Alicia Oshlack

Alicia Yinema Kate Nungarai Oshlack[1][4][5] is an Australian bioinformatician and is Co-Head of Computational Biology at the Peter MacCallum Cancer Centre 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]

Alicia Oshlack
Born
Alicia Yinema Kate Nungarai Oshlack[1]

1975 (age 45–46)[2]
Roleystone, Perth, Western Australia.
NationalityAustralian
Alma materUniversity of Melbourne (BSc, PhD)
Known forGenome wide expression profiling
AwardsRuth Stephens Gani Medal (2011), Millennium Award (2015)[3]
Scientific career
Fields
Institutions
ThesisThe central structure of radio quasars (2002)
Websiteoshlacklab.com

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] In 2019 Oshlack was appointed co-Head of Computational Biology at the Peter MacCallum Cancer Centre.[13]

Research

Gene expression analysis

Oshlack's research[4][5][14] 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,[15] normalisation of microarray data,[16] comparative analysis of RNAseq data[17][18] and normalisation of methylation patterns in human DNA beadchip data.[19]

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.[20] Further related work looked at the expression level changes for these factor across multiple human tissues.[21] For this work Alicia Oshlack was awarded the Ruth Gani Medal for Human Genetics from the Australian Academy of Science in 2011.[22]

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.[23] 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.[24]

Personal life

Oshlack's views on work life balance in science[25] and communicating what bioinformaticians do to a general audience at parties[26] 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 - ), Encyclopedia of Australian Science
  3. Lorne Genome Conference - Awards
  4. Alicia Oshlack publications indexed by Google Scholar
  5. Alicia Oshlack's publications indexed by the Scopus bibliographic database. (subscription required)
  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". Archived from the original on 2014-08-14. Retrieved 2014-08-14.
  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". Archived from the original on 2014-08-14. Retrieved 2014-08-14.
  13. "New co-Head of Computational Biology Program appointed". Peter MacCallum Cancer Centre. Retrieved 13 August 2020.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. "Australian Academy of Science - Awardees for 2011". Archived from the original on 2014-04-15. Retrieved 2014-08-14.
  23. Victorian Clinical Genetics Services (VCGS)
  24. 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.
  25. 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.
  26. Oshlack, A. (2013). "A 10-step guide to party conversation for bioinformaticians". Genome Biology. 14: 104. doi:10.1186/gb-2013-14-1-104. PMC 3663102. PMID 23360612.
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