Helena Oakey

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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	Al-Tamimi, N., Oakey, H., Tester, M., & Negrão, S. (2021). Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. Methods in molecular biology (Clifton, N.J.), 2238, 339-375. 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
  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 Scopus4 WoS4 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
  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	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 Scopus5 WoS5 Europe PMC5
  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 Scopus8 WoS6 Europe PMC3
  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 Scopus82 WoS77 Europe PMC52
  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 Scopus37 WoS36 Europe PMC19
  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 Scopus40 WoS39 Europe PMC28
  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 Scopus54 WoS52 Europe PMC38
  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 Scopus38 WoS34 Europe PMC18
  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 Scopus35 WoS33 Europe PMC23
  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	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 Scopus82 WoS74 Europe PMC52
  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 Scopus30 WoS27 Europe PMC16
  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
  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 Scopus8
  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
  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 Scopus146 WoS138 Europe PMC95
  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 Scopus42 WoS40 Europe PMC22
  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 Scopus114 WoS112 Europe PMC55
  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 Scopus43 WoS42
  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 Scopus77 WoS83
  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 Scopus31 WoS28
  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
  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., & 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 Scopus156
  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.
  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 in Arabidopsis thaliana. 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.

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
  2017	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

• Mentoring

  Date	Topic	Location	Name
  2017 - ongoing	Assessment of Nitrogen and Water co-limitation by remote sensing	University of Adelaide/South Australian Research and Development (SARDI)	Fabio Arsego

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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

• Email: helena.oakey@adelaide.edu.au