Associate Professor Gordon Smyth
Details
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Division: Bioinformatics
Research Overview
Statistical functional genomics in experimental medicine
The genome projects and the accelerated development of high-throughput genomic technologies such as microarrays have revolutionised biology. Making the most of this revolution requires the marriage of researchers from mathematical and biological backgrounds.
In experimental medicine, high-throughput technologies are used in carefully designed experiments. A biological system is perturbed and the resulting expression changes are measured. Designed expression experiments are typically small but complex, with few biological replicates but with multiple experimental factors at varying levels. My lab develops powerful statistical paradigms for analysing these experiments in statistically rigorous ways. This takes us along an exciting path where sophisticated statistical concepts like information borrowing, multivariate analysis and pattern recognition enable insights into molecular pathways and gene function.
Research Projects
Linear models for microarray data
Digital gene expression technologies
Detection of molecular pathways
Bioinformatics resources for medical research
Major Publications
- Smyth GK, Yang YH, Speed T.
Statistical issues in cDNA microarray data analysis.
Methods Mol Biol. 2003;224:111-36 PMID: 12710670 [PubMed - indexed for MEDLINE] - Smyth GK.
Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
Stat Appl Genet Mol Biol. 2004;3:Article3 PMID: 16646809 [PubMed] - Smyth GK, Michaud J, Scott HS.
Use of within-array replicate spots for assessing differential expression in microarray experiments.
Bioinformatics. 2005 May 1;21(9):2067-75 PMID: 15657102 [PubMed - indexed for MEDLINE] - Peart MJ, Smyth GK, van Laar RK, Bowtell DD, Richon VM, Marks PA, Holloway AJ, Johnstone RW.
Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors.
Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3697-702 PMID: 15738394 [PubMed - indexed for MEDLINE] - Shackleton M, Vaillant F, Simpson KJ, Stingl J, Smyth GK, Asselin-Labat ML, Wu L, Lindeman GJ, Visvader JE.
Generation of a functional mammary gland from a single stem cell.
Nature. 2006 Jan 5;439(7072):84-8 PMID: 16397499 [PubMed - indexed for MEDLINE] - Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP.
Expression profiling in primates reveals a rapid evolution of human transcription factors.
Nature. 2006 Mar 9;440(7081):242-5 PMID: 16525476 [PubMed - indexed for MEDLINE] - Ritchie ME, Diyagama D, Neilson J, van Laar R, Dobrovic A, Holloway A, Smyth GK.
Empirical array quality weights in the analysis of microarray data.
BMC Bioinformatics. 2006 May 19;7:261 PMID: 16712727 [PubMed - indexed for MEDLINE] - Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK.
A comparison of background correction methods for two-colour microarrays.
Bioinformatics. 2007 Oct 15;23(20):2700-7 PMID: 17720982 [PubMed - indexed for MEDLINE] - Robinson MD, Smyth GK.
Moderated statistical tests for assessing differences in tag abundance.
Bioinformatics. 2007 Nov 1;23(21):2881-7 PMID: 17881408 [PubMed - indexed for MEDLINE]
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Current Laboratory Members
Faculty Member: Gordon Smyth, BSc(Hons) UWA PhD ANU
Scientific Coordinator/Alliance Manager: Fiona McGrath, BAppSc(Hons) RMIT (Jointly with Molecular Medicine Division)
Administrative Assistant: Maria Markovic, BA RMIT DipEd LaT (Jointly with Molecular Medicine Division)
Senior Postdoctoral Fellow: Alicia Oshlack, BSc(Hons) PhD Melb
Postdoctoral Fellow: Matthew Ritchie, BSc(Hons) Central Qld PhD Melb
Postdoctoral Fellow: Wei Shi, BE MS PhD Harbin
Computational Scientist: Yifang Hu, BESoftEng BSc Melb
Computational Scientist: Keith Satterley, BSc Melb DipCompSci LaT DipEd Melb
Computational Scientist: Matt Young, BA(Hons) BSc(Hons) Melb
Postgraduate Student: Carolyn de Graaf, BInfTech Swinburne BBiomedSc BSc(Hons) Melb (Jointly with Molecular Medicine Division)
Postgraduate Student: Charity Law, BSc(Hons) Melb
Postgraduate Student: Joshy George, ME Bangalore
Postgraduate Student: Belinda Phipson, BSc(Hons) MSc KwaZulu-Natal
Postgraduate Student: Di Wu, MSc Case Western Reserve
Visiting BSc(Honours) Student: Davis McCarthy, BA BSc Melb