Alicia Oshlack

Alicia Oshlack
Born	Alicia Yinema Kate Nungarai Oshlack[1] 1975 (age 40–41)[2] Roleystone, Perth, Australia.
Nationality	Australian
Fields	Bioinformatics RNA-seq ChIP-seq Clinical genomics[3]
Institutions	University of Melbourne Walter and Eliza Hall Institute Murdoch Childrens Research Institute
Alma mater	University of Melbourne (BSc, PhD)
Thesis	The central structure of radio quasars (2002)
Known for	Genome wide expression profiling
Notable awards	Ruth Stephens Gani Medal (2011), Millennium Award (2015) [4]
Website www.mcri.edu.au/research/core-facilities/bioinformatics

Alicia Yinema Kate Nungarai Oshlack^[1][3][5] is an Australian bioinformatician and is Head of Bioinformatics at the Murdoch Children's Research Institute at the Royal Children's Hospital in Melbourne, Victoria, Australia. She is best known for her work developing methods for the analysis of transcriptome data^[6] as a measure of gene expression. She has characterized the role of gene expression in human evolution by comparisons of humans, chimpanzees, orangutans, and rhesus macaques, and works collaboratively in data analysis to improve the use of clinical sequencing of RNA samples by RNAseq for human disease diagnosis.^[7]

Early Life and Education

Alicia Oshlack was born in Roleystone, Perth in 1975. She graduated dux from Warrnambool College Victoria, Australia in 1993.^[8] She completed a Bachelor of Science (Hons) (1994–98) from the University of Melbourne, majoring in physics. She remained at the University of Melbourne to complete a PhD in astrophysics, which she completed on the topic of the central structure of radio quasars (1999-2003).^[1][9]

Career

Oshlack made a career transition to apply her mathematics to genetics after moving to the Walter and Eliza Hall Institute where she worked as a research officer (2003–07) and then senior research officer (2007–11) in the Bioinformatics Division.^[10] Oshlack moved to the Murdoch Children's Research Institute in Melbourne in 2011 to take up the post of Head of Bioinformatics. She was appointment as the co-chair of the Genomics and Bioinformatics advisory group for The Melbourne Genomics Health Alliance ^[11] in 2013. She was also on the organising committee of Beyond the Genome in 2013.^[12]

Research

Gene Expression Analysis

Oshlack's research^[3][5][13] has focused on methods for the analysis of genome expression, notably computational and statistical analysis of transcriptome data. This includes work on background correction methods for two-colour microarrays,^[14] normalisation of microarray data,^[15] comparative analysis of RNAseq data^[16][17] and normalisation of methylation patterns in human DNA beadchip data.^[18]

Human Evolution

Oshlack's methodology has enabled gene expression levels between humans and other primates to be analysed in an unbiased manner. Her work comparing gene expression levels from liver tissues of five individuals from four different primate species: humans, chimpanzees, orangutans, and rhesus macaques, identified the rapid evolution of transcription factors in humans.^[19] Further related work looked at the expression level changes for these factor across multiple human tissues.^[20] For this work Alicia Oshlack was awarded the Ruth Gani Medal for Human Genetics from the Australian Academy of Science in 2011.^[21]

Clinical Gene Expression Analysis

Oshlack has developed a software pipeline for performing clinical grade analysis of DNA sequencing data for diagnostic purposes. These tools are currently being used for the analysis of sequencing data in the diagnosis of cardiomyopathies at the Victorian Clinical Genetics Service.^[22] She has also developed tools for the analysis of tumour data, specifically detecting mutations caused by rearrangement of the tumour genome resulting in oncogenic fusion genes.^[23]

Personal life

Oshlack's views on work life balance in science^[24] and communicating what bioinformaticians do to a general audience at parties^[25] have been published.

References

1. Oshlack, Alicia Yinema Kate Nungarai. (2015). The central structure of radio quasars (PhD thesis). University of Melbourne.
2. BIOGRAPHICAL ENTRY Oshlack, Alicia (1975 - ), Encylopedia of Australian Science
3. Alicia Oshlack's publications indexed by Google Scholar, a service provided by Google
4. Lorne Genome Conference - Awards
5. Alicia Oshlack's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
6. Oshlack, A; Wakefield, M. J. (2009). "Transcript length bias in RNA-seq data confounds systems biology". Biology Direct 4: 14. doi:10.1186/1745-6150-4-14. PMC 2678084. PMID 19371405.
7. Interview with Alicia Oshlack2013-10-22 on YouTube
8. Australian Academy of Science - Dr Alicia Oshlack
9. Oshlack, A. Y. K. N.; Webster, R. L.; Whiting, M. T. (2002). "Black Hole Mass Estimates of Radio-selected Quasars". The Astrophysical Journal 576 (1): 81–8. arXiv:astro-ph/0205171. Bibcode:2002ApJ...576...81O. doi:10.1086/341729.
10. Women In Astronomy: Career Profiles: Astronomer to Head of Bioinformatics
11. Melbourne Genomics
12. Alicia Oshlack | Beyond the Genome 2013 | Mission Bay | San Francisco
13. Young, M. D.; Wakefield, M. J.; Smyth, G. K.; Oshlack, A (2010). "Gene ontology analysis for RNA-seq: Accounting for selection bias". Genome Biology 11 (2): R14. doi:10.1186/gb-2010-11-2-r14. PMC 2872874. PMID 20132535.
14. Ritchie, M. E.; Silver, J; Oshlack, A; Holmes, M; Diyagama, D; Holloway, A; Smyth, G. K. (2007). "A comparison of background correction methods for two-colour microarrays". Bioinformatics 23 (20): 2700–7. doi:10.1093/bioinformatics/btm412. PMID 17720982.
15. Holloway, A. J.; Oshlack, A; Diyagama, D. S.; Bowtell, D. D.; Smyth, G. K. (2006). "Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis". BMC Bioinformatics 7: 511. doi:10.1186/1471-2105-7-511. PMC 1664592. PMID 17118209.
16. Robinson, M. D.; Oshlack, A (2010). "A scaling normalization method for differential expression analysis of RNA-seq data". Genome Biology 11 (3): R25. doi:10.1186/gb-2010-11-3-r25. PMC 2864565. PMID 20196867.
17. Oshlack, A; Robinson, M. D.; Young, M. D. (2010). "From RNA-seq reads to differential expression results". Genome Biology 11 (12): 220. doi:10.1186/gb-2010-11-12-220. PMC 3046478. PMID 21176179.
18. Maksimovic, J; Gordon, L; Oshlack, A (2012). "SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 Bead Chips". Genome Biology 13 (6): R44. doi:10.1186/gb-2012-13-6-r44. PMC 3446316. PMID 22703947.
19. Gilad, Y.; Oshlack, A.; Smyth, G. K.; Speed, T. P.; White, K. P. (2006). "Expression profiling in primates reveals a rapid evolution of human transcription factors". Nature 440 (7081): 242–245. Bibcode:2006Natur.440..242G. doi:10.1038/nature04559. PMID 16525476.
20. Blekhman, R; Oshlack, A; Chabot, A. E.; Smyth, G. K.; Gilad, Y (2008). "Gene regulation in primates evolves under tissue-specific selection pressures". PLoS Genetics 4 (11): e1000271. doi:10.1371/journal.pgen.1000271. PMC 2581600. PMID 19023414.
21. Australian Academy of Science - Awardees for 2011
22. Victorian Clinical Genetics Services (VCGS)
23. Majewski, I. J.; Mittempergher, L.; Davidson, N. M.; Bosma, A.; Willems, S. M.; Horlings, H. M.; De Rink, I.; Greger, L.; Hooijer, G. K.; Peters, D.; Nederlof, P. M.; Hofland, I.; De Jong, J.; Wesseling, J.; Kluin, R. J.; Brugman, W.; Kerkhoven, R.; Nieboer, F.; Roepman, P.; Broeks, A.; Muley, T. R.; Jassem, J.; Niklinski, J.; Van Zandwijk, N.; Brazma, A.; Oshlack, A.; Van Den Heuvel, M.; Bernards, R. (2013). "Identification of recurrentFGFR3fusion genes in lung cancer through kinome-centred RNA sequencing". The Journal of Pathology 230 (3): 270–276. doi:10.1002/path.4209.
24. Dean, Caroline; Osborn, Mary; Oshlack, Alicia; Thornton, Janet (2012). "Women in science". Genome Biology 13 (3): 148. doi:10.1186/gb4005. PMC 3439960. PMID 22405408.
25. Oshlack, A. (2013). "A 10-step guide to party conversation for bioinformaticians". Genome Biology 14: 104. doi:10.1186/gb-2013-14-1-104. PMID 23360612.