/ Home

Publications

Publications prior to 2003

2003

Smyth, G. K., Yang, Y.-H., Speed, T. P. (2003). Statistical issues in cDNA microarray data analysis. Methods in Molecular Biology 224, 111-136. [PubMed Abstract] [Publisher Full Text] [Preprint PDF] (Published March 2003)
Smyth, G. K. (2003). Pearson's goodness of fit statistic as a score test statistic. In: Science and Statistics: A Festschrift for Terry Speed, D. R. Goldstein (ed.), IMS Lecture Notes - Monograph Series, Volume 40, Institute of Mathematical Statistics, Beachwood, Ohio, pages 115-126. [Preprint PDF] (Published March 2003)
Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273. [PubMed Abstract] [Publisher Full Text] [Preprint PDF] (Published December 2003)

2004

Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3. [Publisher Full Text] [Reprint PDF with corrections] (Published Feb 2004)
Elso, C. M., Roberts, L. J., Smyth, G. K., Thomson, R. J., Baldwin, T. M., Foote, S. J., and Handman, E. (2003). Leishmaniasis host response loci (lmr1–3) modify disease severity through a Th1/Th2-independent pathway. Genes and Immunity 5, 93-100. (Published 1 Mar 2004)
Elso, C., Kumar, B., Smyth, G. K., Foote, S., and Handman, E. (2004). Dissociation of disease susceptibility, inflammation and cytokine profile in lmr1/2 congenic mice infected with Leishmania major. Genes and Immunity 5, 188-196. (Published 1 May 2004)
Domenighetti, A. A., Ritchie, M., Smyth, G., Pedrazzini, T., Proietto, J., Delbridge. L. M. D. (2004). Gene expression profiling reveals distinct sets of genes altered during hormonally and metabolically induced cardiac hypertrophies. Journal of Molecular and Cellular Cardiology 37 (1), 303-304. (Meeting abstract, Published July 2004)
Beissbarth, T., Hyde, L., Smyth, G. K., Job, C., Boon, W. M., Tan, S. S., Scott, H. S., Speed, T. P. (2004). Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics 20 Supplement 1, i31-i39. DOI: 10.1093/bioinformatics/bth924 [Publisher Full Text] (Published Aug 2004)
Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706. [Publisher Full Text] (Published 5 Aug 2004)
Gentleman, R. C., Cary, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A. J., Sawitzki, G., Smith, C., Smyth, G. K., Tierney, L., Yang, J. Y. H., and Zhang, J. (2004). Bioconductor: a software development project. Genome Biology 5, R80. [Publisher Full Text] (Published 15 Sep 2004)
Podlich, H. M., Faddy, M. J., and Smyth, G. K. (2004). Semi-parametric extended Poisson process models. Statistics and Computing 14, 311-321. [Preprint PDF] (Published Oct 2004)
Smyth, G. K. (2004). Numerical analysis. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 3762-3767. (Published Oct 2004)
Smyth, G. K. (2004). Numerical integration. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 3766-3773. (Published Oct 2004)
Smyth, G. K. (2004). Optimization and nonlinear equations. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 3857-3863. (Published Oct 2004)
Smyth, G. K. (2004). Polynomial approximation. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 4136-4140. (Published Oct 2004)
Boon, W.-M., Beissbarth, T., Hyde, L., Smyth, G. K., Gunnersen, J., Denton, D. A., Scott, H., and Tan, S.-S. (2004). A comparative analysis of transcribed genes in the mouse hypothalamus and neocortex reveals chromosomal clustering. PNAS 101, 14972–14977. [Publisher Full Text] (Published 12 Oct 2004)

2005

Cox, M. E., Moss, A., and Smyth, G. K. (2005). Water quality condition and trend in North Queensland waterways. Marine Pollution Bulletin 51, 89-98. (doi:10.1016/j.marpolbul.2004.10.039) (Published March 2005)
Peart, M. J., Smyth, G. K., van Laar, R. K., Richon, V. M., Holloway, A. J., Johnstone, R. W. (2005). Identification and functional significance of genes regulated by structurally diverse histone deacetylase inhibitors. Proceedings of the National Academy of Sciences of the United States of America 102, 3697-3702. [Publisher Full Text] (Published 8 March 2005)
Smyth, G. K. (2005). Individual channel analysis of two-colour microarray data. Invited Session IPM 11: Computational Tools For Microarray Analysis, 55th Session of the International Statistics Institute, 5-12 April 2005, Sydney Convention & Exhibition Centre, Sydney, Australia (CD Paper 116). (PDF) (Published 5 April 2005)
Smyth, G. K., Michaud, J., and Scott, H. (2005). The use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21(9), 2067-2075. (Supplementary Information, Online, PDF, Errata) (Published 1 May 2005) (Recommended by Biology Faculty of 1000)
Beißbarth, T., Tye-Din, J. A., Smyth, G. K., Speed, T. P., and Anderson, R. P. (2005). A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. Bioinformatics 21 (Supplement 1), i29-i37. (Online) (Published 7 June 2005)
Dwyer, J. P., Ritchie, M. E., Smyth, G. K., Delbridge, L. M., Domenighetti, A. A., Harrap, S. B., and Di Nicolantonio, R. (2005). Differentially expressed genes in cardiac tissue from the hypertrophic heart rat. Clinical and Experimental Pharmacology and Physiology 32 (7), A13-A14. (Meeting abstract, Published July 2005)
Francis, A., Matawie, K., Oshlack, A., and Smyth, G. K. (2005). Statistical Solutions to Modern Problems: Proceedings of the 20th International Workshop on Statistical Modelling, Sydney, 10-15 July 2005. University of Western Sydney Press, Sydney, ISBN 1-74108-101-7. (Published 10 July 2005)
Beißbarth, T., Tye-Din, J. A., Smyth, G. K., Anderson, R. P., and Speed, T. P. (2005). Modelling and analysis of T-cell epitope screening data. In: Statistical Solutions to Modern Problems: Proceedings of the 20th International Workshop on Statistical Modelling, Sydney, 10-15 July 2005. Francis, A., Matawie, K., Oshlack, A., and Smyth, G. K. (eds.), University of Western Sydney Press, pages 101-108. (Published 10 July 2005)
Ritchie, M. E., and Smyth, G. K. (2005). Estimating shared parameters using many small data sets. In: Statistical Solutions to Modern Problems: Proceedings of the 20th International Workshop on Statistical Modelling, Sydney, 10-15 July 2005, Francis, A., Matawie, K., Oshlack, A., and Smyth, G. K. (eds.), University of Western Sydney Press, pages 419-427. (Published 10 July 2005)
Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420. (Publisher web site, PDF) (Published 8 August 2005)
Dunn, P. K., and Smyth, G. K. (2005). Series evaluation of Tweedie exponential dispersion models. Statistics and Computing 15, 267-280. (Preprint PDF) (Accepted 1 March 2005, Published October 2005)

2006

Shackleton, M., Vaillant, F., Simpson, K. J., Stingl, J., Smyth, G. K., Asselin-Labat, M.-L., Wu, L., Lindeman, G. J., and Visvader, J. E. (2006). Generation of a functional mammary gland from a single stem cell. Nature 439, 84-88. [Publisher Full Text] (Published 5 January 2006) (Rated Exceptional by Biology Faculty of 1000)
Gilad, Y., Oshlack, A., Smyth, G. K., Speed, T. P., and White, K. P. (2006). Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440, 242-245. [Publisher Full Text] (Published 9 March 2006) (Rated Exceptional by Biology Faculty of 1000)
Wettenhall, J. M., Simpson, K. M., Satterley, K., and Smyth, G. K. (2006). affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics 22, 897-899. [Publisher Full Text] (Published 1 April 2006)
de Silva, M. G., Hildebrand, M. S., Christopoulos, H., Newman, M. R., Bell, K., Ritchie, M., Smyth. G. K., Dahl, H.-H. M. (2006). Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway. Acta Oto-Laryngologica 126, 1148-1157. [Publisher Full Text] (Published online 12 May 2006, print Dec 2006).
Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights for microarray data. BMC Bioinformatics 7, Article 261. [PubMed Abstract] [Publisher Full Text] [Supplementary Information] (Published 19 May 2006)
Lahoud, M. H., Proietto, A. I., Gartlan, K., Kitsoulis, S., Curtis, J., Wettenhall, J., Sofi, M., Daunt, M., O’Keeffe, M., Caminschi, I., Satterley, K., Rizzitelli, A., Schnorrer, P., Hinohara, A., Yamaguchi, Y., Wu, L., Smyth, G. K., Handman, E., Shortman, K. and Wright., M. D. (2006). Sirp molecules are differentially expressed by CD8-dendritic cells. J. Immunol 177, 372-382. [PubMed Abstract] (Published July 2006)
Wormald, S., Hilton, D. J., Smyth, G. K., and Speed, T. P. (2006). Proximal genomic localization of STAT1 binding and regulated transcriptional activity. BMC Genomics 7, 254. [Publisher Full Text] (Published 11 October 2006)
Holloway, A. J., Oshlack, A., Diyagama, D. S., Bowtell, D. D. L., and Smyth, G. K. (2006). Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. BMC Bioinformatics 7, Article 511. [PubMed Abstract] [Publisher Full Text] (Published 22 Nov 2006)

2007

Oshlack, A., Emslie, D., Corcoran, L., and Smyth, G. K. (2007). Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biology 8, R2. [PubMed Abstract] [Publisher Full Text] (Published 4 Jan 2007)
Greenawalt, D. M., Duong, C., Smyth, G. K., Ciavarella, M. L., Thompson, N. J., Tiang, T., Murray, W. K., Thomas, R. J S., and Phillips, W. A. (2007). Gene expression profiling of esophageal cancer: comparative analysis of Barrett’s esophagus, adenocarcinoma and squamous cell carcinoma. International Journal of Cancer 120, 1914-1921. [PubMed Abstract] [Publisher Full Text] (Published 1 May 2007).
Oshlack, A., Chabot, A. E., Smyth, G. K., and Gilad, Y. (2007). Using DNA microarrays to study gene expression in closely related species. Bioinformatics 23, 1235-1242. [PubMed Abstract] [Publisher Full Text] (Published 23 March 2007).
Smyth, G. K. (one of a panel of 9 experts) (2007). The cDNA Microarray Tech Guide. Genome Technology Magazine, Supplement April 2007, pages 1-15. [Publisher Full Text] (Published 2 April 2007)
Baldwin, T., Sakthianandeswaren, A., Curtis, J., Kumar, B., Smyth, G. K., Foote, S., and Handman, E. (2007). Wound healing response is a major contributor to the severity of cutaneous leishmaniasis in the ear model of infection. Parasite Immunology 29, 501–513. [Publisher Full Text] (Accepted 25 July 2007, Published October 2007).
Ritchie, ME, Silver, J, Oshlack, A, Holmes, M, Diyagama, D, Holloway, A, and Smyth, GK (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics 23, 2700-2707. [Publisher Full Text] [Supplementary Information] (Published online 25 August 2007, Published 15 October 2007)
Robinson, MD, and Smyth, GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887. [Publisher Full Text] [Supplementary information] [Software] (Published online 19 September 2007, Published 1 November 2007)

2008

Huggins, CE, Domenighetti, AA, Ritchie, ME, Khalil, N, Favaloro, JM, Proietto, J, Smyth, GK, Pepe, S, Delbridge, LMD (2008). Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention. Journal of Molecular and Cellular Cardiology 44, 270-280. (Accepted 30 Nov 2007, Published 1 February 2008)
Pridans, C, Holmes, ML, Polli, M, Wettenhall, JM, Dakic, A, Corcoran, LM, Smyth, GK, and Nutt, SL (2008). Identification of Pax5 target genes in early B cell differentiation. Journal of Immunology 180, 1719-1728. [Publisher Full Text] (Accepted 5 December 2007, Published 1 February 2008)
Berkovic, SF, Dibbens, LM, Oshlack, A, Silver, JD, Katerelos, M, Vears, DF, Lüllmann-Rauch, R, Blanz, J, Zhang, KW, Stankovich, J, Kalnins, RM, Dowling, JP, Andermann, E, Andermann, F, Faldini, E, D’Hooge, R, Vadlamudi, L, Macdonell, RA, Hodgson, BL, Bayly, MA, Savige, J, Mulley, JC, Smyth, GK, Power, DA, Saftig, P, Bahlo, M. (2008). Array-based gene discovery with 3 unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis. American Journal of Human Genetics 82, 673-684. [Publisher Full Text] [Nature Review Genetics Research Highlight] (Accepted 28 December 2007, Published 28 February 2008)
Dunn, PK, and Smyth, GK (2008). Evaluation of Tweedie exponential dispersion model densities by Fourier inversion. Statistics and Computing 18, 73-86. [Preprint] (Accepted 15 September 2007, Published online 17 October 2007, Published 1 March 2008)
Ling, K-H, Hewitt, CA, Kinkel, SA, Smyth, GK, and Scott, HS (2008). High-throughput and complex gene expression validation using the Universal Probe Library and the LightCycler 480 System. Biochemica No 2 (2008), 23-26. [Publisher Full Text] (Published 1 March 2008)
Robinson, M., and Smyth, G. K. (2008). Small sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9, 321-332. [Publisher Full Text] [Preprint] (Accepted 19 July 2007, Published online 29 August 2007, Published 1 April 2008)
Majewski, IJ, Blewitt, ME, de Graaf, CA, McManus, EJ, Bahlo, M, Hilton, AA, Hyland, CD, Smyth, GK, Corbin, JE, Metcalf, D, Alexander, WS, and Hilton, DJ (2008). Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activity. PLoS Biology 6, e93. (Accepted 4 March 2008, Published 15 April 2008)
Dwyer, JP, Ritchie, ME, Smyth, GK, Harrap, SB, Delbridge, LMD, Domenighetti, AA, Di Nicolantonio, R (2008). Myocardial gene expression associated with genetic cardiac hypertrophy in the absence of hypertension. Hypertension Research 31, 941-955. [Publisher Full Text] (Accepted 28 November 2007, Published May 2008)
Ellis, L, Pan, Y, Smyth, GK, George, DJ, McCormack, C, Williams-Traux, R, Mita, M, Beck, J, Ryan, G, Atadja, P, Butterfoss, D, Dugan, M, Culver, K, Johnstone, RW, Prince, HM (2008). The histone deacetylase inhibitor panobinostat induces clinical responses with associated alterations in gene expression profiles in cutaneous T cell lymphoma. Clinical Cancer Research 14, 4500-4510. [Publisher Full Text] (Published 14 July 2008)
Michaud, J, Simpson, KM, Escher, R, Buchet-Poyau, K, Beissbarth, T, Carmichael, C, Ritchie, ME, Schutz, F, Cannon, P, Liu, M, Shen, X, Ito, Y, Raskind, WH, Horwitz, MS, Osato, M, Turner, DR, Speed, TP, Kavallaris, M, Smyth, GK, and Scott, HS (2008). Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics 9, 363. [Publisher Full Text] (Published 31 July 2008)
Barker, HE, Smyth, GK, Wettenhall, J, Ward, TA, Bath, ML, Lindeman, GJ, and Visvader, JE (2008). Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland. BMC Developmental Biology 8, 94. [Publisher Full Text] (Published 1 October 2008)
Blekhman, R, Oshlack, A, Chabot AE, Smyth, GK and Gilad, Y (2008). Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genetics 4, e1000271. [Publisher Full Text] (Published 21 November 2008)

2009

McMorran, BJ, Marshall, VM, de Graaf, C, Drysdale, KE, Shabbar, M, Smyth, GK, Corbin, JE, Alexander, WS, Foote, SJ (2009). Platelets kill intraerythrocytic malarial parasites and mediate survival to infection. Science 323, 797-800. [Publisher Full Text] (Published 6 Feb 2009)
Bryant, PA, Smyth, GK, Robins-Browne, R, Curtis, N (2009). Detection of gene expression in an individual cell type within a cell mixture using microarray analysis. PLoS ONE 4, e4427. [Publisher Full Text] (Published 12 Feb 2009)
McCarthy, DJ, and Smyth, GK (2009). Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25, 765-771. [Publisher Full Text] (Epub 28 January 2009, Published 15 March 2009)
Silver, JD, Ritchie, ME, and Smyth, GK (2009). Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics 10, 352-363. [Publisher Full Text] (Epub 8 Dec 2008, Published Apr 2009)
Hubert, F-X, Kinkel, SA, Crewther, PE, Cannon, PZF, Webster, KE, Link, M, Uibo, R, Meager, A, Forehan, SP, Smyth, GK, Mittaz, L, Antonarakis, SE, Peterson, P, Heath, WR, and Scott, HS (2009). Aire-deficient C57BL/6 mice mimicking the common human 13-bp deletion mutation present with only a mild autoimmune phenotype. Journal of Immunology 182, 3902-3918. (Published 1 April 2009)
Michalak, EM, Jansen, ES, Happo, L, Cragg, MS, Tai, L, Smyth, GK, Strasser, A, Adams, JM, and Scott, CL (2009). Puma and to a lesser extent Noxa are suppressors of Myc-induced lymphomagenesis. Cell Death and Differentiation 16, 684-696. (Epub 16 January 2009, Published May 2009).
Parish, IA, Rao, S, Smyth, GK, Juelich, T, Denyer, GS, Davey, GM, Strasser, A, and Heath, WR (2009). The molecular signature of CD8+ T cells undergoing deletional tolerance. Blood 113, 4575-4585. [Publisher Full Text] (Epub 9 February 2009, Published 7 May 2009)
D’Costa, K, Emslie, D, Metcalf, D, Smyth, GK, Karnowski, A, Kallies, A, Nutt, SL, and Corcoran, LM (2009). Blimp1 is limiting for transformation in a mouse plasmacytoma model. Blood 113(23), 5911-5919. (Epub 27 March 2009, Published 4 June 2009)
Hu, Y, and Smyth, GK (2009). ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. Journal of Immunological Methods. [Publisher Full Text] (Accepted 20 June 2009, Epub 27 June 2009)
Smyth, GK, and Verbyla, AP (2009). Leverage adjustments for dispersion modelling in generalized nonlinear models. Australian and New Zealand Journal of Statistics. (Accepted 10 November 2008)