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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. [Publisher Site] [Full Text PDF] [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 Site] [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 Volume 3, Issue 1, Article 3. [Publisher Full Text] or [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. Proceedings of the National Academy of Sciences of the United States of America 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). Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21(9), 2067-2075. [Supplementary Information] [Publisher Full Text] [Preprint 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. [Publisher Full Text] (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] [Preprint 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] (AOP 12 May 2006, Published 1 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). Signal regulatory protein molecules are differentially expressed by CD8-dendritic cells. Journal of Immunology 177, 372-382. [PubMed Abstract] (Published 1 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 February 2009)
Recommended by Faculty of 1000
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 February 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] (AOP 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] (AOP 8 Dec 2008, Published 1 April 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. (AOP 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] (AOP 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. (AOP 27 March 2009, Published 4 June 2009)
Lim, E, Vaillant, F, Wu, D, Forrest, NC, Pal, B, Hart, AH, Asselin-Labat, M-L, Gyorki, DE, Ward, T, Partanen, A, Feleppa, F, Huschtscha, LI, Thorne, HJ, kConFab, Fox, SB, Yan, M, French, JD, Brown, MA, Smyth, GK, Visvader, JE, and Lindeman, GJ (2009). Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carrier. Nature Medicine 15, 907-913. [Publisher Full Text] (Published 2 August 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 347, 70-78. [Publisher Full Text] [Preprint PDF] (Accepted 20 June 2009, AOP 27 June 2009, Published 15 August 2009)
Smyth, G. K. (one of a panel of 5 experts) (2009). Traditional and Digital Gene Expression. A trouble-shooting guide: experts share their advice on QPCR, microarrays and sequencing. Genome Technology Magazine, 30 Sep 2009, 16 pages. [Publisher Full Text]
Ling, KH, Hewitt, CA, Beissbarth, T, Hyde, L, Banerjee, K, Cheah, PS, Cannon, PZ, Hahn, CN, Thomas, PQ, Smyth, GK, Tan, SS, Thomas, T and Scott, HS (2009). Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 sense and antisense transcripts revealed by transcriptome profiling. Genome Biology 10, R104. [Publisher Full Text] (Accepted 25 September 2009, Published 2 October 2009)
Liang, D, Wong, CE, Singh, MB, Beveridge, CA, Phipson, B, Smyth, GK, and Bhalla, PL (2009). Molecular dissection of pea shoot apical meristem. Journal Of Experimental Botany 60, 4201–4213. (Accepted 31 July 2009, AOP 25 August 2009, Published 14 October 2009)
Metcalf, D, Ng, AP, Loughran, SJL, Phipson, B, Smyth, GK, Di Rago, L, Mifsud, S (2009). Murine hematopoietic blast colony-forming cells and their progeny have distinctive membrane marker profiles. Proceedings of the National Academy of Sciences of the United States of America 106, 19102-19107. [Publisher Full Text] (Accepted 24 September 2009, AOP 23 October 2009, Published 10 November 2009)
Shi, W, Banerjee, A, Ritchie, ME, Gerondakis, S, and Smyth, GK (2009). Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics 10, 372. [Publisher Full Text] (Accepted 19 October 2009, Published 11 November 2009)
Smyth, GK, and Verbyla, AP (2009). Leverage adjustments for dispersion modelling in generalized nonlinear models. Australian and New Zealand Journal of Statistics 51, 433-448. [Publisher Full Text] (Accepted 10 November 2008, AOP 28 September 2009, Published 1 December 2009)

2010

Robinson, M, McCarthy, DJ, Smyth, GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. [Publisher Full Text] (Accepted 23 October 2009, AOP 11 November 2009, Published 1 January 2010)
Young, MD, Wakefield, MJ, Smyth, GK, Oshlack, A (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11, R14. [Publisher Full Text] (Published 4 February 2010)
Lim, E, Wu, D, Pal, B, Bouras, T, Asselin-Labat, M-L, Vaillant, F, Yagita, H, Lindeman, GJ, Smyth, GK, Visvader, JE (2010). Transcriptome analyses of mouse and human mammary cell subpopulations reveals multiple conserved genes and pathways. Breast Cancer Research 12, R21. [Publisher Full Text] (Published 26 March 2010)
Shi, W, de Graaf, C, Kinkel, S, Achtman, A, Baldwin, T, Schofield, L, Scott, H, Hilton, D, Smyth, GK (2010). Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Research 38, 2168-2176. [Publisher Full Text] (Accepted 12 December 2009, AOP 7 January 2010, Published 1 April 2010)
Guipponi, M, Li, Q-X, Hyde, L, Beissbarth, T, Smyth, GK, Masters, CL, Scott, HS (2010). SAGE analysis of genes differentially expressed in pre-symptomatic TgSOD1G93A transgenic mice identified cellular processes involved in early stage of ALS pathology. Journal of Molecular Neuroscience 41, 172–182. [Publisher Full Text] (Accepted 16 November 2009, AOP 2 December 2009, Published 1 May 2010)
Sakthianandeswaren, A, Curtis, JM, Elso, C, Kumar, B, Baldwin, TM, Lopaticki, S, Kedzierski, L, Smyth, GK, Foote, SJ, and Handman, E (2010). Fine Mapping of Leishmania major susceptibility locus lmr2 and evidence of a role for Fli1 in disease and wound healing. Infection and Immunity 78, 2734-2744. (Accepted 30 March 2010, AOP 5 April 2010, Published 1 June 2010)
Asselin-Labat, M-L, Vaillant, F, Sheridan, J, Pal, B, Wu, D, Simpson, ER, Yasuda, H, Smyth, GK, Martin, TJ, Lindeman, GJ, Visvader, JE (2010). Control of mammary stem cell function by steroid hormone signaling. Nature 465, 798–802. [Publisher Full Text] (AOP 11 April 2010, Published 10 June 2010)
Wentworth JM, Naselli G, Brown WA, Phipson B, Smyth GK, O’Brien PE, Harrison LC (2010). Pro-inflammatory CD11c⁺CD206⁺ adipose tissue macrophages are associated with insulin resistance in human obesity. Diabetes 59, 1648-1656. (Accepted 16 March 2010, AOP 31 March 2010, Published 1 July 2010)
Hewitt, CA, Ling, K-H, Merson, TD, Simpson, KM, Ritchie, ME, King, SL, Pritchard, MA, Smyth, GK, Thomas, T, Scott, HS, Voss, AK (2010). Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of down syndrome. PLoS ONE 5, e11561. [Publisher Full Text] (Accepted 31 May 2010, Published 16 July 2010)
Majewski, IJ, Ritchie, ME, Phipson, B, Corbin, J, Pakusch, M, Ebert, A, Busslinger, M, Koseki, H, Hu, Y, Smyth, GK, Alexander, WS, Hilton, DJ, and Blewitt, ME (2010. Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells. Blood 116, 731-739. (Accepted 21 April 2010, AOP 5 May 2010, Published 5 August 2010)
Wu, D, Lim, E, Vaillant, F, Asselin-Labat, M-L, Visvader, JE, and Smyth, GK (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26, 2176-2182. [Publisher Full Text] (Accepted 4 July 2010, AOP 7 July 2010, Published 1 September 2010)
Gorringe, KL, George, J, Anglesio, MS, Ramakrishna, M, Etemadmoghadam, D, Cowin, P, Sridhar, A, Williams, LH, Boyle, SE, Yanaihara, N, Okamoto, A, Urashima, M, Australian Ovarian Cancer Study, Smyth, GK, Campbell, IG, Bowtell, DDL (2010). Copy number analysis identifies novel interactions between genomic loci in ovarian cancer. PLoS ONE 5(9): e11408. [Publisher Full Text] (Accepted 16 April 2010, Published 10 September 2010)
Phipson, B, and Smyth, GK (2010). Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn. Statistical Applications in Genetics and Molecular Biology Volume 9, Article 39. [Publisher Full Text] [Technical Report with Corrections] (Accepted 13 September 2010, Published 31 October 2010)
Lindeman, G, Smyth, G, Visvader, J, Wu, D (2011). Gene expression profiles and uses thereof. International Patent Application No. PCT/AU2010/000524, Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Melbourne, Victoria 3052, Australia. (Published 11 November 2010)
Etemadmoghadam D, George J, Cowin PA, Cullinane C, Kansara M, Australian Ovarian Cancer Study Group, Gorringe, KL, Smyth, GK, Bowtell, DDL (2010). Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer. PLoS ONE 5(11), e15498. doi:10.1371/journal.pone.0015498 (Published 12 November 2010)
Shi, W, Oshlack, A, and Smyth, GK (2010). Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression BeadChips. Nucleic Acids Research 38, e204. [Publisher Full Text] (Accepted 16 September 2010, AOP 6 October 2010, Published 1 December 2010)
Tan, IKL, Mackin, L, Wang, N, Papenfuss, AT, Elso, CM, Ashton, MP, Quirk, F, Phipson, B, Bahlo, M, Speed, TP, Smyth, GK, Grant Morahan, G, Brodnicki, TC (2010). A recombination hotspot leads to sequence variability within a novel gene and contributes to complex disease susceptibility. Genome Research 20, 1629-1638. (Accepted 24 August 2010, AOP 4 November 2010, Published 1 December 2010)
Happo, L, Cragg, MS, Phipson, B, Haga, JM, Jansen, E, Herold, MJ, Dewson, G, Michalak, EM, Vandenberg, CJ, Smyth, GK, Strasser, A, Cory, S, and Scott, CL (2010). Maximal killing of lymphoma cells by DNA-damage inducing therapy requires not only the p53 targets Puma and Noxa but also Bim. Blood 116, 5256-5267. (Accepted 21 August 2010, AOP 9 September 2010, Published 9 December 2010)
de Graaf CA, Kauppi M, Baldwin T, D Hyland C, Metcalf D, Willson TA, Carpinelli MR, Smyth GK, Alexander WS, Hilton DJ. (2010). Regulation of hematopoietic stem cells by their mature progeny. Proc Natl Acad Sci USA 107, 21689-21694. [Publisher Full Text] (AOP 29 November 2010, Published 14 December 2010)

2011

Ling, K-H, Hewitt, CA, Beissbarth, T, Hyde, L, Cheah, P-S, Smyth, GK, Tan, S-S, Hahn, CN, Thomas, T, Thomas, PQ, and Scott, HS (2011). Spatio-temporal regulation of multiple overlapping sense and novel natural antisense transcripts at the Nrgn and Camk2n1 gene loci during mouse cerebral corticogenesis. Cerebral Cortex 21, 683-697. [Publisher Full Text] (Accepted 30 June 2010, AOP 6 August 2010, Published 1 March 2011)
Cretney, E, Xin, A, Shi, W, Minnich, M, Masson, F, Miasari, M, Belz, G, Smyth, GK, Meinrad Busslinger, M, Nutt, SL, Kallies, A (2011). The transcription factors Blimp1 and IRF4 jointly control differentiation and function of effector regulatory T cells. Nature Immunology 12, 304-311. [PubMed] (Accepted 21 January 2011, AOP 6 March 2011, Published 1 April 2011)
Gordon, L, Joo, J-HE, Andronikos, R, Ollikainen, M, Wallace, EM, Umstad, MP, Permezel, M, Oshlack, A, Morley, R, Carlin, JB, Saffery, R, Smyth, GK, and Craig, JM (2011). Expression discordance of monozygotic twins at birth: Effect of intrauterine environment and a possible mechanism for fetal programming. Epigenetics 6, 579-592. (Accepted 5 February 2011, Published 1 May 2011)
Helland, Å, Anglesio, MS, George, J, Cowin, PA, Johnstone, CN, House, CM, Sheppard, KE, Dariush Etemadmoghadam, D, Melnyk, N, Rustgi, AK, Phillips, WA, Johnsen, H, Holm, R, Kristensen, GB, Australian Ovarian Cancer Study Group, Pearson, RB, Børresen-Dale, A-L, Huntsman, DG, Anna deFazio, A, Creighton, CJ, Smyth, GK, and Bowtell, DDL (2011). MYCN, Let-7 and HMGA2 copy number change and altered gene expression in a specific molecular subtype of high-grade serous ovarian cancer. PLoS ONE 6, e18064. (Accepted 25 February 2011, Published 13 April 2011)
Zamudio, NM, Scott, HS, Wolski, K, Lo, C-Y, Law, C, Leong, D, Kinkel, SA, Chong, S, Jolley D, Smyth GK, de Kretser, D, Whitelaw, E, O’Bryan, MK (2011). DNMT3L is a regulator of X chromosome compaction and post-meiotic gene transcription. PLoS ONE 6, e18276. [Publisher Full Text] (Accepted 1 March 2011, Published 31 March 2011)
Hubert, F-X, Kinkel, SA, Davey, GM, Phipson, B, Mueller, SN, Liston, A, Proietto, AI, Cannon, PZF, Forehan, S, Smyth, GK, Wu, L, Goodnow, CC, Carbone, FR, Scott, HS, and Heath, WR (2011). Aire regulates transfer of antigen from mTEC to dendritic cells for induction of thymic tolerance. Blood 118(9), 2462-2472. (Accepted 23 March 2011, AOP 19 April 2011, Published 1 September 2011)
Jackson, JT, Hu, Y, Liu, R, Masson, F, D'Amico, A, Carotta, S, Xin, A, Camilleri, MJ, Mount, AM, Kallies, A, Wu, L, Smyth, GK, Nutt, SL, and Belz, GT (2011). Id2 expression delineates differential checkpoints in the genetic program of CD8α+ and CD103+ dendritic cell lineages. The EMBO Journal 30, 2690-2704. (Accepted 28 April 2011, Published 17 May 2011)
Bryant, PA, Smyth, GK, Robins-Browne, R, Curtis, N (2011). Technical variability is greater than biological variability in a microarray experiment but both are outweighed by changes induced by stimulation. PLoS ONE 6, e19556. (Accepted 13 May 2011, Published 31 May 2011)
Ng, AP, Loughran, SJ, Metcalf, D, Hyland, CD, de Graaf, CA, Hu, Y, Smyth, GK, Hilton, DJ, Kile, BT, and Alexander, WS (2011). Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice. Blood 118, 2454-2461. (Accepted 22 May 2011, AOP 14 June 2011, Published 1 September 2011)
Campbell, DJ, Zhang, Y, Kelly, DJ, Gilbert, RE, McCarthy, DJ, Shi, W, Smyth, GK (2011). Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart. Clinical and Experimental Pharmacology and Physiology 38, 623-631. (Accepted 1 July 2011, AOP 7 July 2011, Published 1 September 2011)
Lahoud, MH, Ahmet, F, Kitsoulis, S, Wan, SS, Vremec, D, Lee, C-N, Phipson, B, Shi, W, Smyth, GK, Lew, AM, Kato, Y, Mueller, S, Davey, GM, Heath, WR, Shortman, K, Caminschi, I (2011). Targeting antigen to mouse dendritic cells via Clec9A induces potent CD4 T cell responses biased toward a follicular helper phenotype. Journal of Immunology 187, 842-850. (Accepted 18 May 2011, AOP 15 June 2011, Published 15 July 2011)
Croker BA, O'Donnell JA, Nowell CJ, Metcalf D, Dewson G, Campbell KJ, Rogers KL, Hu Y, Smyth GK, Zhang JG, White M, Lackovic K, Cengia LH, O'Reilly LA, Bouillet P, Cory S, Strasser A, Roberts AW. (2011). Fas-mediated neutrophil apoptosis is accelerated by Bid, Bak, and Bax and inhibited by Bcl-2 and Mcl-1. Proceedings of the National Academy of Sciences of the United States of America 108, 13135-13140. (Accepted 10 July 2011, AOP 18 July 2011, Published 9 August 2011)
Kraft, M, Cirstea, IC, Voss, AK, Thomas, T, Goehring, I, Sheikh, B, Gordon, L, Scott, HS, Smyth, GK, Ahmadian, MR, Trautmann, U, Zenker, M, Tartaglia, M, Ekici, A, Reis, A, Dörr, H-G, Rauch, A, Thiel, CT (2011). Disruption of the histone acetyltransferase MYST4 leads to a Noonan syndrome-like phenotype and hyperactivated MAPK signaling. Journal of Clinical Investigation 121, 3479-3491. [Publisher Full Text] (Accepted 8 June 2011, AOP 1 August 2011, Published 1 September 2011)
Asselin-Labat, M-L, Sutherland, KD, Vaillant, F, Gyorki, DE, Wu, D, Holroyd, S, Breslin, K, Ward, T, Shi, W, Bath, ML, Deb, S, Fox, SB, Smyth, GK, Lindeman, GJ, Visvader, JE (2011). Gata-3 negatively regulates the tumor-initiating capacity of mammary luminal progenitor cells and targets the putative tumor suppressor caspase-14. Molecular and Cellular Biology 31, 4609-4622. (Accepted 12 September 2011, AOP 19 September 2011, Published 1 November 2011).

2012

Young, MD, McCarthy, DJ, Wakefield, MJ, Smyth, GK, Oshlack, A, Robinson, MD (2012). Differential expression for RNA-Seq data: mapping, summarization, statistics and experimental design. Chapter 10 of Bioinformatics for High Throughput Sequencing (AM Aransay, ML Hackenberg and N Rodriguez-Ezpeleta, editors), Springer, New York, pages 169--190. [Publisher Site] (Accepted 28 June 2011, AOP 25 October 2011, Copyright year 2012)
Oakes, SR, Vaillant, F, Lim, E, Lee, L, Breslin, K, Feleppa, F, Deb, S, Ritchie, ME, Takano, E, Fox, SB, Daniele Generali, D, Smyth, GK, Strasser, A, Huang, DCS, Visvader, JE, and Lindeman, GJ (2011). Sensitization of BCL-2-expressing breast tumors to chemotherapy by the BH3-mimetic ABT-737. Proceedings of the National Academy of Sciences of the United States of America 109, 2766-2771. (Accepted 22 June 2012, AOP 18 July 2011, Published 21 Feb 2012)
Smyth, GK (one of a panel of eight experts) (2012). Transcriptomics Technical Guide. Genome Technology Magazine, 1 April. [Publisher Full Text] (Accepted 25 February 2012, Published 1 April 2012)
McCarthy, DJ, Chen, Y, Smyth, GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297. [Publisher Full Text] (Accepted 10 January 2012, AOP 28 January 2012, Published 10 May 2012)
Happo, L, Phipson, B, Smyth, GK, Strasser, A and Scott, CL (2012). Neither loss of Bik alone, nor combined loss of Bik and Noxa, accelerate murine lymphoma development or render lymphoma cells resistant to DNA damaging drugs. Cell Death and Disease 3, e306. doi: 10.1038/cddis.2012.42. (Accepted 29 February 2012, Published 10 May 2012)
Achtman, AH, Pilat, S, Law, CW, Lynn, DJ, Janot, L, Mayer, ML, Ma, S, Kindrachuk, J, Finlay, BB, Brinkman, FSL, Smyth, GK, Hancock, REW, Schofield, L (2012). Effective adjunctive therapy by an innate defense regulatory peptide in a pre-clinical model of severe malaria. Science Translational Medicine 4(135):135ra64. (Accepted 31 March 2012, Published 23 May 2012)
Leong, DW, Komen, JC, Hewitt, CA, Arnaud, E, McKenzie, M, Phipson, B, Bahlo, M, Laskowski, A, Kinkel, SA, Davey, GM, Heath, WR, Voss, AK, Zahedi, RP, Pitt, JJ, Roman Chrast, R, Sickmann, A, Ryan, MT, Smyth, GK, Thorburn, DR, Scott, HS (2012). Proteomic and metabolomic analyses of a mitochondrial complex I deficient mouse model generated by spontaneous B2 Short Interspersed Nuclear Element (SINE) insertion into the NADH dehydrogenase (ubiquinone) Fe-S protein 4 (Ndufs4) gene. The Journal of Biological Chemistry 287, 20652-20663. [PubMed] (Accepted 23 April 2012, AOP 25 April 2012, Published 8 June 2012)
Wu, D, Smyth, GK (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 40, e133. [Publisher Full Text] (Accepted 1 May 2012, AOP 25 May 2012, Published 1 September 2012)
Wakim, LM, Woodward-Davis, A, Liu, R, Hu, Y, Villadangos, J, Smyth, GK and Bevan MJ (2012). The molecular signature of tissue resident memory CD8+ T cells isolated from the brain. Journal of Immunology 189, 3462-3471. [PubMed] (Accepted 30 July 2012, AOP 24 Aug 2012, Published 1 October 2012)
Lund, SP, Nettleton, D, McCarthy, DJ, Smyth, GK (2012). Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Statistical Applications in Genetics and Molecular Biology Volume 11, Issue 5, Article 8. [Preprint PDF] (Accepted 31 July 2012, Published 22 October 2012)

2013

Pal, B, Bouras, T, Shi, W, Vaillant, F, Sheridan, J, Fu, N, Breslin, K, Jiang, K, Ritchie, ME, Young, M, Lindeman, GJ, Smyth, GK, and Visvader, JE (2013). Ezh2 coordinates global changes in the mammary epigenome induced by hormonal cues and controls mammary progenitor activity. Cell Reports 3, 411-326. [Pubmed] (Accepted 1 January 2013, AOP 31 January 2013, Published 21 February 2013)
Bolden, JE, Shi, W, Jankowski, K, Kan, C-Y, Cluse, L, MacKenzie, KL, Smyth, GK, and Johnstone, RW (2013). HDAC inhibitors induce tumor cell-selective pro-apoptotic transcriptional responses. Cell Death and Disease 4, e519. [Pubmed] (Accepted 31 December 2012, Published 28 February 2013)
Leong, HS, Chen, K, Hu, Y, Lee, S, Corbin, J, Pakusch, M, Murphy, JM, Majewski, IJ, Smyth, GK, Alexander, WS, Hilton, DJ, and Blewitt, ME (2013). Epigenetic regulator Smchd1 functions as a tumor suppressor. Cancer Research 73, 1591-1599. [Pubmed] (Accepted 22 December 2012, AOP 26 December 2012, Published 1 March 2013)
Tang, JZ, Carmichael, CL, Shi, W, Metcalf, D, Ng, AP, Hyland, CD, Jenkins, NA, Copeland, NG, Howell, VM, Zhao, ZJ, Smyth, GK, Kile, BT, and Alexander, WS (2013). Transposon mutagenesis reveals cooperation of ETS family transcription factors with signaling pathways in erythro-megakaryocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America. [Pubmed] (Accepted 12 March 2013, AOP 26 March 2013)
Liao, Y, Smyth, GK, and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research 41, 1-17. [Pubmed] [Publisher Full Text] (Accepted 8 March 2013, AOP 4 April 2013)
George, J, Gorringe, KL, Smyth, GK, and Bowtell, DDL (2013). Identification of associated genomic alterations by integrated CNV and expression profiling analysis. Methods in Molecular Biology, Ovarian Cancer: Methods and Protocols. (Accepted 21 February 2012, to be published Spring 2013)
Wu, D, Hu, Y, Tong, S, Williams, BRG, Smyth, GK, and Gantier, MP (2013). The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease. RNA 19. (Accepted 6 April 2013)
George, J, Alsop, K, Etemadmoghadam, D, Hondow, H, Mikeska, T, Dobrovic, A, The Australian Ovarian Cancer Study Group, Smyth, GK, Levine, DA, Mitchell, G, and David Bowtell, D (2013). Non-equivalent gene expression and copy number alterations in high-grade serous ovarian cancers with BRCA1 and BRCA2 mutations. Clinical Cancer Research. [PubMed] (Accepted 27 April 2013, AOP 30 April 2013)
Smyth, GK, and Altman, NS (2013). Separate-channel analysis of two-channel microarrays: recovering inter-spot information. BMC Bioinformatics. (Accepted 10 May 2013)

Submitted

Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts. Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. [Preprint 1 May 2013]
Phipson, B, Lee, S, Majewski, IJ, Alexander, WS, Smyth, GK (2013). Empirical Bayes in the presence of exceptional cases, with application to microarray data. Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. [Preprint 22 May 2013]

AOP = Advance Online Publication (aka Epub ahead of print)