Helena Oakey

Adelaide Medical School

Faculty of Health and Medical Sciences

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

My Research
Career
Publications
Grants and Funding
Teaching
Supervision
Professional Activities
Contact

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.

Appointments

Date	Position	Institution name
2019 - ongoing	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 Child and Adolescent Health Pregnancy and Birth

Journals

Year	Citation
2022	Wentworth, J. M., Oakey, H., Craig, M. E., Couper, J. J., Cameron, F. J., Davis, E. A., . . . Harrison, L. C. (2022). Decreased occurrence of ketoacidosis and preservation of beta cell function in relatives screened and monitored for type 1 diabetes in Australia and New Zealand. Pediatric Diabetes, 23(8), 1594-1601. DOI
2022	Bandala-Sanchez, E., Roth-Schulze, A. J., Oakey, H., Penno, M. A. S., Bediaga, N. G., Naselli, G., . . . ENDIA Study Group. (2022). Women with type 1 diabetes exhibit a progressive increase in gut Saccharomyces cerevisiae in pregnancy associated with evidence of gut inflammation.. Diabetes research and clinical practice, 184, 109189. DOI Scopus2
2022	Hall, M., Oakey, H., Penno, M. A. S., McGorm, K., Anderson, A. J., Ashwood, P., . . . Cavenett, L. (2022). Mental Health During Late Pregnancy and Postpartum in Mothers With and Without Type 1 Diabetes: The ENDIA Study. Diabetes Care, 45(5), 1082-1090. DOI Scopus1 WoS1
2022	McGorm, K. J., Brown, J. D., Thomson, R. L., Oakey, H., Moore, B., Hendry, A., . . . Penno, M. A. S. (2022). A Long-Term Evaluation of Facebook for Recruitment and Retention in the ENDIA Type 1 Diabetes Pregnancy-Birth Cohort Study. Journal of Diabetes Science and Technology, 19322968221079867. DOI
2022	McEwin, R. A., Hebart, M. L., Oakey, H., Tearle, R., Grose, J., Popplewell, G., & Pitchford, W. S. (2022). Comparison of Methods to Select Candidates for High-Density Genotyping; Practical Observations in a Cattle Breeding Program. Agriculture (Switzerland), 12(2), 10 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 Scopus1
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), 1-52. DOI Scopus8 WoS8 Europe PMC5
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.. The Plant journal : for cell and molecular biology, 107(2), 544-563. DOI Scopus7 WoS7 Europe PMC4
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, 38(11), e14638-1-e14638-4. DOI Europe PMC1
2021	Facy, M. L., Hebart, M. L., Oakey, H., McEwin, R. A., Popplewell, G., & Pitchford, W. S. (2021). Evaluation of dominance in tropically adapted composite beef cattle. Animal Production Science, 61(18), 1811-1817. 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), 167-1-167-21. DOI Scopus16 WoS15 Europe PMC9
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 Scopus2 WoS2 Europe PMC2
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 Scopus14 WoS14 Europe PMC4
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 Scopus5 WoS5 Europe PMC3
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 Scopus3 WoS3 Europe PMC1
2020	Awlia, M., Alshareef, N., Saber, N., Korte, A., Oakey, H., Panzarová, K., . . . Julkowska, M. M. (2020). Genetic mapping of the early responses to salt stress in Arabidopsis thaliana. 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 Scopus22 WoS20 Europe PMC9
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 Scopus10 WoS8 Europe PMC7
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 Scopus71 WoS67 Europe PMC43
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 Scopus136 WoS124 Europe PMC76
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 Scopus58 WoS55 Europe PMC32
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 Scopus79 WoS78 Europe PMC59
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 Scopus56 WoS53 Europe PMC41
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 Scopus54 WoS50 Europe PMC24
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 Scopus98 WoS89 Europe PMC63
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 Scopus36 WoS32 Europe PMC19
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 Scopus10
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 Scopus187 WoS175 Europe PMC122
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(S1), 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 Scopus56 WoS55 Europe PMC32
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 Scopus141 WoS138 Europe PMC70
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 Scopus57 WoS51
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 Scopus97 WoS96
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 Scopus42 WoS39
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 Scopus41 WoS39 Europe PMC26
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 Scopus30 WoS29
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 Scopus178
1992	Carey, A. H., Claussen, U., Lüdecke, 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 Scopus16 WoS17 Europe PMC11
-	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
-	Facy, M. L., Hebart, M. L., Oakey, H., McEwin, R. A., & Pitchford, W. S. (n.d.). Genetic Correlations between Days to Calving across Joinings and Lactation Status in a Tropically Adapted Composite Beef Herd. Agriculture, 13(1), 37. DOI
-	Shafiei, R., Hooper, M., McClellan, C., Oakey, H., Stephens, J., Lapierre, C., . . . Halpin, C. (n.d.). Downregulation of barley ferulate 5-hydroxylase dramatically alters straw lignin structure without impact on mechanical properties. Frontiers in Plant Science, 13. DOI

Books

Year Citation
2021 Rice Genome Engineering and Gene Editing (2021). . Springer US.
DOI
2021 Rice Genome Engineering and Gene Editing (2021). . Springer US.
DOI

Year	Citation
2021	Rice Genome Engineering and Gene Editing (2021). . Springer US. DOI
2021	Rice Genome Engineering and Gene Editing (2021). . Springer US. 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 Scopus3 Europe PMC2

Conference Papers

Year	Citation
2022	Haynes, A., Tully, A., Smith, G. J., Penno, M. A. S., Craig, M. E., Wentworth, J. M., . . . Davis, E. A. (2022). Continuous glucose monitoring identifies early dysglycaemia in very young children at risk of type 1 diabetes being followed in the Australian ENDIA pregnancy cohort study. In DIABETOLOGIA Vol. 65 (pp. S173-S174). Stockholm, SWEDEN: SPRINGER.
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. In ANIMAL PRODUCTION SCIENCE Vol. 61 (pp. 1751-1759). Clayton, Victoria: CSIRO PUBLISHING. DOI Scopus1 WoS1

Report for External Bodies

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

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

2023 - 2025 Leona M. and Harry B. Helmsley Charitable Trust Research Grant (3-SRA-2023-1374-M-N) "ENDIA Follow Up" (Couper, J.; Penno, M.; Craig, M.; Wentworth, J.; Colman, P.; Harrison, L.; Davis, E.; Haynes, A.; Harris, M.; Soldatos, G.; Oakey, H.; Sinnott, R.; Thomson, R.; McGorm, K.; Vuillermin, P. AUD$8,977,646
2021-2023 JDRFA Research Grant "Using 3D genomics to functionally connect genetic risk of Type 1 diabetes to the genes that drive loss of immune tolerance" (Barry S, Wong Y, Penno M, Sadlon T, Couper J, Breen J, Oakey H). AUD$505,085
2021-2023 Leona M. and Harry B. Helmsley Charitable Trust - Research Grant (R-2103-05117) "Environmental determinants of islet autoimmunity (ENDIA) Expanded Support" (Penno M, Couper J, Oakey H Thomson R, Ashwood P, Brown J, Sinnott R, Harrison L, Colman P, Wentworth J, Soldatos, G, Vuillermin P, Craig M, Rawlinson W, Harris M, Davis E, Haynes A) AUD$1,428,543
2021-2023 Leona M. and Harry B. Helmsley Charitable Trust - Research Grant (R-2112-04908) "Environmental determinants of islet autoimmunity (ENDIA) Science Continuation " (Couper J, Penno M, Harrison L, Craig M, Oakey H, Kim K, Rawlinson W, Morahan G) AUD$2,067,727
2011-2013 NHMRC (51301001) "Prenatal repeat corticosteroids in women at risk of preterm birth for improving neonatal health - an individual patient data review" (Crowther C, Askie L, Oakey H, Middleton P) AUD$447,280
2010-2011 NHMRC "Magnesium sulphate in women at risk of preterm birth for fetal neuroprotection - an individual patient data review" (Crowther C, Doyle L, Middleton P, Oakey H, Askie L) AUD$268,751

Short courses and workshops I have prepared and taught

Experimental design and analysis of variance using R

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

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

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

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

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.

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

Committee Memberships

Date	Role	Committee	Institution	Country
2020 - ongoing	Member	ENDIA Steering Committee	University of Adelaide	Australia
2020 - 2023	Member	Women's & Children's Health Network HREC committee	Women's and Children's Hospital	Australia
2019 - ongoing	Council	Statistical Society of Australia -SA Branch	University of Adelaide	Australia

Memberships

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

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

Email: helena.oakey@adelaide.edu.au