Helena Oakey

Helena Oakey

Adelaide Medical School

Faculty of Health and Medical Sciences

Eligible to supervise Masters and PhD - email supervisor to discuss availability.

Helena is working as a Senior Research Fellow with the ENDIA T1D study. Her expertise includes advanced knowledge of the design and analysis of agronomic trials, laboratory experiments and health science studies (eg. clinical trials and cohort studies).  Her research interests cover the development and improvement of statistical genetic methodology, including genomic selection and association mapping. She has a particular interest in the design and analysis of 'omics studies.

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  • Appointments
    Date Position Institution name
    2019 Senior Research Fellow University of Adelaide
    2017 - 2020 Senior Research Fellow University of Adelaide
    2015 - 2016 Senior Statistician Biomathematics and Statistics Scotland, Edinburgh
    2010 - 2016 Senior Biological Statistician University of Dundee/James Hutton Institute

  • Education
    Date Institution name Country Title
    2008 University of Adelaide Australia PhD
    1998 University of Southampton United Kingdom MSc Statistics with Applications in Medicine
    1994 University of Southampton United Kingdom BSc (Hons) Mathematics with Statistics

  • Research Interests
    Agriculture Applied Statistics Genomics
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  • Journals
    Year Citation
    2021 Awlia, M., Alshareef, N., Saber, N., Korte, A., Oakey, H., Panzarová, K., . . . Julkowska, M. M. (2021). Genetic mapping of the early responses to salt stress in Arabidopsis thaliana. Plant Journal, 107(2), 544-563.
    DOI
    2021 Penno, M. A., Anderson, A. J., Thomson, R. L., McGorm, K., Barry, S. C., Colman, P. G., . . . ENDIA Study Group. (2021). Evaluation of protocol amendments to the Environmental Determinants of Islet Autoimmunity (ENDIA) study during the COVID-19 pandemic. Diabetic medicine : a journal of the British Diabetic Association, 38(11), e14638-1-e14638-4.
    DOI Europe PMC1
    2021 Facy, M. L., Hebart, M. L., Oakey, H., McEwin, R. A., Popplewell, G. I., & Pitchford, W. S. (2021). Evaluation of dominance in tropically adapted composite beef cattle. Animal Production Science, 7 pages.
    DOI
    2021 Roth-Schulze, A. J., Penno, M. A. S., Ngui, K. M., Oakey, H., Bandala-Sanchez, E., Smith, A. D., . . . Harrison, L. C. (2021). Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome. Microbiome, 9(1), 21 pages.
    DOI
    2021 McEwin, R. A., Hebart, M. L., Oakey, H., & Pitchford, W. S. (2021). Within-breed selection is sufficient to improve terminal crossbred beef marbling: A review of reciprocal recurrent genomic selection. Animal Production Science, 9 pages.
    DOI
    2021 Hope, C. M., Huynh, D., Wong, Y. Y., Oakey, H., Perkins, G. B., Nguyen, T., . . . Barry, S. C. (2021). Optimization of blood handling and peripheral blood mononuclear cell cryopreservation of low cell number samples. International Journal of Molecular Sciences, 22(17), 9129-1-9129-19.
    DOI
    2021 Stanschewski, C. S., Rey, E., Fiene, G., Craine, E. B., Wellman, G., Melino, V. J., . . . Tester, M. (2021). Quinoa phenotyping methodologies: An international consensus. Plants, 10(9), 52 pages.
    DOI
    2020 Penno, M. A., Oakey, H., Augustine, P., Taranto, M., Barry, S. C., Colman, P. G., . . . Couper, J. J. (2020). Changes in pancreatic exocrine function in young at-risk children followed to islet autoimmunity and type 1 diabetes in the ENDIA study. Pediatric Diabetes, 21(6), 945-949.
    DOI WoS1 Europe PMC1
    2020 Houston, K., Jiaen, Q., Wege, S., Oakey, H., Hrmova, M., Qu, Y., . . . Waugh, R. (2020). Barley sodium content is regulated by natural variants of the Na+ transporter HvHKT1;5. Communications Biology, 3(1), 258-1-258-9.
    DOI Scopus6 WoS6 Europe PMC2
    2020 Barakate, A., Keir, E., Oakey, H., & Halpin, C. (2020). Stimulation of homologous recombination in plants expressing heterologous recombinases. BMC plant biology, 20(1), 336.
    DOI Scopus1 WoS2 Europe PMC1
    2020 Nguyen, D. T., Gomez, L. D., Harper, A., Halpin, C., Waugh, R., Simister, R., . . . McQueen-Mason, S. J. (2020). Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw. BIOTECHNOLOGY FOR BIOFUELS, 13(1), 16 pages.
    DOI
    2019 Daly, P., McClellan, C., Maluk, M., Oakey, H., Lapierre, C., Waugh, R., . . . Halpin, C. (2019). RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. Plant Biotechnology Journal, 17(3), 594-607.
    DOI Scopus12 WoS13 Europe PMC6
    2019 Ward, B., Brien, C., Oakey, H., Pearson, A., Negrão, S., Schilling, R. K., . . . Van Den Hengel, A. (2019). High‐throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare). The Plant Journal, 98(3), 555-570.
    DOI Scopus7 WoS6 Europe PMC6
    2016 Saade, S., Maurer, A., Shahid, M., Oakey, H., Schmöckel, S., Negraõ, S., . . . Tester, M. (2016). Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Scientific Reports, 6(1), 32586-1-32586-9.
    DOI Scopus55 WoS51 Europe PMC34
    2016 Al-Tamimi, N., Brien, C., Oakey, H., Berger, B., Saade, S., Ho, Y., . . . Negrão, S. (2016). Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communications, 7(1), 13342-1-13342-11.
    DOI Scopus108 WoS97 Europe PMC57
    2016 Oakey, H., Cullis, B., Thompson, R., Comadran, J., Halpin, C., & Waugh, R. (2016). Genomic selection in multi-environment crop trials. G3: Genes, Genomes, Genetics, 6(5), 1313-1326.
    DOI Scopus44 WoS43 Europe PMC23
    2015 Phillips, D., Jenkins, G., Macaulay, M., Nibau, C., Wnetrzak, J., Fallding, D., . . . Ramsay, L. (2015). The effect of temperature on the male and female recombination landscape of barley. New Phytologist, 208(2), 421-429.
    DOI Scopus65 WoS63 Europe PMC47
    2014 Barakate, A., Higgins, J., Vivera, S., Stephens, J., Perry, R., Ramsay, L., . . . Halpin, C. (2014). The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley. Plant Cell, 26(2), 729-740.
    DOI Scopus44 WoS42 Europe PMC32
    2014 Houston, K., Russell, J., Schreiber, M., Halpin, C., Oakey, H., Washington, J., . . . Waugh, R. (2014). A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys. BMC Genomics, 15(1), 907-1-907-15.
    DOI Scopus46 WoS40 Europe PMC21
    2013 Oakey, H., Shafiei, R., Comadran, J., Uzrek, N., Cullis, B., Gomez, L., . . . Halpin, C. (2013). Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling. Biotechnology for Biofuels, 6(1), 185-1-185-12.
    DOI Scopus11 WoS11 Europe PMC8
    2012 Dodd, J. M., Crowther, C. A., Haslam, R. R., & Robinson, J. S. (2012). Elective birth at 37 weeks of gestation versus standard care for women with an uncomplicated twin pregnancy at term: the Twins Timing of Birth Randomised Trial. Obstetrical and Gynecological Survey, 67(11), 675-676.
    DOI
    2012 Crowther, C., Dodd, J., Hiller, J., Haslam, R., & Robinson, J. (2012). Planned vaginal birth or elective repeat caesarean: patient preference restricted cohort with nested randomised trial. PLoS Medicine, 9(3), 1-10.
    DOI Scopus86 WoS76 Europe PMC54
    2012 Grivell, R., Reilly, A., Oakey, H., Chan, A., & Dodd, J. (2012). Maternal and neonatal outcomes following induction of labor: a cohort study. Acta Obstetricia et Gynecologica Scandinavica, 91(2), 198-203.
    DOI Scopus33 WoS30 Europe PMC18
    2011 Evans, K., Gomez, D., Jones, M., Oakey, H., & Roush, R. (2011). Pathogenicity of Phragmidium violaceum isolates on European blackberry clones and on leaves of different ages. Plant Pathology, 60(3), 532-544.
    DOI Scopus9
    2010 Gillman, M., Oakey, H., Baghurst, P., Volkmer, R., Robinson, J., & Crowther, C. (2010). Effect of treatment of gestational diabetes mellitus on obesity in the next generation. Diabetes Care, 33(5), 964-968.
    DOI Scopus163 WoS156 Europe PMC104
    2010 Middleton, P. F., Crowther, C. A., Doyle, L. W., Bubner, T., Oakey, H., Morris, J., . . . Flenady, V. (2010). S44– Rapid development and implementation of guidelines for infant neuroprotection with antenatal magnesium sulfate (MgSO4). Otolaryngology–Head and Neck Surgery, 143(1_suppl), 33-34.
    DOI
    2007 Oakey, H., Verbyla, A., Cullis, B., Wei, X., & Pitchford, W. (2007). Joint modeling of additive and non-additive (genetic line) effects in multi-environment trials. Theoretical and Applied Genetics, 114(8), 1319-1332.
    DOI Scopus47 WoS46 Europe PMC24
    2006 Oakey, H., Verbyla, A., Pitchford, W., Cullis, B., & Kuchel, H. (2006). Joint modeling of additive and non-additive genetic line effects in single field trials. Theoretical and Applied Genetics, 113(5), 809-819.
    DOI Scopus120 WoS117 Europe PMC58
    2005 Skouroumounis, G., Kwiatkowski, M., Francis, I., Oakey, H., Capone, D., Peng, Z., . . . Waters, E. (2005). The influence of ascorbic acid on the composition, colour and flavour properties of a Riesling and a wooded Chardonnay wine during five years' storage. Australian Journal of Grape and Wine Research, 11(3), 355-368.
    DOI Scopus47 WoS45
    2005 Skouroumounis, G., Kwiatkowski, M., Francis, I., Oakey, H., Capone, D., Duncan, B., . . . Waters, E. (2005). The impact of closure type and storage conditions on the composition, colour and flavour properties of a Riesling and a wooded Chardonnay wine during five years' storage. Australian Journal of Grape and Wine Research, 11(3), 369-377.
    DOI Scopus83 WoS89
    2005 John, S., Wicks, T., Hunt, J., Lorimer, M., Oakey, H., & Scott, E. (2005). Protection of grapevine pruning wounds from infection by Eutypa lata using Trichoderma harzianum and Fusarium lateritium. Australasian Plant Pathology, 34(4), 569-575.
    DOI Scopus34 WoS31
    2004 Zhu, B., Walker, S., Oakey, H., Setchell, B., & Maddocks, S. (2004). Effect of paternal heat stress on the development in vitro of preimplantation embryos in the mouse. Andrologia, 36(6), 384-394.
    DOI Scopus40 Europe PMC25
    2001 Barker, D., Capone, D., Pollnitz, A., McLean, H., Francis, I., Oakey, H., & Sefton, M. (2001). Absorption of 2,4,6-trichloroanisole by wine corks via the vapour phase in an enclosed environment. Australian Journal of Grape and Wine Research, 7(1), 40-46.
    DOI Scopus27 WoS27
    2000 Soden, A., Francis, I. L., & Oakey, H. (2000). The effect of mixed yeast species fermentation on the composition and aroma of chardonnay wine.. Australian Journal of Grape and Wine Research, 6, 21-30.
    2000 Soden, A., Francis, I. L., Oakey, H., & Henschke, P. A. (2000). Effects of co-fermentation with Candida stellata and Saccharomyces cerevisiae on the aroma and composition of Chardonnay wine. Australian Journal of Grape and Wine Research, 6(1), 21-30.
    DOI Scopus167
    1992 Carey, A. H., Claussen, U., L�decke, H. -J., Horsthemke, B., Ellis, D., Oakey, H., . . . Scambler, P. J. (1992). Interstitial deletions in DiGeorge syndrome detected with microclones from 22q11. Mammalian Genome, 3(2), 101-105.
    DOI
    — Awlia, M., Alshareef, N., Saber, N., Korte, A., Oakey, H., Panzarová, K., . . . Julkowska, M. M. (n.d.). Genetic mapping of the early responses to salt stress inArabidopsis thaliana.
    DOI
    — McGorm, K. J., Brown, J. D., Thomson, R. L., Oakey, H., Moore, B., Hendry, A. B., . . . Penno, M. A. S. (n.d.). A long-term evaluation of Facebook for recruitment and retention in the ENDIA type 1 diabetes pregnancy-birth cohort study (Preprint).
    DOI

  • Book Chapters
    Year Citation
    2021 Al-Tamimi, N., Oakey, H., Tester, M., & Negrão, S. (2021). Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping.. In J. M. Walker (Ed.), Rice Genome Engineering and Gene Editing (Vol. 2238, pp. 339-375). United States: Springer.
    DOI

  • Report for External Bodies
    Year Citation
    2010 Crowther, C., Middleton, P., Bubner, T., & Oakey, H. (2010). Antenatal magnesium sulphate for neeroprotection guideline development panel.

BBSRC Other countries partnering awards: Australia-UK Interdisciplinary partnership to speed cereal breeding 2016

 

Short courses and workshops I have prepared and taught
Experimental design and analysis of variance using R (2016)

A two day course which introduces the principals of experimental design and analysis of experiments with practical examples using R. Aimed at post-graduates and researchers.

Introduction to simple designs and their analysis (2015)

A half day course that introduces simple designs such as CRD, RCBD and split plot: why design is important, how to generate and analyse them in R using relevant examples. Aimed at scientists.

Introduction to spatial designs for field trials and their analysis (2015)

A half day course that introduces spatial designs such as unreplicated, partially replicated and row-column designs: why design is important, how to generate and analyse them in R and ASReml. Aimed at scientists.

Association mapping in R (2015)

A half day course that introduces Association mapping with interactive lectures and practical sessions so that by the end of the course participants should feel confident in performing an Association mapping analysis on their own data using GAPIT. Aimed at scientists.

Introduction to Medical Statistics (2008-2010)

A series of one hour interactive lectures/workshops for clinical trials departmental staff with little or no experience of statistics. These included data cleaning, introduction to randomised control trials, means and standard deviation, p-values and confidence intervals and the principles of the analysis of randomised control trials. Aimed at wide audience.

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  • Current Higher Degree by Research Supervision (University of Adelaide)
    Date Role Research Topic Program Degree Type Student Load Student Name
    2020 Co-Supervisor Using existing private data set containing both genotypes and phenotypes for growth, fertility, carcase and novel traits investigate heterosis and effects of sperm traits in composite cattle. Doctor of Philosophy Doctorate Full Time Miss Maddie Louise Facy
    2019 Co-Supervisor Genomic Selection in Barley Doctor of Philosophy Doctorate Full Time Mrs Silvina Baraibar Pedersen

  • Past Higher Degree by Research Supervision (University of Adelaide)
    Date Role Research Topic Program Degree Type Student Load Student Name
    2017 - 2021 Co-Supervisor Genomic Selection for High Quality Beef Production Doctor of Philosophy Doctorate Full Time Miss Rudi Adrianna McEwin

  • Other Supervision Activities
    Date Role Research Topic Location Program Supervision Type Student Load Student Name
    2015 - 2020 Co-Supervisor Genomic selection for accelerated barley breeding University of Dundee — Doctorate Full Time Ruth Hamilton
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  • Committee Memberships
    Date Role Committee Institution Country
    2019 - ongoing Council Statistical Society of Australia -SA Branch University ofAdelaide Australia

  • Memberships
    Date Role Membership Country
    2018 - ongoing Member Statistical Society of Australia Australia
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