorectal cancer. Carcinogenesis, 41(11), 1507-1517. doi: 10.1093/carcin/bgaa102
Mayyas, I. M., Weeks, R. J., Day, R. C., Magrath, H. E., O’Connor, K. M., Kardailsky, O., Hore, T. A., Hampton, M. B., & Morison, I. M. (2020). Hairpin-bisulfite sequencing of cells exposed to decitabine documents the process of DNA demethylation. Epigenetics. Advance online publication. doi: 10.1080/15592294.2020.1861169
Aitchison, A., Hakkaart, C., Day, R. C., Morrin, H. R., Frizelle, F. A., & Keenan, J. I. (2020). APC mutations are not confined to hotspot regions in early-onset colorectal cancer. Cancers, 12, 3829. doi: 10.3390/cancers12123829
Chapter in Book - Research
Day, R., & Macknight, R. (2014). Screening for imprinted genes using high-resolution melting analysis of PCR amplicons. In C. Spillane & P. C. McKeown (Eds.), Plant epigentics and epigenomics: Methods and protocols. (pp. 71-83). Humana Press. doi: 10.1007/978-1-62703-773-0_5
Macknight, R. C., Herridge, R. P., & Day, R. C. (2012). Using transcriptomics to reveal gene networks of seed development in Arabidopsis. In G. K. Agrawal & R. Rakwal (Eds.), Seed development: OMICS technologies toward Improvement of seed quality and crop yield. (pp. 99-110). Dordrecht, The Netherlands: Springer. doi: 10.1007/978-94-007-4749-4_6
Day, R. C. (2010). Laser microdissection of paraffin-embedded plant tissues for transcript profiling. In L. Hennig & C. Köhler (Eds.), Plant developmental biology: Methods and protocols. (pp. 321-346). New York: Spinger. doi: 10.1007/978-1-60761-765-5_22
Journal - Research Article
Begemann, A., Sticht, H., Begtrup, A., Vitobello, A., Faivre, L., Siddharth, B., … Day, R., … Sadleir, L. G., … Rauch, A. (2020). New insights into the clinical and molecular spectrum of the novel CYFIP2-related neurodevelopmental disorder and impairment of the WRC-mediated actin dynamics. Genetics in Medicine. Advance online publication. doi: 10.1038/s41436-020-01011-x
Aitchison, A., Hakkaart, C., Day, R. C., Morrin, H. R., Frizelle, F. A., & Keenan, J. I. (2020). APC mutations are not confined to hotspot regions in early-onset colorectal cancer. Cancers, 12, 3829. doi: 10.3390/cancers12123829
Mayyas, I. M., Weeks, R. J., Day, R. C., Magrath, H. E., O’Connor, K. M., Kardailsky, O., Hore, T. A., Hampton, M. B., & Morison, I. M. (2020). Hairpin-bisulfite sequencing of cells exposed to decitabine documents the process of DNA demethylation. Epigenetics. Advance online publication. doi: 10.1080/15592294.2020.1861169
Zou, D., Day, R., Cocadiz, J. A., Parackal, S., Mitchell, W., Black, M. A., … Jackson, C., & Guilford, P. (2020). Circulating tumor DNA is a sensitive marker for routine monitoring of treatment response in advanced colorectal cancer. Carcinogenesis, 41(11), 1507-1517. doi: 10.1093/carcin/bgaa102
Marsman, J., Gimenez, G., Day, R. C., Horsfield, J. A., & Jones, G. T. (2020). A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. Human Molecular Genetics, 29(4), 554-565. doi: 10.1093/hmg/ddz256
Ortega-Recalde, O., Day, R. C., Gemmell, N. J., & Hore, T. A. (2019). Zebrafish preserve global germline DNA methylation while sex-linked rDNA is amplified and demethylated during feminisation. Nature Communications, 10, 3053. doi: 10.1038/s41467-019-10894-7
Hakkaart, C., Ellison-Loschmann, L., Day, R., Sporle, A., Koea, J., Harawira, P., … Guilford, P. (2019). Germline CDH1 mutations are a significant contributor to the high frequency of early-onset diffuse gastric cancer cases in New Zealand Māori. Familial Cancer, 18(1), 83-90. doi: 10.1007/s10689-018-0080-8
Parackal, S., Zou, D., Day, R., Black, M., & Guilford, P. (2019). Comparison of Roche Cell-Free DNA collection Tubes® to Streck Cell-Free DNA BCT®s for sample stability using healthy volunteers. Practical Laboratory Medicine, 16, e00125. doi: 10.1016/j.plabm.2019.e00125
Clare, A. J., Day, R. C., Empson, R. M., & Hughes, S. M. (2018). Transcriptome profiling of layer 5 intratelencephalic projection neurons from the mature mouse motor cortex. Frontiers in Molecular Neuroscience, 11, 410.
Schmid, J., Day, R., Zhang, N., Dupont, P.-Y., Cox, M. P., Schardl, C. L., … Zhou, Y. (2017). Host tissue environment directs activities of an Epichloë endophyte, while it induces systemic hormone and defense responses in its native perennial ryegrass host. Molecular Plant-Microbe Interactions, 30(2), 138-149. doi: 10.1094/mpmi-10-16-0215-r
Tantirigama, M. L. S., Oswald, M. J., Clare, A. J., Wicky, H. E., Day, R. C., Hughes, S. M., & Empson, R. M. (2016). Fezf2 expression in layer 5 projection neurons of mature mouse motor cortex. Journal of Comparative Neurology, 524(4), 829-845. doi: 10.1002/cne.23875
Dupont, P.-Y., Eaton, C. J., Wargent, J. J., Fechtner, S., Solomon, P., Schmid, J., Day, R. C., … Cox, M. P. (2015). Fungal endophyte infection of ryegrass reprograms host metabolism and alters development. New Phytologist, 208(4), 1227-1240. doi: 10.1111/nph.13614
Zhang, H., Luo, M., Day, R. C., Talbot, M. J., Ivanova, A., Ashton, A. R., … Macknight, R. C., … Koltunow, A. M. (2015). Developmentally regulated HEART STOPPER, a mitochondrially targeted L18 ribosomal protein gene, is required for cell division, differentiation, and seed development in Arabidopsis. Journal of Experimental Botany, 66(19), 5867-5880. doi: 10.1093/jxb/erv296
Herridge, R. P., Day, R. C., & Macknight, R. C. (2014). The role of the MCM2-7 helicase complex during Arabidopsis seed development. Plant Molecular Biology, 86(1-2), 69-84. doi: 10.1007/s11103-014-0213-x
Butler, M. I., Stockwell, P. A., Black, M. A., Day, R. C., Lamont, I. L., & Poulter, R. T. M. (2013). Pseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China. PLoS ONE, 8(2), e57464. doi: 10.1371/journal.pone.0057464
Jones, T. E. M., Day, R. C., & Beck, C. W. (2013). Attenuation of bone morphogenetic protein signaling during amphibian limb development results in the generation of stage-specific defects. Journal of Anatomy, 223(5), 474-488. doi: 10.1111/joa.12098
Herridge, R. P., Day, R. C., Baldwin, S., & Macknight, R. C. (2011). Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery. Plant Methods, 7. doi: 10.1186/1746-4811-7-3
Day, R. C., & Beck, C. W. (2011). Transdifferentiation from cornea to lens in Xenopus laevis depends on BMP signalling and involves upregulation of Wnt signalling. BMC Developmental Biology, 11, 54. doi: 10.1186/1471-213x-11-54
Fenby, N., Pu, H., Pennell, R., Praekelt, U., Day, R., & Scott, R. (2010). An uncoupling screen for autonomous embryo mutants in Arabidopsis thaliana. Sexual Plant Reproduction, 23, 255-264. doi: 10.1007/s00497-010-0142-z
Day, R. C., Mueller, S., & Macknight, R. C. (2009). Identification of cytoskeleton-associated genes expressed during arabidopsis syncytial endosperm development. Plant Signaling & Behavior, 4(9), 883-886.
Pearl, E. J., Barker, D., Day, R. C., & Beck, C. W. (2008). Identification of genes associated with regenerative success of Xenopus laevis hindlimbs. BMC Developmental Biology, 8, 66. doi: 10.1186/1471-213X-8-66
Day, R. C., Herridge, R. P., Ambrose, B. A., & Macknight, R. C. (2008). Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiology, 148(4), 1964-1984. doi: 10.1104/pp.108.128108
Day, R. C., McNoe, L., & Macknight, R. C. (2007). Evaluation of global RNA amplification and its use for high-throughput transcript analysis of laser-microdissected endosperm. International Journal of Plant Genomics, 2007, 61028.
Day, R. C., McNoe, L. A., & MacKnight, R. C. (2007). Transcript analysis of laser microdissected plant cells. Physiologia Plantarum, 129(2), 267-282.
Journal - Research Other
Antony, J., Gimenez, G., Taylor, T., Khatoon, U., Day, R., Morison, I. M., & Horsfield, J. A. (2020). BET inhibition prevents aberrant RUNX1 and ERG transcription in STAG2 mutant leukaemia cells. Journal of Molecular Cell Biology, 12(5), 397-399. doi: 10.1093/jmcb/mjz114
