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Department of Biochemistry profile

Dr Rob Day

PositionResearch Fellow
DepartmentDepartment of Biochemistry
QualificationsPhD
Research summaryAgricultural science, developmental biology, cancer biology, genomics and technology development
MembershipsExecutive 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

Rob is Acting Operations Manager for Otago Genomics Facility.

Publications

Jamieson, S. A., Pudjihartono, M., Horne, C. R., Salamanca Viloria, J., Dunlop, J. L., McMillan, H. D., Day, R. C., … Mace, P. D. (2022). Nanobodies identify an activated state of the TRIB2 pseudokinase. Structure. Advance online publication. doi: 10.1016/j.str.2022.08.006

Jeunen, G.-J., von Ammon, U., Cross, H., Ferreira, S., Lamare, M., Day, R., Treece, J., … Gemmell, N. J., & Stanton, J.-A. L. (2022). Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction. Environmental DNA. Advance online publication. doi: 10.1002/edn3.356

Lubbe, P., Rawlence, N. J., Kardailsky, O., Robertson, B. C., Day, R., Knapp, M., & Dussex, N. (2022). Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida). Zoological Journal of the Linnean Society. Advance online publication. doi: 10.1093/zoolinnean/zlac060

Hudson, D. T., Bromell, J. S., Day, R. C., McInnes, T., Ward, J. M., & Beck, C. W. (2022). Gene expression analysis of the Xenopus laevis early limb bud proximodistal axis. Developmental Dynamics. Advance online publication. doi: 10.1002/dvdy.517

Harfoot, R., Lawley, B., Hernández, L. C., Kuang, J., Grant, J., Treece, J. M., LeQueux, S., Day, R., Jack, S., Stanton, J.-A. L., Bostina, M., Ussher, J. E., & Quiñones‑Mateu, M. E. (2022). Characterization of the first SARS-CoV-2 isolates from Aotearoa New Zealand as part of a rapid response to the COVID-19 pandemic. Viruses, 14, 366. doi: 10.3390/v14020366

Marsman, J., Day, R. C., & Gimenez, G. (2022). Circular chromosome conformation capture sequencing (4C-Seq ) in primary adherent cells. In J. Horsfield & J. Marsman (Eds.), Chromatin: Methods and protocols: Methods in molecular biology (Vol. 2458). (pp. 301-320). New York, NY: Springer. doi: 10.1007/978-1-0716-2140-0_16

Chapter in Book - Research

Smith, J., Day, R. C., & Weeks, R. J. (2022). Next-generation bisulfite sequencing for targeted DNA methylation analysis. In J. Horsfield & J. Marsman (Eds.), Chromatin: Methods and protocols: Methods in molecular biology (Vol. 2458). (pp. 47-62). New York, NY: Springer. doi: 10.1007/978-1-0716-2140-0_3

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

Chapter in Book - Research

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

Chapter in Book - Research

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

Chapter in Book - Research

Harfoot, R., Lawley, B., Hernández, L. C., Kuang, J., Grant, J., Treece, J. M., LeQueux, S., Day, R., Jack, S., Stanton, J.-A. L., Bostina, M., Ussher, J. E., & Quiñones‑Mateu, M. E. (2022). Characterization of the first SARS-CoV-2 isolates from Aotearoa New Zealand as part of a rapid response to the COVID-19 pandemic. Viruses, 14, 366. doi: 10.3390/v14020366

Journal - Research Article

Hudson, D. T., Bromell, J. S., Day, R. C., McInnes, T., Ward, J. M., & Beck, C. W. (2022). Gene expression analysis of the Xenopus laevis early limb bud proximodistal axis. Developmental Dynamics. Advance online publication. doi: 10.1002/dvdy.517

Journal - Research Article

Jamieson, S. A., Pudjihartono, M., Horne, C. R., Salamanca Viloria, J., Dunlop, J. L., McMillan, H. D., Day, R. C., … Mace, P. D. (2022). Nanobodies identify an activated state of the TRIB2 pseudokinase. Structure. Advance online publication. doi: 10.1016/j.str.2022.08.006

Journal - Research Article

Jeunen, G.-J., von Ammon, U., Cross, H., Ferreira, S., Lamare, M., Day, R., Treece, J., … Gemmell, N. J., & Stanton, J.-A. L. (2022). Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction. Environmental DNA. Advance online publication. doi: 10.1002/edn3.356

Journal - Research Article

Lubbe, P., Rawlence, N. J., Kardailsky, O., Robertson, B. C., Day, R., Knapp, M., & Dussex, N. (2022). Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida). Zoological Journal of the Linnean Society. Advance online publication. doi: 10.1093/zoolinnean/zlac060

Journal - Research Article

Almomani, S. N., Alsaleh, A. A., Weeks, R. J., Chatterjee, A., Day, R. C., Honda, I., … Fukuzawa, R., Slatter, T. L., Hung, N. A., Devenish, C., Morison, I. M., & Macaulay, E. C. (2021). Identification and validation of DNA methylation changes in pre-eclampsia. Placenta, 110, 16-23. doi: 10.1016/j.placenta.2021.05.005

Journal - Research Article

Begemann, A., Sticht, H., Begtrup, A., Vitobello, A., Faivre, L., Siddharth, B., … Day, R., … Sadleir, L. G., … Rauch, A. (2021). 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, 23(3), 543-554. doi: 10.1038/s41436-020-01011-x

Journal - Research Article

Hudson, D. T., Chapman, P. A., Day, R. C., Morgan, X. C., & Beck, C. W. (2021). Complete genome sequences of Kinneretia sp. strain XES5, Shinella sp. strain XGS7, and Vogesella sp. strain XCS3, ssolated from Xenopus laevis skin. Microbiology Resource Announcements, 10(50), e01050-21. doi: 10.1128/mra.01050-21

Journal - Research Article

Lawley, B., Grant, J., Harfoot, R., Treece, J. M., Day, R., Hernández, L. C., Stanton, J.-A. L., Ussher, J. E., & Quiñones‑Mateu, M. E. (2021). Rapid response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a diagnostic test and characterization of the first COVID-19 cases in the South Island. Viruses, 13(11), 2222. doi: 10.3390/v13112222

Journal - Research Article

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. (2021). Hairpin-bisulfite sequencing of cells exposed to decitabine documents the process of DNA demethylation. Epigenetics, 16(11), 1251-1259. doi: 10.1080/15592294.2020.1861169

Journal - Research Article

Smith, J., Banerjee, R., Waly, R., Urbano, A., Gimenez, G., Day, R., Eccles, M. R., Weeks, R. J., & Chatterjee, A. (2021). Locus-specific DNA methylation editing in melanoma cell lines using a CRISPR-based system. Cancers, 13, 5433. doi: 10.3390/cancers13215433

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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. doi: 10.3389/fnmol.2018.00410

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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.

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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 Article

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.

Journal - Research Article

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

Journal - Research Other

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