The Walter and Eliza Hall Institute of Medical Research

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 Interests

• Linear models for microarray data
• Digital gene expression technologies
• Detection of molecular pathways
• Bioinformatics resources for medical research

Selected Publications

1. 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]
2. 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]
3. 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]
4. 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]
5. 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]
6. 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]
7. 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]
8. 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]
9. 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

Laboratory Head: Gordon Smyth BSc(Hons) UWA PhD ANU

Senior Postdoctoral Fellow: Matthew Ritchie BAppSc(Hons) Qld PhD Melbourne

Senior Postdoctoral Fellow: Wei Shi BECompEng Harbin MS Harbin PhD Harbin

Research Assistant: Yang Liao Melbourne BCompSc Tsinghua

Research Assistant: Cynthia Liu BSc Melbourne

Postgraduate Student: Andy Chen BSc(Hons) Melbourne

Postgraduate Student: Joshy George ME Bangalore

Postgraduate Student: Charity Law BSc(Hons) Melbourne

Postgraduate Student: Aaron Lun BSc(Hons) Sydney

Postgraduate Student: Belinda Phipson BSc(Hons) KwaZulu-Natal MSc KwaZulu-Natal

Undergraduate Student: Jenny Dai

Administrative Officer: Maria Markovic BA RMIT DipEd LaTrobe

Senior Programmer: Keith Satterley BSc Melbourne DipEd Melbourne DipCompSci LaTrobe

Software Engineer: Yifang Hu BESoftEng Melbourne BSc Melbourne