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Gordon Smyth Home - Publications to 2002

Publications since 2003

From April 2023, this page is no longer actively maintained. The new page can be found at http://gksmyth.github.io/pubs/index.html.

2023

• You Y, Dong X, Wee YK, Maxwell MJ, Alhamdoosh M, Smyth GK, Hickey PF, Ritchie ME, Law CW (2022). Modelling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data. Genome Biology. (Accepted 28 April 2023)
• Li M, Smyth GK (2023). Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics. Bioinformatics btad200, https://doi.org/10.1093/bioinformatics/btad200. [PMID: 37067487] (Accepted 12 April 2023, Epub 17 April 2023)
• Baldoni PL, Chen Y, Hediyeh-zadeh S, Liao Y, Dong X, Ritchie ME, Shi W, Smyth GK (2023). Dividing out quantification uncertainty allows efficient assessment of differential transcript expression. bioRxiv doi: 10.1101/2023.04.02.535231. (Published 4 April 2023)
• Abdulla H, Alserihi R, Flensburg C, Abeysekera W, Luo M, Gray DHD, Gordon Smyth GK, Alexander WS, Majewski, IJ McCormack MP (2023). Overexpression of Lmo2 initiates T-lymphoblastic leukemia via impaired thymocyte competition. Journal of Experimental Medicine 220(6), e20212383. (Accepted 22 February 2023, Epub 15 March 2023, Published 5 June 2023) [PMID: 36920307]
• Chan WF, Coughlan HD, Ruhle M, Iannarella N, Alvarado C, Groom JR, Keenan CR, Kueh AJ, Wheatley AK, Smyth GK, Allan RS, Johanson TM (2022). Survey of activation-induced genome architecture reveals a novel enhancer of Myc. Immunology and Cell Biology 101(4), 345-357. [PMID: 36710659] (Accepted 27 January 2023, Epub, 14 February 2023, Published 1 April 2023)
• Kueh AJ#, Bergamasco M#, Quaglieri A, Phipson B, Li-Wai-Suen CSN, Lönnstedt IM, Hu Y, Feng Z-P, Woodruff C, May RE, Wilcox S, Garnham AL, Snyder MP, Smyth GK, Speed TP, Thomas T*, Voss AK* (2022). Stem cell plasticity, acetylation of H3K14 and de novo gene activation rely on KAT7. Cell Reports 42(1), 111980. [PMID: 36641753] (Accepted 21 November 2022, Epub 14 January 2023, Published 31 January 2023)

2022

• Chan WF, Coughlan HD, Chen Y, Keenan CR, Smyth GK, Perkins AC, Johanson TM, Allan RS (2022). Activation of stably silenced genes by recruitment of a synthetic de-methylating module. Nature Communications 13(1), 5582. [PMID: 36151095] (Accepted 7 September 2022, Published 23 September 2022)
• Chan WF, Coughlan HD, Ruhle M, Iannarella N, Alvarado C, Groom JR, Keenan CR, Kueh AJ, Wheatley AK, Smyth GK, Allan RS, Johanson TM (2022). Survey of activation-induced genome architecture reveals a novel enhancer of Myc. bioRxiv doi: 10.1101/2022.09.14.508046. (Published 20 September 2022)
• You Y, Dong X, Wee YK, Maxwell MJ, Alhamdoosh M, Smyth GK, Hickey PF, Ritchie ME, Law CW (2022). Modelling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data. bioRxiv doi: 10.1101/2022.09.12.507511. (Published 14 September 2022)
• Dong X, Du MRM, Gouil Q, Tian L, Baldoni PL, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME (2022). Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. bioRxiv doi: 10.1101/2022.07.22.501076. (Published 22 July 2022)
• Wichmann J, Pitt C, Eccles S, Garnham AL, Li-Wai-Suen CSN, May R, Allan E, Wilcox S, Herold MJ, Smyth GK, Monahan BJ, Thomas T, Voss AK (2022). Loss of TIP60 abolishes H2AZ lysine 7 acetylation and causes p53, INK4A and ARF-independent cell cycle arrest. Cell Death & Disease 13(7), 627. [PMID: 35853868] (Accepted 30 June 2022, Published 20 July 2022)
• Li M, Smyth GK (2022). Missing values are informative in label-free shotgun proteomics data: estimating the detection probability curve. bioRxiv doi: 10.1101/2022.07.02.498573. (Published 4 July 2022)
• Haeusler GM, Garnham AL, Li-Wai-Suen CSN, Clark JE, Babl FE, Allaway Z, Slavin MA, Mechinaud F, Smyth GK, Phillips B, Thursky KA, Pellegrini M*, Doerflinger M* (2022). Blood transcriptomics identifies immune signatures indicative of infectious complications in childhood cancer patients with febrile neutropenia. Clinical & Translational Immunology 11(5), e1383. [PMID: 35602885] (Accepted 10 March 2022, Published 17 May 2022)
• Studniberg SI, Ioannidis LJ, Utami RAS, Trianty L, Liao Y, Abeysekera W, Li-Wai-Suen CSN, Pietrzak HM, Healer J, Puspitasari AM, Apriyanti D, Coutrier F, Poespoprodjo JR, Kenangalem E, Andries B, Prayoga P, Sariyanti N, Smyth GK, Cowman AF, Price RN, Noviyanti R, Shi W, Garhnham AL, Hansen DS (2022). Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria. Molecular Systems Biology 18(4), e10824. [PMID: 35475529] (Accepted 1 April 2022, Published 27 April 2022)
• El-Saafin F, Bergamasco MI, Chen Y, May RE, Esakky P, Hediyeh-zadeh S, Dixon M, Wilcox S, Davis MJ, Strasser A, Smyth GK, Thomas T*, Voss AK* (2022). Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death. Cell Death and Differentiation 29(5), 1013-1027. [PMID: 35361962] (Accepted 10 March 2022, Epub 31 March 2022, Published 1 May 2022)
• Chen Y, Pal B, Lindeman GJ, Visvader JE, Smyth GK (2022). R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue. Scientific Data 9(1), 96. [PMID: 35322042] (Accepted 24 February 2022, Published 23 March 2022)
• Heitink L, Whittle JR, Vaillant F, Capaldo BD, Dekkers JF, Dawson CA, Milevskiy MJG, Tsai M, Chen H-R, Christie M, Chen Y, Smyth GK, Herold MJ, Strasser A, Lindeman GJ*, Visvader JE* (2022). In vivo genome-editing screen identifies tumor suppressor genes that cooperate with Trp53 loss during mammary tumorigenesis. Molecular Oncology 16(5), 1119-1131. [PMID: 35000262] (Accepted 13 December 2021, Epub 9 January 2022, Published 1 March 2022)
• Bediaga NG, Garnham AL, Naselli G, Bandala-Sanchez E, Stone NL, Cobb J, Harbison JE, Wentworth JM, Ziegler AG, Couper JJ, Smyth GK, Harrison LC (2022). Cytotoxicity-related gene expression and chromatin accessibility define a subset of CD4+ T cells that mark progression to type 1 diabetes. Diabetes 71(3), 566-577. [PMID: 35007320] (Accepted 12 December 2021, Epub 7 January 2022, Published 1 March 2022)
• Yang Y, Kueh AJ, Grant ZL, Abeysekera W, Garnham AL, Wilcox S, Hyland CD, Di Rago L, Metcalf D, Alexander WS, Coultas L, Smyth GK, Voss AK*, Thomas T* (2022). The histone lysine acetyltransferase HBO1 regulates hematopoietic stem cell quiescence and self-renewal. Blood 139(6), 845-858. [PMID: 34724565] (Accepted 14 October 2021, Epub 1 November 2021, Published 10 February 2022)
• Heinlein M, Gandolfo LC, Zhao K, Teh CE, Nguyen N, Baell JB, Goldfarb Y, Abramson J, Wichmann J, Voss AK, Strasser A, Smyth GK, Thomas T, Gray DHD (2022). The acetyltransferase KAT7 is required for thymic epithelial cell expansion, expression of AIRE target genes and thymic tolerance. Science Immunology 7(67), eabb6032. [PMID: 35061506] (Accepted 22 December 2021, Published 21 January 2022)

2021

• Zotos D, Quast I, Li-Wai-Suen CSN, McKenzie CI, Robinson MJ, Kan A, Smyth GK, Hodgkin P, Tarlinton DM (2021). The distribution of cell cycle phases and zone composition change in concert in germinal centers, regulated by IL21. Nature Communications 12(1), 7160. [PMID: 34887406] (Accepted 19 November 2021, Published 9 December 2021)
• Chen Y, Pal B, Lindeman GJ, Visvader JE, Smyth GK (2021). R code and downstream analysis objects for the scRNA-seq atlas of human breast spanning normal, preneoplastic and tumorigenic states. bioRxiv doi: https://doi.org/10.1101/2021.11.30.470523. (Published 1 December 2021)
• Yip RKH, Rimes JS#, Capaldo BD#, Vaillant F, Mouchemore KA, Pal B, Chen Y, Surgenor E, Murphy AJ, Anderson RL, Smyth GK, Lindeman GJ, Hawkins ED*, Visvader JE* (2021). Mammary tumour cells remodel the bone marrow vascular microenvironment to support metastasis. Nature Communications 12(1), 6920. [PMID: 34836954] (Accepted 27 September 2021, Published 26 November 2021)
• Peters TJ, Buckley MJ, Chen Y, Smyth GK, Goodnow CC, Clark SJ (2021). Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate. Nucleic Acids Research 49(19), e109. [PMID: 34320181] (Accepted 13 July 2021, Epub 28 July 2021, Published 8 November 2021)
• Grant ZL, Hickey PF, Abeysekera W, Whitehead L, Lewis SM, Symons RCA, Baldwin TM, Amann-Zalcenstein D, Garnham AL, Naik SH, Smyth GK, Thomas T, Voss AK, Coultas L (2021). The histone acetyltransferase HBO1 (KAT7) promotes efficient tip cell sprouting during angiogenesis. Development 148(20), dev199581. [PMID: 34550360, Correction PMID: 34927679] (Accepted 15 September 2021, Epub 22 September 2021, Published 26 October 2021)
• Zhan Y, Zhang Y, Zhang S, Coughlan H, Baldoni PL, Jacquelot N, Cao WJH, Preston S, Louis C, Rautela J, Pellegrini M, Wicks IP, Alexander WS, Harrison LC, Lew AM, Smyth GK, Nutt SL, Chopin M (2021). Differential requirement for the Polycomb repressor complex 2 in dendritic cell and tissue-resident myeloid cell homeostasis. Science Immunology 6(63), eabf7268. [PMID: 34533976] (Accepted 18 August 2021, Published 17 September 2021)
• Roth-Schulze AJ, Penno MAS, Ngui KM, Oakey H, Bandala-Sanchez E, Smith AD, Allnutt TR, Thomson RL, Vuillermin PJ, Craig ME, Rawlinson WD, Davis EA, Harris M, Soldatos G, Colman PG, Wentworth JM, Haynes A, Barry SC, Sinnott RO, Morahan G, Bediaga NG, Smyth GK, Papenfuss AT, Couper JJ, Harrison L (2021). Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome. Microbiome 9(1), 167. [PMID: 34362459] (Accepted 14 May 2021, Published 6 August 2021)
• Ioannidis LJ, Pietrzak HM, Ly A, Utami RAS, Eriksson EM, Studniberg SI, Abeysekera W, Li-Wai-Suen CSN, Sheerin D, Healer J, Puspitasari AM, Apriyanti D, Coutrier F, Poespoprodjo JR, Kenangalem E, Prayoga A, Sariyanti N, Smyth GK, Trianty L, Cowman AF, Price RN, Noviyanti R, Hansen DS (2021). High dimensional mass cytometry identifies T cell and B cell signatures predicting reduced risk of Plasmodium vivax malaria. JCI Insight 6(14), 148086. [PMID: 34128836] (Accepted 25 May 2021, Epub 15 June 2021, Published 22 July 2021)
• Pal B#, Chen Y#, Milevskiy MJG#, Vaillant F, Prokopuk L, Dawson C, Capaldo BD, Song X, Jackling F, Timpson P, Lindeman GJ, Smyth GK*, Visvader JE* (2021). Single cell transcriptome atlas of mouse mammary epithelial cells across development. Breast Cancer Research 23(1), 69. [PMID: 34187545] (Accepted 28 May 2021, Published 29 June 2021)
• Pal B#, Chen Y#, Vaillant F#, Capaldo BD, Joyce R, Song X, Bryant VL, Penington JS, Di Stefano L, Ribera NT, Wilcox S, Mann GB, kConFab, Papenfuss AT, Lindeman GJ, Smyth GK*, Visvader JE* (2021). A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast. EMBO Journal 40(11), e3107333. [PMID: 33950524] (Accepted 17 March 2021, Epub 5 May 2021, Published 1 June 2021)
• Doerflinger M, Haeusler GM, Li-Wai-Suen CSN, Clark JE, Slavin MA, Babl FE, Allaway Z, Mechinaud F, Smyth GK, De Abreu Lourenco R, Phillips B, Pellegrini M, Thursky KA (2021). Procalcitonin and Interleukin-10 may assist in early prediction of bacteraemia in children with cancer and febrile neutropenia. Frontiers in Immunology 12, 641879. [PMID: 34093531] (Accepted 27 April 2021, Published 20 May 2021)
• Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, Raviram R, Myers RM, Costacurta M, Todorovski I, Pijpers L, Bjelosevic S, Williams T, Huskins SN, Kearney CJ, Devlin JR, Jabbari JS, Martin BP, Fareh M, Kelly MJ, Dupere-Richer D, Sandow JJ, Feran B, Knight D, Khong T, Spencer A, Harrison SJ, Gregory G, Wickramasinghe VO, Webb AI, Taberlay PC, Bromberg KD, Lai A, Papenfuss AT, Smyth GK, Allan RA, Licht JD, Landau DA, Abdel-Wahab O, Shortt J, Vervoort SJ, Johnstone RW (2021). Targeting P300/CBP reveals discrete regulation of transcription and chromatin accessibility by histone acetylation. Molecular Cell 81(10), 2183-2200.e13. [PMID: 34019788] (Accepted 26 March 2021, Published 20 May 2021)
• Foers AD, Garnham AL, Chatfield S, Smyth GK, Cheng L, Hill AF, Wicks IP, Pang KC (2021). Extracellular vesicles in synovial fluid from rheumatoid arthritis patients contain miRNAs with capacity to modulate inflammation. International Journal of Molecular Sciences 22(9), 4910. [PMID: 34066338] (Accepted 5 May 2021, Published 6 May 2021)
• Zhang S, Coughlan HD, Ashayeripanah M, Seizova S, Kueh AJ, Brown DV, Cao W, Jacquelot N, D'Amico A, Lew AM, Zhan T, Tonkin CJ, Villadangos JA, Smyth GK, Chopin M, Nutt SL (2021). Type 1 conventional dendritic cell fate and function are controlled by DC-SCRIPT. Science Immunology 6(58), eabf4432. [PMID: 33811060] (Accepted 3 March 2021, Published 2 April 2021)
• Keenan CR, Mlodzianoski MJ, Coughlan HD, Bediaga NG, Naselli G, Lucas EC, Wang Q, de Graaf CA, Hilton DJ, Harrison LC, Smyth GK, Rogers KL, Boudier T, Allan RS, Johanson TM (2021). Chromosomes distribute randomly to, but not within, human neutrophil nuclear lobes. iScience 24(3), 102161. [PMID: 33665577] (Accepted 3 February 2021, Epub 6 February 2021, Published 19 March 2021)
• Chan WF, Coughlan HD, Iannarella N, Smyth GK, Johanson TM, Keenan CR, Allan RS (2021). Identification and characterization of the long non-coding RNA Dreg1 as a novel regulator of Gata3. Immunology and Cell Biology 99(3), 323-332. [PMID: 32970351] (Accepted 23 September 2020, Epub 24 September 2020, Published 1 March 2021)
• Chan WF#, Coughlan HD#, Zhou JHS, Keenan CR, Bediaga N, Hodgkin PD, Smyth GK*, Johanson TM*, Allan RS* (2021). Pre-mitotic genome re-organisation bookends the B cell differentiation process. Nature Communications 12(1), 1344. [PMID: 33637722] (Accepted 2 February 2021, Published 26 February 2021)
• Bediaga NG, Coughlan HD, Johanson TM, Garnham AL, Naselli G, Schröder J, Fearnley LG, Bandala-Sanchez E, Allan RS, Smyth GK, Harrison LC (2021). Multi-level remodelling of chromatin underlying activation of human T cells. Scientific Reports 11(1), 528. [PMID: 33436846] (Accepted 15 December 2020, Published 12 January 2021)

2020

• Law CW, Zeglinski K, Dong X, Alhamdoosh M, Smyth GK*, Ritchie ME* (2020). A guide to creating design matrices for gene expression experiments. F1000Research 9, 1444. [PMID: 33604029] [Full Text] [Workflow version] (Accepted 26 November 2020, Published 10 December 2020)
• Foers AD, Garnham AL, Smyth GK, Proudman SM, Cheng L, Hill AF, Pang KC, Wicks IP (2020). Circulating small non-coding RNA biomarkers of response to triple disease-modifying antirheumatic drug therapy in white women with early rheumatoid arthritis. Journal of Rheumatology 47(12), 1746-1751. [PMID: 32541082] (Accepted 5 May 2020, Epub 15 June 2020, Published 1 December 2020)
• Tong L, Wu PY, Phan JH, Hassazadeh HR, Jones WD, Shi L, Fischer M, Mason CE, Li S, Xu J, Shi W, Wang J, Thierry-Mieg J, Thierry-Mieg D, Hertwig F, Berthold F, Hero B, Liao Y, Smyth GK, Kreil D, Labaj PP, Megherbi D, Schroth G, Fang H, Tong W, Wang MD (2020). Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction. Scientific Reports 10(1), 17925. [PMID: 33087762] (Accepted 27 August 2020, Published 21 October 2020)
• Lalaoui N, Merino D, Giner G, Vaillant F, Chau D, Liu L, Pal B, Whittle JR, Etemadi N, Berthelet J, Gräsel J, Hall C, Ritchie ME, Ernst M, Smyth GK, Vaux DL, Visvader JE, Lindeman GJ, Silke J, Kratina T (2020). Targeting triple negative breast cancers with the Smac-mimetic birinapant. Cell Death and Differentiation 27(10):2768-2780. [PMID: 32341449] (Accepted 27 March 2020, Epub 27 April 2020, Published 1 October 2020)
• Keenan CR#, Coughlan HD#, Iannarella N, Johanson TM, Chan WF, Garnham AL, Smyth GK*, Allan RS* (2020). Suv39h-catalysed H3K9me3 is critical for euchromatic genome organisation and the maintenance of gene transcription. bioRxiv 2020.08.13.249078; doi: 10.1101/2020.08.13.249078. (Epub 14 August 2020)
• Whittle JR, Vaillant F, Surgenor E, Policheni AN, Giner G, Capaldo BD, Chen H-R, Liu HK, Dekkers JF, Sachs N, Clevers H, Fellowes A, Green T, Xu H, Fox S, Herold MJ, Smyth GK, Gray DHD, Visvader JE, Lindeman GJ (2020). Dual targeting of CDK4/6 and BCL2 pathways in estrogen receptor positive breast cancer. Clinical Cancer Research 26(15), 4120-4134. [PMID: 32245900] (Accepted 20 March 2020, Epub 3 April 2020, Published 1 August 2020)
• Ng AP, Coughlan HD, Hediyeh-zadeh S, Behrens K, Johanson TM, Low MSY, Bell CC, Gilan O, Chan YC, Kueh AJ, Boudier T, Feltham R, Gabrielyan A, DiRago L, Hyland CD, Ierino H, Mifsud S, Viney E, Willson T, Dawson MA, Allan RS, Herold MJ, Rogers K, Tarlinton DM, Smyth GK, Davis MJ, Nutt SL, Alexander WS (2020). An Erg-driven transcriptional program controls B-lymphopoiesis. Nature Communications 11(1), 3013. [PMID: 32541654] (Accepted 13 April 2020, Published 15 June 2020)
• Dawson CA, Pal B, Vaillant F, Gandolfo LC, Liu Z, Bleriot C, Ginhoux F, Smyth GK, Lindeman GJ, Mueller SN, Rios AC, Visvader JE (2020). Tissue-resident ductal macrophages survey the mammary epithelium and facilitate gland remodelling during involution. Nature Cell Biology 22(5), 546-558. [PMID: 32341550] (Accepted 6 March 2020, Epub 27 April 2020, Published 1 May 2020)
• Chappaz S, Law CW, Dowling M, Carey KT, Lane RM, Ngo LH, Wickramasinghe VO, Smyth GK, Ritchie ME, Kile BT (2020). Germline heterozygous mutations in Nxf1 perturb RNA metabolism and trigger thrombocytopenia and lymphopenia in mice. Blood Advances 4(7), 1270-1283. [PMID: 32236527] (Accepted 29 February 2020, Published 14 April 2020)
• Roth-Schulze AJ, Penno MAS, Ngui KM, Oakey H, Thomson RL, Vuillermin PJ, Craig ME, Rawlinson WD, Davis EA, Harris M, Soldatos G, Colman PG, Wentworth JM, Haynes A, Morahan G, Bediaga NG, Smyth GK, Papenfuss AT, Couper JJ, Harrison L (2020). Changes in the composition and function of the gut microbiome accompany type 1 diabetes in pregnancy. Research Square doi:10.21203/rs.3.rs-18520/v1. PPR:PPR121947. (Preprint 24 March 2020)
• Seillet, C, Luong, K, Tellier, J, Jacquelot, N, Shen, RD, Hickey, P, Wimmer, VC, Whitehead, L, Rogers, K, Smyth, GK, Garnham, AL, Ritchie, ME, Belz, GT (2020). The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity. Nature Immunology 21(2), 168-177. [PMID: 31873294] (Accepted 19 October 2019, Epub 23 December 2019, Published 1 February 2020)
• Kueh AJ, Eccles S, Tang L, Garnham AL, May RE, Herold MJ, Smyth GK, Voss AK, Thomas T (2020). HBO1 (KAT7) does not have an essential role in cell proliferation, DNA replication, or histone 4 acetylation in human cells. Molecular and Cellular Biology 40(4), e00506-e00519. [PMID: 31767635] (Accepted 11 November 2019, Epub 25 November 2019, Published 30 January 2020)
• Sidwell, T, Liao, Y, Garnham AL, Vasanthakumar, A, Gloury, R, Blume, J, Teh, PP, Chisanga, D, Thelemann, C, de Labastida Rivera, F, Engwerda, CR, Corcoran, L, Kometani, K, Kurosaki, T, Smyth, GK, Shi, W, Kallies, A (2020). Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis. Nature Communications 11(1), 252. [PMID: 31937752] (Accepted 7 November 2019, Published 14 January 2020)

2019

• Koçhan N, Tutuncu GY, Smyth GK, Gandolfo LC, Giner G (2019). qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data. PeerJ 7, e8260. [PMID: 31976167] [Full Text] (Accepted 20 November 2019, Published 18 December 2019)
• Bhuva, DD, Cursons, J, Smyth, GK, Davis, MJ (2019). Differential co-expression based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer. Genome Biology 20(1), 236. [PMID: 31727119] (Accepted 2 October 2019, Published 14 November 2019)
• Vrahnas C, Blank M, Dite TA, Tatarczuch L, Ansari N, Crimeen-Irwin B, Nguyen H, Forwood MR, Hu Y, Ikegame M, Bambery KR, Petibois C, Mackie EJ, Tobin MJ, Smyth GK, Oakhill JS, Martin TJ, Sims NA (2019). Increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary mineralization and brittle bone. Nature Communications 10(1), 3436. [PMID: 31366886] (Accepted 3 July 2019, Published 31 July 2019)
• Vanyai HK, Garnham AL, May RE, McRae HM, Collin C, Wilcox S, Smyth GK, Thomas T, Voss AK (2019). MOZ directs the distal-less homeobox gene expression program during craniofacial development. Development 146(14) dev175042. [PMID: 31340933] (Accepted 17 June 2019, Epub 24 July 2019)
• Stock AT, Collins N, Smyth GK, Hu Y, Hansen JA, D'Silva DB, Jama H, Lew AM, Gebhardt T, Wicks IP (2019). The selective expansion and targeted accumulation of bone-marrow derived macrophages drives cardiac vasculitis. Journal of Immunology 202(11), 3282-3296. [PubMed] (Accepted 29 March 2019, Epub 19 April 2019, Published 1 June 2019)
• Liao, Y, Smyth, GK, Shi, W (2019). The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research 47(8), e47. [PubMed] (Accepted 12 February 2019, Epub 20 February 2019, Published 7 May 2019)
• McRae HM, Garnham AL, Hu Y, Witkowski MT, Corbett MA, Dixon MP, May RE, Sheikh BN, Chiang W, Kueh AJ, Nguyen TA, Man K, Gloury R, Aubrey BJ, Policheni A, Di Rago L, Alexander WS, Gray DHD, Strasser A, Hawkins ED, Wilcox S, Gécz J, Kallies A, McCormack MP, Smyth GK, Voss AK, Thomas T (2019). PHF6 regulates hematopoietic stem and progenitor cells and its loss synergizes with expression of TLX3 to cause leukemia. Blood 133(16), 1729-1741. [PubMed] (Accepted 23 January 2019, Epub 12 February 2019, Published 18 April 2019)
• Rios AC, Capaldo BD, Vaillant F, Pal B, van Ineveld R, Dawson CA, Chen Y, Nolan E, Fu NY, 3DTCLSM Group, Jackling FC, Devi S, Clouston D, Whitehead L, Smyth GK, Mueller SN, Lindeman GJ, Visvader JE (2019). Intraclonal plasticity in mammary tumors revealed through large-scale single-cell resolution 3D imaging. Cancer Cell 35(4), 618-632. [PubMed] (Accepted 27 February 2019, Epub 28 March 2019, Published 15 April 2019)
• Delbridge ARD, Kueh AJ, Ke F, Zamudio NM, El-Saffin F, Jansz N, Wang G-Y, Iminitoff M, Beck T, Haupt S, Hu Y, May RE, Whitehead L, Tai L, Chiang W, Herold MJ, Haupt Y, Smyth GK, Blewitt ME, Thomas T, Strasser A, Voss AK (2019). Loss of p53 causes stochastic aberrant X-chromosome inactivation and female-specific neural tube defects. Cell Reports 27(2), 442-454. [PubMed] (Accepted 26 February 2019, Published 9 April 2019)
• Lok SW, Whittle JR, Vaillant F, Teh CE, Lo LL, Policheni AN, Bergin ART, Desai J, Ftouni S, Gandolfo LC, Liew D, Liu HK, Mann GB, Moodie K, Murugasu A, Pal B, Roberts AW, Rosenthal MA, Shackleton K, Silva MJ, Siow ZR, Smyth GK, Taylor L, Travers A, Yeo B, Yeung M, Bujak AZ, Dawson SJ, Gray DHD, Visvader JE, Lindeman GJ (2019). A phase 1b dose-escalation and expansion study of the BCL-2 inhibitor venetoclax combined with tamoxifen in ER and BCL-2-positive metastatic breast cancer. Cancer Discovery 9(3), 354-369. [PubMed] (Accepted 4 November 2018, Epub 5 December 2018, Published 1 March 2019)
• Merino D, Weber TS, Serrano A, Vaillant F, Liu K, Pal B, di Stefano L, Schroeder J, Lin D, Chen Y, Asselin-Labat ML, Schumacher TN, Cameron D, Smyth GK, Papenfuss AT, Lindeman GJ, Visvader JE, Naik SH (2019). Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer. Nature Communications 10(1), 766. [PubMed] (Accepted 18 January 2019, Published 15 February 2019)
• Bediaga NG, Coughlan HD, Johanson TM, Garnham AL, Naselli G, Schroeder J, Fearnley LG, Bandala-Sanchez E, Smyth GK, Allan RS, Harrison L (2019). Multi-Level Chromosome Remodeling Underlying Activation of Human T Cells. Cell Press Sneak Peek doi: 10.2139/ssrn.3329249. (Posted 5 February 2019)
• Chopin M, Lun ATL, Zhan Y, Schroeder J, Coughlan HD, D'Amico A, Mielke LA, Almeida FF, Kueh AJ, Dickins RA, Belz GT, Naik SH, Lew AM, Bouillet P, Herold MJ, Smyth GK, Corcoran LM, Nutt SL (2019). Transcription factor PU.1 promotes conventional dendritic cell identity and function via induction of transcriptional regulator DC-SCRIPT. Immunity 50(1), 77-90. [PubMed] (Accepted 9 October 2018, Epub 2 January 2019, Published 15 January 2019)

2018

• Kim, ML, Martin, WJ, Minigo, G, Keeble, JL, Garnham, AL, Pacini, G, Smyth, GK, Speed, TP, Carapetis J, Wicks, IP (2018). A dysregulated IL-1beta-GM-CSF axis in acute rheumatic fever that is limited by hydroxychloroquine. Circulation 138(23), 2648-2661. [PubMed] (Accepted 27 July 2018, Published 4 December 2018)
• Fu, NY, Pal, B, Chen, Y, Jackling, F, Milevskiy, M, Vaillant, F, Capaldo, B, Guo, F, Liu, KH, Rios, AC, Lim, NL, Kueh, AJ, Virshup, DM, Herold, MJ, Tucker, HO, Smyth, GK, Lindeman, GJ, Visvader, JE (2018). Foxp1 is indispensable for ductal morphogenesis and controlling the exit of mammary stem cells from quiescence. Developmental Cell 47(5), 629-644. [PubMed] (Accepted 1 October 2018, Epub 25 Oct 2018, Published 3 December 2018)
• Dunn PK, Smyth GK (2018). Generalized linear models with examples in R. Springer, New York, NY. DOI: 10.1007/978-1-4419-0118-7. ISBN: 978-1-4419-0118-7. (Accepted 16 December 2017, Published 17 November 2018)
• Aw, WC, Towarnicki SG, Melvin, RG, Youngson, NA, Garvin, MR, Hu, Y, Nielsen, S, Thomas, T, Pickford, R, Bustamante, S, Vila-Sanjurjo, A, Smyth, GK, Ballard, JWO (2018). Genotype to phenotype: diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLOS Genetics 14(11), e1007735. [PubMed] (Accepted 2 October 2018, Published 6 November 2018)
• Aubrey, BJ, Janic, A, Chen, Y, Chang, C, Lieschke, EC, Diepstraten, ST, Kueh, AJ, Bernardini, JP, Dewson, G, O'Reilly, LA, Whitehead, L, Voss, AK, Smyth, GK, Strasser, A, Kelly, GL (2018). Mutant TRP53 exerts a target gene selective dominant negative effect to drive tumor development. Genes and Development 32(21-22), 1420-1429. [PubMed] (Accepted 20 September 2018, Epub 26 October 2018, Published 1 November 2018)
• Johanson, TM, Lun, ATL, Coughlan, HD, Tan, T, Smyth, GK, Nutt, SL, Allan, RS (2018). Transcription factor-mediated supervision of global genome architecture maintains B cell identity. Nature Immunology 19(11), 1257-1264. [PubMed] (Accepted 5 September 2018, Epub 15 October 2018, Published 1 November 2018)
• Michalak, EM, Milevskiy, MJG, Joyce, RM, Dekkers, JF, Jamieson, PR, Pal, B, Dawson, CA, Hu, Y, Orkin, SH, Alexander, WS, Lindeman, GJ, Smyth, GK, Visvader, JE (2018). Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids. PLOS Biology 16(8), e2004986. [PubMed] (Accepted 26 July 2018, Published 6 August 2018)
• Baell, JB, Leaver, DJ, Hermans, SJ, Kelly, GL, Brennan, MS, Downer, NL, Nguyen, N, Wichmann, J, McRae, HM, Yang, Y, Cleary, B, Lagiakos, HR, Mieruszynski, S, Pacini, G, Vanyai, HK, Bergamasco, MI, May, RE, Davey, BK, Morgan, KJ, Sealey, AJ, Wang, B, Zamudio, N, Wilcox, S, Garnham, AL, Sheikh, BN, Aubrey, BJ, Doggett, K, Chung, MC, de Silva, M, Bentley, J, Pilling, P, Hattarki, M, Dolezal, O, Dennis, M, Falk, H, Ren, B, Charman, SA, White, KL, Rautela, J, Newbold, A, Hawkins, ED, Johnstone, RW, Huntington, ND, Peat, TS, Heath, JK, Strasser, A, Parker, MW, Smyth, GK, Street, IP, Monahan, BJ, Voss, AK, Thomas, T (2018). Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumor growth. Nature 560(7717), 253-257. [PubMed] (Accepted 21 June 2018, Published 1 August 2018)
• Johanson TM#, Coughlan HD#, Lun ATL, Bediaga NG, Naselli G, Garnham AL, Harrison LC, Smyth GK, Allan RS (2018). Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development. PLOS Genetics 14(6), e1007431. [PubMed] (Accepted 18 May 2018, Published 8 June 2018)
• O'Reilly, LA, Putoczki, TL, Mielke, LA, Low, JT, Lin, A, Preaudet, A, Herold, MJ, Yaprianto, K, Tai, L, Kueh, A, Pacini, G, Ferrero, RL, Gugasyan, R, Hu, Y, Christie, M, Wilcox, S, Grumont, R, O'Connor, L, Smyth, GK, Ernst, M, Waring, P, Gerondakis, S, Strasser, A (2018). Loss of NF-kB1 function causes gastric cancer by deregulating STAT1 dependent control of inflammation and immune checkpoints. Immunity 48(3), 570-583. [PubMed] (Accepted 18 January 2018, Published 20 March 2018)
• Xin A#, Lee M#, Hu Y#, Ignjatovic V, Shi W, Shipp A, Praporski S, Kallies A, Weintraub R, Monagle P, Smyth GK*, Konstantinov I* (2018). Identifying low-grade cellular rejection after heart transplantation in children using gene expression profiling. Physiological Genomics 50(3), 190-196. [PubMed] (Accepted 8 December 2017, Epub 20 December 2017, Published 1 March 2018)
• Vrahnas, C, Dite, TA, Ansari, N, Crimeen-Irwin, B, Nguyen, H, Forwood, MR, Hu, Y, Ikegame, M, Bambery, KR, Petibois, C, Tobin, MJ, Smyth, GK, Oakhill, JS, Martin, TJ, Sims, NA (2018). Increased autophagy in ephrinB2 deficient osteocytes is associated with hypermineralized, brittle bones. bioRxiv 260711; doi: 10.1101/260711. (Preprint 5 February 2018, revised 1 March 2018)

2017

• Jain, R, Sheridan, JM, Policheni, A, Heinlein, M, Gandolfo, LC, Dewson, G, Smyth, GK, Sansom, SN, Fu, NY, Visvader, JE, Holländer, GA, Strasser, A, Gray, DHD (2017). A critical epithelial survival axis regulated by MCL-1 maintains thymic function in mice. Blood 130(23), 2504-2515. [PubMed] (Accepted 22 September 2017, Epub 29 September 2017, Published 7 December 2017)
• Wentworth, J, Zhang, J-G, Bandala-Sanchez, E, Naselli, G, Liu, R, Ritchie, ME, Smyth, GK, O'Brien, PE, Harrison, LC (2017). Interferon-gamma released from omental adipose tissue of insulin-resistant humans alters adipocyte phenotype and impairs response to insulin and adiponectin release. International Journal of Obesity 41(12), 1782-1789. [PubMed] (Accepted 17 July 2017, Epub 3 August 2017, Published 1 December 2017)
• Chen, Y, Pal, B, Visvader, JE, Smyth, GK (2017). Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research 6, 2055. [PubMed] [Corrected preprint, code and data] (Published 28 Nov 2017, Version 2 published 8 Oct 2018)
• Pal B#, Chen Y#, Vaillant F#, Jamieson P, Gordon L, Rios AC, Wilcox S, Fu N, Liu KH, Jackling FC, Davis MJ, Lindeman GJ, Smyth GK*, Visvader JE* (2017). Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling. Nature Communications 8(1), 1627. [PubMed] (Accepted 28 September 2017, Published 20 November 2017)
• Johanson TM#, Coughlan HD#, Lun ATL, Bediaga NG, Naselli G, Garnham AL, Harrison LC, Smyth GK, Allan RS (2017). No kissing in the nucleus: unbiased analysis reveals no evidence of trans chromosomal regulation of mammalian immune development. bioRxiv 212985; doi: 10.1101/212985. (Epub 2 November 2017)
• Williams, SP, Odell, AF, Karnezis, T, Farnsworth, RH, Gould, CM, Li, J, Paquet-Fifield, S, Harris, NC, Walter, A, Gregory, JL, Lamont, SF, Liu, R, Takano, EA, Nowell, CJ, Bower, NI, Resnick, D, Smyth, GK, Coultas, L, Hogan, BM, Fox, SB, Mueller, SN, Simpson, KJ, Achen, MG, Stacker, SA (2017). Genome-wide functional analysis reveals central signaling regulators of lymphatic endothelial cell migration and remodeling. Science Signaling 10(499), eaal2987. [PubMed] (Accepted 15 August 2017, Published 3 October 2017)
• Kueh, AJ, Pal, M, Tai, L, Liao, Y, Smyth, GK, Shi, W, Herold, MJ (2017). An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles. Cell Death and Differentiation 24(10), 1821-1822. [PubMed] (Accepted 19 June 2017, Epub 28 July 2017, Published 1 October 2017)
• Nguyen, TA, Smith, BRC, Tate, MD, Belz, GT, Barrios, MH, Elgass, KD, Weisman, AS, Baker, PJ, Preston, S, Whitehead, L, Garnham, AL, Lundie, RJ, Smyth, GK, Pellegrini, M, O'Keeffe, M, Wicks, IP, Masters, SL, Hunter, CP, Pang, KC (2017). SIDT2 transports extracellular dsRNA into the cytoplasm for innate immune recognition. Immunity 47(3), 498-509. [PubMed] (Accepted 31 July 2017, Epub 12 September 017, Published 19 September 2017)
• Vasanthakumar A, Liao Y, Teh P, Pascutti MF, Oja AE, Garnham AL, Gloury R, Tempany JC, Sidwell T, Cuadrado E, Tuijnenburg P, Kuijpers TW, Lalaoui N, Mielke LA, Bryant VL, Hodgkin PD, Silke J, Smyth GK, Nolte MA, Shi W, Kallies A. (2017). The TNF receptor superfamily-NF-κB axis is critical to maintain effector regulatory T cells in lymphoid and non-lymphoid tissues. Cell Reports 20(12), 2906-2920. [PubMed] (Epub 7 September 2017, Published 19 September 2017)
• Merino, D, Whittle, JR, Vaillant, F, Serrano, A, Gong, J-N, Giner, G, Maragno, AL, Chanrion, M, Schneider, E, Pal, B, Li, X, Dewson,, G, Gräsel, J, Liu, K, Lalaoui, N, Segal, D, Herold, MJ, Huang, DCS, Smyth, GK, Geneste, O, Lessene, G, Visvader, JE, Lindeman, GJ (2017). Synergistic action of the MCL-1 inhibitor S63845 with current therapies in preclinical models of triple negative and HER2-amplified breast cancer. Science Translational Medicine 9(401), eaam7049. [PubMed] (Accepted 29 June 2017, Published 2 August 2017)
• Lun ATL, Smyth GK (2017). No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data. Statistical Applications in Genetics and Molecular Biology 16(2), 83-93. [PubMed] [Preprint] (Accepted 26 April 2017, Published 25 May 2017)
• Piovesan, D, Tempany, J, Di Pietro, A, Baas, I, Yiannis, C, O'Donnell, K, Chen, Y, Peperzak, V, Belz, GT, Mackay, CR, Smyth, GK, Groom, JR, Tarlinton, DM, Good-Jacobson, KL (2017). c-Myb regulates the T-bet-dependent differentiation program in B cells to coordinate antibody responses. Cell Reports 19(3), 461-470. [PubMed] (Accepted 6 March 2017, Published 18 April 2017)
• Vasanthakumar, A, Xu, D, Lun, ATL, Kueh, AJ, van Gisbergen, KPJM, Iannarella, N, Li, X, Yu, L, Wang, D, Williams, BRG, Lee, SCW, Majewski, IJ, Godfrey, DI, Smyth, GK, Alexander, WS, Herold, MJ, Kallies, A, Nutt, SL, Allan, RS (2017). A non-canonical function for Ezh2 in the preservation of immune homeostasis. EMBO Reports 18(4), 619-631. [PubMed] (Accepted 23 January 2017, Epub 21 February 2017, Published 1 April 2017)
• Holik AZ#, Law CW#, Liu R, Wang Z, Wang W, Ahn J, Marie-Liesse A-L, Smyth GK, Ritchie ME (2017). RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods. Nucleic Acids Research 45(5), e30. [PubMed] (Accepted 19 October 2016, Epub 29 November 2016, Published 17 March 2017)
• Witkowski, MT, Hu, Y, Roberts, KG, Boer, JM, McKenzie, MD, Liu, GJ, Le Grice, OD, Tremblay, CS, Ghisi, M, Willson, TA, Horstmann, MA, Aifantis, I, Cimmino, L, Frietze, S, den Boer, ML, Mullighan, CG, Smyth, GK, Dickins, RA (2017). Conserved IKAROS-regulated genes associated with B-progenitor acute lymphoblastic leukemia outcome. Journal of Experimental Medicine 214(3), 773-791. [PubMed] (Accepted 22 November 2016, Epub 10 February 2017, Published 6 March 2017)
• Fu, NY, Rios, AC, Pal, B, Law, CW, Jamieson, P, Liu, R, Vaillant, F, Jackling, F, Liu, KH, Smyth, GK, Lindeman, GJ, Ritchie, ME, Visvader, JE (2017). Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive. Nature Cell Biology 19(3), 164-176. [PubMed] (Accepted 11 January 2017, Epub 13 February 2017, Published 1 March 2017)
• Weeden, CE, Chen, Y, Ma, SB, Hu, Y, Ramm, G, Sutherland, KD, Smyth, GK, Asselin-Labat, ML (2017). Lung basal stem cells rapidly repair DNA damage using the error-prone non-homologous end-joining pathway. PLOS Biology 15(1), e2000731. [PubMed] (Accepted 23 December 2016, Published 26 January 2017)
• Dias, S, D'Amico, A, Cretney, E, Liao, Y, Tellier, J, Bruggeman, CW, Almeida, FF, Leahy, J, Belz, GT, Smyth, GK, Shi, W, Nutt, SL (2017). Effector regulatory T cell differentiation and immune homeostasis depend on the transcription factor Myb. Immunity 46(1), 78-91. [PubMed] (Accepted 23 November 2016, Published 17 January 2017)
• Gregory, JL, Walter, A, Alexandre, YO, Hor, JL, Liu, R, Ma, J, Devi, S, Tokuda, N, Owada, Y, Mackay, LK, Smyth, GK, Heath, WR, Mueller, SN (2017). Infection programs sustained lymphoid stromal cell responses and shapes lymph node remodeling upon secondary challenge. Cell Reports 18(2), 406-418. [PubMed] (Accepted 12 December 2016, Published 10 January 2017)

2016

• Teh, C, Lalaoui, N, Jain, R, Policheni, A, Heinlein, M, Alvarez-Diaz, S, Sheridan, J, Rieser, E, Deuser, S, Darding, M, Koay, HF, Hu, Y, Kupresanin, F, O'Reilly, L, Godfrey, D, Smyth, GK, Bouillet, P, Strasser, A, Walczak, H, Silke, J, Gray, D (2016). The linear ubiquitin chain assembly complex coordinates late thymic T cell differentiation and regulatory T cell homeostasis. Nature Communications 7, 13353. [PubMed] (Accepted 26 September 2016, Published 18 November 2016)
• Walker, EC, Johnson, RW, Hu, Y, Brennan, HJ, Poulton, IJ, Zhang, J-G, Jenkins, BJ, Smyth, GK, Nicola, NA, Sims, NA (2016). Murine Oncostatin M acts via Leukemia Inhibitory Factor Receptor to phosphorylate STAT3 but not STAT1, an effect that protects bone mass. Journal of Biological Chemistry 291(41), 21703-21716. [PubMed] (Accepted 17 August 2016, Epub 18 August 2016, Published 7 October 2016)
• Newman DM, Sakaguchi S, Lun ATL, Preston S, Pellegrini M, Khamina K, Bergthaler A, Nutt SL, Smyth GK, Voss AK, Thomas T, Ellmeier W, Belz GT, Allan RS (2016). Acetylation of the Cd8 locus by KAT6A determines memory T cell diversity. Cell Reports 16(12), 3311-3321. [PubMed] (Accepted 18 August 2016, Published 20 September 2016)
• de Graaf, CA, Choi, J, Baldwin, TM, Bolden, JE, Fairfax, KA, Robinson, AJ, Biben, C, Morgan, C, Ramsay, K, Ng, AP, Kauppi, M, Kruse, EA, Sargeant, TJ, Seidenman, N, D'Amico, A, D'Ombrain, MC, Lucas, EC, Koernig, S, Morelli, AB, Wilson, MJ, Dower, SK, Williams, B, Heazlewood, SY, Hu, Y, Nilsson, SK, Wu, L, Smyth, GK, Alexander, WS, Hilton, DJ (2016). Haemopedia: an expression atlas of murine hematopoietic cells. Stem Cell Reports 7(3), 571-582. [PubMed] (Accepted 10 July 2016, Epub 4 August 2016, Published 13 September 2016)
• Giner G, Smyth GK (2016). statmod: probability calculations for the inverse Gaussian distribution. R Journal 8(1), 339-351. [Full text] (Accepted 28 April 2016, Published 31 August 2016)
• Nolan E, Vaillant F, Branstetter D, Pal B, Giner G, Whitehead L, Lok SW, Mann GB, kConFab, Rohrbach K, Huang LY, Soriano R, Smyth GK, Dougall WC, Visvader JE, Lindeman GJ (2016). RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers. Nature Medicine 22(8), 933-939. [PubMed] (Accepted 6 May 2016, Epub 20 June 2016, Published 1 August 2016)
• Phipson B, Lee S, Majewski IJ, Alexander WS, Smyth GK (2016). Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. Annals of Applied Statistics 10, 946-963. [PubMed] [Full text] [arXiv preprint] (Accepted 25 February 2016, Published 31 June 2016)
• Chen Y, Lun ATL, Smyth GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438. [PubMed] [Full text] [Preprint] [Data and R code] (Published 20 June 2016)
• Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK*, Ritchie ME* (2016). RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research 5, 1408. [PubMed] [Full text] (Published 17 June 2016, Revised 1 January 2017 and 28 December 2018)
• Taberlay PC, Achinger-Kawecka J, Lun ATL, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O'Donoghue SI, Clark SJ (2016). Three-dimensional disorganisation of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Research 26(6), 719-731. [PubMed] (Accepted 5 April 2016, Epub 6 April 2016, Published 1 June 2016)
• Chopin M, Preston SP, Lun ATL, Tellier J, Smyth GK, Pellegrini M, Belz GT, Corcoran LM, Visvader JE, Wu L, Nutt SL (2016). RUNX2 mediates plasmacytoid dendritic cell egress from the bone marrow and controls viral immunity. Cell Reports 15, 866-878. [PubMed] (Accepted 3 March 2016, Epub 13 April, Published 26 April 2016)
• Xin A, Masson F, Liao Y, Preston S, Guan T, Gloury R, Olshansky M, Lin JX, Li P, Speed TP, Smyth GK, Ernst M, Leonard WJ, Pellegrini M, Kaech SM, Nutt SL, Shi W, Belz GT, Kallies A (2016). A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet. Nature Immunology 17, 422-432. [PubMed] (Accepted 7 December 2015, Epub 7 March 2016, Published 1 April 2016)
• Wentworth JM, Naselli G, Ngui K, Smyth GK, Liu R, O'Brien PE, Bruce C, Weir J, Cinel M, Meikle PJ, Harrison LC (2016). GM3 ganglioside and phosphatidylethanolamine-containing lipids are adipose tissue markers of insulin resistance in obese women. International Journal of Obesity 40, 706-713. [PubMed] (Epub 26 October 2015, Published 1 April 2016)
• Lun ATL, Chen Y, Smyth GK (2016). It's DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. Methods in Molecular Biology 1418, 391-416. [PubMed] [Preprint 8 April 2015] (Accepted 9 October 2015, Published 24 March 2016)
• Lun ATL, Smyth GK (2016). csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Research 44, e45. [PubMed] (Accepted 24 October 2015, Epub 17 November 2015, Published 18 March 2016)
• Tellier, J, Shi, W, Minnich, M, Liao, Y, Crawford, S, Smyth, GK, Kallies, A, Busslinger, M, Nutt, SL (2016). Blimp1 controls plasma cell function through regulation of immunoglobulin secretion and the unfolded protein response. Nature Immunology 17, 323-330. [PubMed] (Accepted 30 September 2015, Epub 18 January 2016, Published 1 March 2016)
• Rankin, LC, Girard-Madoux, MJH, Seillet, C, Mielke, LA, Kerdiles, Y, Fenis, A, Wieduwild, E, Putoczki, T, Mondot, S, Lantz, O, Demon, D, Papenfuss, AT, Smyth, GK, Lamkanfi, M, Carotta, S, Renauld, J-C, Shi, W, Carpentier, S, Soos, T, Arendt, C, Ugolini, S, Huntington, ND, Belz, GT, Vivier, E 2015. Complementarity and redundancy of IL-22-producing innate lymphoid cells. Nature Immunology 17, 179-186. [PubMed] (Accepted 16 October 2015, Epub 30 November 2015, Published 1 February 2016)
• Shields, BJ, Jackson, JT, Metcalf, D, Shi, W, Huang, Q, Garnham, AL, Glaser, SP, Beck, D, Pimanda, JE, Bogue, CW, Smyth, GK, Alexander, WS, McCormack, MP (2016). Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a. Genes & Development 30, 78-91. [PubMed] (Accepted 24 November 2015, Published 1 January 2016)

2015

• Etemadi, N, Chopin, M, Anderton, H, Tanzer, MC, Rickard, JA, Abeysekra, W, Hall, C, Spall, SK, Wang, B, Xiong, Y, Hla, T, Pitson, SM, Bonder, CS, Wong, WW, Ernst, M, Smyth, GK, Vaux, DL, Nutt, SL, Nachbur, U, Silke, J (2015). TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine Kinase 1. eLife 4, e10592. [PubMed] (Accepted 21 December 2015, Published 23 December 2015)
• Sheikh, BN, Phipson, B, El-Saafin, F, Vanyai, HK, Downer, NL, Bird, MJ, Kueh, AJ, May, RE, Smyth, GK, Voss, AK and Thomas, T (2015). MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway. Oncogene 34, 5807-5820. [PubMed] (Accepted 23 January 2015, Epub 16 March 2015, Published 19 November 2015)
• Coffey, MJ, Sleebs, BE, Uboldi, AD, Garnham, AL, Franco, M, Marino, ND, Panas, MW, Ferguson, DJP, Enciso, M, O'Neill, MT, Lopaticki, S, Stewart, RJ, Dewson, G, Smyth, GK, Smith, BJ, Masters, SL, Boothroyd, JC, Boddey, JA, Tonkin, CJ 2015. An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell. eLife 4, e10809. [PubMed] (Accepted 18 November 2015, Published 18 November 2015)
• Lun, ATL, Smyth, GK (2015). From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data. F1000Research 4, 1080. doi: 10.12688/f1000research.7016.2. [PubMed] (Published 16 Oct 2015)
• Khong, JJ, Wang, LY, Smyth, GK, McNab, AA, Hardy, TG, Selva, D, Llamas, B, Jung, C-H, Sharma, S, Burdon, KP, Ebeling, PR, Craig, JE (2015). Gene expression profiling of orbital adipose tissue in thyroid orbitopathy. Investigative Ophthalmology & Visual Science 56, 6438-6447. [PubMed] (Accepted 9 August 2015, Published 1 October 2015)
• Liu, X, Liu, R, Croker, BA, Lawlor, KE, Smyth, GK, and Wicks, IP (2015). Distinctive pro-inflammatory gene signatures induced in articular chondrocytes by oncostatin M and IL-6 are regulated by Suppressor of Cytokine Signaling-3. Osteoarthritis and Cartilage 23, 1743-1754. [PubMed] (Accepted 21 May 2015, Epub 2 June 2015, Published 1 October 2015)
• Liu, R, Holik, AZ, Su, S, Jansz, N, Chen, K, Leong, HS, Blewitt, ME, Asselin-Labat, M-L, Smyth, GK, Ritchie, ME (2015). Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research 43, e97. [PubMed] (Accepted 17 April 2015, Epub 29 April 2015, Published 3 September 2015)
• Lun, ATL, and Smyth, GK (2015). diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics 16, 258. [PubMed] (Accepted 21 July 2015, Published 19 August 2015)
• Pal, B, Chen, Y, Bert, A, Hu, Y, Beck, T, Sheridan, JM, Shi, W, Satterley, K, Jamieson, P, Goodall, GJ, Lindeman, GJ, Smyth, GK, and Visvader, JE (2015). Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits. Breast Cancer Research 17, 85. [PubMed] (Accepted 2 May 2015, Published 18 June 2015)
• Shi W, Liao Y, Willis, SN, Taubenheim, N, Inouye, M, Tarlinton, DM, Smyth, GK, Hodgkin, PD, Nutt, SL and Corcoran, LM (2015). Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells. Nature Immunology 16, 663-673. [PubMed] (Accepted 16 February 2015, Epub 20 April 2015, Published 1 June 2015)
• Witkowski, MT, Cimmino, L, Hu, Y, Trimarchi, T, Tagoh, H, McKenzie, MD, Best, SA, Tuohey, L, Willson, TA, Nutt, SL, Meinrad Busslinger, M, Aifantis, I, Smyth, GK, and Dickins, RA (2015). Activated Notch counteracts Ikaros tumor suppression in mouse and human T cell acute lymphoblastic leukemia. Leukemia 29, 1301-1311. [PubMed] (Accepted 29 January 2015, Epub 6 February 2015, Published 1 June 2015)
• Ng AP, Hu Y, Metcalf D, Hyland CD, Ierino H, Phipson B, Wu D, Baldwin TM, Kauppi M, Kiu H, Di Rago L, Hilton DJ, Smyth GK, Alexander WS (2015). Early lineage priming by trisomy of Erg leads to myeloproliferation in a Down syndrome model. PLOS Genetics 11, e1005211. [PubMed] (Accepted 14 April 2015, Published 14 May 2015)
• Sheikh, BN, Downer, NL, Phipson, B, Vanyai, HK, Kueh, AJ, McCarthy, DJ, Smyth, GK, Thomas, T and Voss, AK (2015). MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo. Proceedings of the National Academy of Sciences of the United States of America 112, 5437-5442. [PubMed] (Accepted 24 March 2015, Epub 14 April 2015, Published 28 April 2015)
• Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47. [PubMed] [Preprint 2 January 2015] (Accepted 6 January 2015, Epub 20 January 2015, Published 20 April 2015)
• Sheridan, JM, Ritchie, ME, Best, SA, Jiang, K, Beck, TJ, Vaillant, F, Liu, K, Dickins, RA, Smyth, GK, Lindeman, GJ, Visvader, JE. (2015). A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1. BMC Cancer 15, 221. [PubMed] (Accepted 12 March 2015, Published 3 April 2015)
• Fu, NY, Rios, AC, Pal, B, Soetanto, R, Lun, AT, Liu, K, Beck, T, Best, SA, Vaillant, F, Bouillet, P, Strasser, A, Preiss, T, Smyth, GK, Lindeman, GJ, and Visvader, J (2015). EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival. Nature Cell Biology 17, 365-375. [PubMed] (Accepted 19 January 2015, Epub 2 March 2015, Published 1 April 2015)
• Smyth, G. K. (2015). Optimization and nonlinear equations. Wiley StatsRef: Statistics Reference Online (edited by W. Piegorsch), John Wiley & Sons, https://doi.org/10.1002/9781118445112.stat05030.pub2, 9 pages. [Preprint 12 November 2014] (Accepted 20 November 2014, Published 31 March 2015)
• Sheikh, BN, Lee, SC, El-Saafin, F, Vanyai, HK, Hu, Y, Pang, SH, Grabow, S, Strasser, A, Nutt, SL, Alexander, WS, Smyth, GK, Voss, AK, and Thomas, T (2015). MOZ regulates B cell progenitors in mice and, consequently, Moz haploinsufficiency dramatically retards MYC-induced lymphoma development. Blood 125, 1910-1921. [PubMed] (Accepted 12 January 2015, Epub 20 January 2015, Published 19 March 2015)
• Vasanthakumar, A, Moro, K, Xin, A, Liao, Y, Gloury, R, Kawamoto, S, Fagarasan, S, Mielke, L, Afshar-Sterle, S, Masters, S, Nakae, S, Saito, H, Wentworth, JM, Li, P, Liao, W, Leonard, WJ, Smyth, GK, Shi, W, Nutt, SL, Koyasu, S, Kallies, A (2015). The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells. Nature Immunology 16, 276-285. [PubMed] (Accepted 8 Dec 2014, Epub 19 January 2015, Published 1 March 2015)
• Huber, W, Carey, VJ, Gentleman, R, Anders, S, Carlson, M, Carvalho, BS, Bravo, HC, Davis, S, Gatto, L, Girke, T, Gottardo, R, Hahne, F, Hansen, KD, Irizarry, RA, Lawrence, M, Love, MI, MacDonald, J, Obenchain, V, Oles, AK, Pagès, H, Reyes, A, Shannon, P, Smyth, GK, Tenenbaum, D, Waldron, L, Morgan, M (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12, 115-121. [PubMed] (Accepted 15 Dec 2014, Epub 29 January 2015, Published 1 February 2015)
• Overview of the csaw package. Bioconductor Newsletter, January 2015. (Published 5 January 2015)

2014

• Shi, W, Man, K, Smyth, GK, Nutt, SL, and Kallies, A (2014). Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells. Genomics Data 2, 396-398. [PubMed] (Accepted 28 October 2014, Epub 1 November 2014, Published 1 December 2014)
• Tan, K-L, Ling, K-H, Hewitt, CA, Cheah, P-S, Simpson, K, Gordon, L, Pritchard, MA, Smyth, GK, Thomas, T, and Scott, HS (2014). Transcriptional profiling of the postnatal brain of the Ts1Cje mouse model of Down syndrome. Genomics Data 2, 314-317. [PubMed] (Accepted 23 September 2014, Epub 2 Oct 2014, Published 1 December 2014)
• Holmes, M, Thong, R, Brady, J, Huntington, N, Hayakawa, Y, Andoniou, C, Fleming, P, Degli-Esposti, M, Belz, G, Kallies, A, Carotta, S, Smyth, M, Shi, W, Smyth, GK, Nutt, S (2014). Peripheral natural killer cell maturation depends on the transcription factor Aiolos. The EMBO Journal 33, 2721-2734. [PubMed] (Accepted 28 August 2014, Epub 15 October 2014, Published 18 November 2014)
• Potts, KS, Sargeant, TJ, Markham, JF, Shi, W, Biben, C, Josefsson, EC, Whitehead, LW, Rogers, KL, Liakhovitskaia, A, Smyth, GK, Kile, BT, Medvinsky, A, Alexander, WS, Hilton, DJ, and Taoudi, S (2014). A lineage of diploid platelet-forming cells precedes polyploid megakaryocyte formation in the mouse embryo. Blood 124(17), 2725-2729. [PubMed] (Accepted 8 Jul 2014, Epub 25 July 2014, Published 23 October 2014)
• Smyth, G. K. (2014). Nonlinear regression – extensions. Wiley StatsRef: Statistics Reference Online (edited by W. Piegorsch), John Wiley & Sons, https://doi.org/10.1002/9781118445112.stat07552. (Originally published in Encyclopedia of Environmetrics, republished in Wiley StatsRef 29 September 2014.)
• Smyth, G. K. (2014). Polynomial approximation. Wiley StatsRef: Statistics Reference Online (edited by T. Colton), John Wiley & Sons, https://doi.org/10.1002/9781118445112.stat05031. [Preprint] (Originally published in Encyclopedia of Biostatistics, republished in Wiley StatsRef 29 September 2014.)
• Smyth, G. K. (2014). Optimization and nonlinear equations. Wiley StatsRef: Statistics Reference Online (edited by T. Colton), John Wiley & Sons, https://doi.org/10.1002/9781118445112.stat05030. (Originally published in Encyclopedia of Biostatistics, republished in Wiley StatsRef 29 September 2014.)
• Smyth, G. K. (2014). Numerical integration. Wiley StatsRef: Statistics Reference Online (edited by T. Colton), John Wiley & Sons, doi: 10.1002/9781118445112.stat05029. https://doi.org/10.1002/9781118445112.stat05029. (Originally published in Encyclopedia of Biostatistics, republished in Wiley StatsRef 29 September 2014.)
• Smyth, G. K. (2014). Numerical analysis. Wiley StatsRef: Statistics Reference Online (edited by T. Colton), John Wiley & Sons, https://doi.org/10.1002/9781118445112.stat05028. (Originally published in Encyclopedia of Biostatistics, republished in Wiley StatsRef 29 September 2014.)
• Maindonald, J. H. and Smyth, G. K. (2014). Matrix computations. Wiley StatsRef: Statistics Reference Online (edited by T. Colton), John Wiley & Sons, https://doi.org/10.1002/9781118445112.stat05025. (Originally published in Encyclopedia of Biostatistics, republished in Wiley StatsRef 29 September 2014.)
• Munro, SA, Lund, SP, Pine, PS, Binder, H, Clevert, D-A, Conesa, A, Dopazo, J, Fasold, M, Hochreiter, S, Hong, H, Jafari, N, Kreil, DP, Labaj, PP, Li, S, Liao, Y, Lin, SM, Meehan, J, Mason, CE, Santoyo, J, Setterquist, RA, Shi, L, Shi, W, Smyth, GK, Stralis-Pavese, N, Su, Z, Tong, W, Wang, C, Wang, J, Xu, J, Ye, Z, Yang, Y, Yu, Y, Salit, M (2014). Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature Communications 5, 5125. [PubMed] (Accepted 14 August 2014, Published 25 September 2014)
• Su, Z, Labaj, PP, Li, S, Thierry-Mieg, J, Thierry-Mieg, D, Shi, W, Wang, C, Schroth, GP, Setterquist, RA, Thompson, JF, Jones, WD, Xiao, W, Xu, W, Jensen, RV, Kelly, R, Xu, J, Conesa, A, Furlanello, C, Gao, H, Hong, H, Jafari, N, Letovsky, S, Liao, Y, Lu, F, Oakeley, EJ, Peng, Z, Praul, CA, Santoyo-Lopez, J, Scherer, A, Shi, T, Smyth, GK, Staedtler, F, Sykacek, P, Tan, X-X, Thompson, A, Vandesompele, J, Wang, MD, Eli, JW, Wolfinger, RD, Zavadil, J, Auerbach, SS, Bao, W, Binder, H, Blomquist, T, Brilliant, MH, Bushel, PR, Cai, W, Catalano, JG, Chang, C-W, Chen, T, Chen, G, Chen, R, Chierici, M, Chu, T-M, Clevert, D-A, Deng, Y, Derti, A, Devanara, V, Dong, Z, Dopazo, J, Du, T, Fang, H, Fang, Y, Fasold, M, Fernandez, A, Fischer, M, Furió-Tarí, P, Fuscoe, JC, Gaj, S, Gandara, J, Gao, H, Ge, W, Gondo, Y, Gong, B, Gong, M, Gong, Z, Green, B, Guo, C, Guo, L, Guo, L-W, Hadfield, J, Hellemans, J, Hochreiter, S, Jia, M, Jian, M, Johnson, CD, Kay, S, Kleinjans, J, Lababidi, S, Levy, S, Li, Q-Z, Li, L, Li, P, Li, Y, Li, H, Li, J, Li, S, Lin, SM, López, FJ, Lu, X, Luo, H, Ma, X, Meehan, J, Megherbi, DB, Mei, N, Mu, B, Ning, B, Pandey, A, Pérez-Florido, J, Perkins, RG, Peters, R, Phan, JH, Pirooznia, M, Qian, F, Qing, T, Rainbow, L, Rocca-Serra, P, Sambourg, L, Sansone, S-A, Schwartz, S, Shah, R, Shen, J, Smith, TM, Stegle, O, Stralis-Paves, N, Stupka, E, Suzuki, Y, Szkotnicki, LT, Tinning, M, Tu, B, van, J, Vela, A, Venturini, E, Walker, SJ, Wan, L, Wang, W, Wang, J, Wang, J, Wieben, ED, Willey, JC, Wu, P-Y, Xuan, J, Yang, Y, Ye, Z, Yin, Y, Yu, Y, Yuan, Y-C, Zhang, J, Zhang, KK, Zhang, W, Zhang, W, Zhang, Y, Zhao, C, Zheng, Y, Zhou, Y, Zumbo, P, Tong, W, Kreil, DP, Mason, CE, and Shi, L (2014). A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology 32(9), 903-914. [PubMed] (Accepted 11 May 2014, Epub 24 August 2014, Published 1 September 2014)
• Ling, K-H, Hewitt, CA, Tan, K-L, Cheah, P-S, Vidyadaran, S, Lai, M-I, Lee, H-C, Simpson, K, Hyde, L, Pritchard, MA, Smyth, GK, Thomas, T, and Scott, HS (2014). Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks. BMC Genomics 15, 624. [PubMed] (Accepted 16 July 2014, Published 22 July 2014)
• Good-Jacobson, KL, Chen, Y, Voss, AK, Smyth, GK, Thomas, T, and Tarlinton, DM (2014). Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ. PNAS 111, 9585-9590. [PubMed] (Accepted 28 May 2014, Epub 16 June 2014, Published 1 July 2014)
• Chen, Y, Lun, ATL, and Smyth, GK (2014). Differential expression analysis of complex RNA-seq experiments using edgeR. In: Statistical Analysis of Next Generation Sequence Data, Somnath Datta and Daniel S Nettleton (eds), Springer, New York, pages 51--74. [Publisher] [Preprint 31 January 2014] (Accepted 8 February 2014, Published 1 July 2014)
• Lun, ATL and Smyth, GK (2014). De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly. Nucleic Acids Research 42, e95. [Publisher] [PubMed] (Accepted 14 Apr 2014, Epub 22 May 2014, Published 17 June 2014)
• Liu, GJ, Cimmino, L, Jude, JG, Hu, Y, Witkowski, MT, McKenzie, MD, Kartal-Kaess, M, Best, SA, Tuohey, L, Liao, Y, Shi, W, Mullighan, CG, Farrar, MA, Nutt, SL, Smyth, GK, Zuber, J, and Dickins, RA (2014). Pax5 loss imposes a reversible differentiation block in B progenitor acute lymphoblastic leukemia. Genes & Development 28, 1337-1350. [PubMed] (Accepted 16 May 2014, Published 15 June 2014)
• Giner, G, and Smyth, GK (2014). A monotonically convergent Newton iteration for the quantiles of any unimodal distribution, with application to the inverse Gaussian distribution. [Preprint 28 May 2014] [See arXiv:1603.06687 for a later version of this manuscript.]
• Chevrier, S, Emslie, D, Shi, W, Kratina, T, Wellard, C, Karnowski, A, Erikci, E, Smyth, GK, Chowdhury, K, Tarlinton, D, and Corcoran, LM (2014). The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity. Journal of Experimental Medicine 211, 827-840. [PubMed] (Accepted 10 February 2014, Epub 7 April 2014, Published 5 May 2014)
• Willis, SN, Good-Jacobson, KL, Curtis, J, Light, A, Tellier, J, Shi, W, Smyth, GK, Tarlinton, DM, Belz, GT, Corcoran LM, Kallies, A, and Nutt, SL (2014). Transcription factor IRF4 regulates germinal center cell formation through a B-cell intrinsic mechanism. Journal of Immunology 192, 3200-3206. [PubMed] (Accepted 28 January 2014, Epub 3 March 2014, Published 1 April 2014)
• Liao Y, Smyth GK, Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7), 923-930. [PubMed] (Accepted 7 November 2013, Epub 13 November 2013, Published 1 April 2014)
• Law, CW, Chen, Y, Shi, W, and Smyth, GK (2014). Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 15, R29. [PubMed] [Supplementary Information] [Preprint with corrections] [F1000Prime review] (Accepted 9 January 2014, Published 3 February 2014)
• Bryant, PA, Smyth, GK, Gooding, T, Oshlack, A, Harrington, Z, Currie, B, Carapetis, J, Robins-Browne, R, and Curtis, N (2014). Susceptibility to acute rheumatic fever: differential expression of genes involved in cytotoxicity, chemotaxis and apoptosis. Infection and Immunity 82, 753-761. [PubMed] (Accepted 24 November 2013, Epub 2 December 2013, Published 1 February 2014)
• Dagley, LF, White, CA, Liao, Y, Shi, W, Smyth, GK, Orian, JM, Emili, A, and Purcell, AW (2014). Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain. Proteomics 14, 241-261. [PubMed] (Accepted 11 November 2013, Epub 20 November 2013, Published 1 February 2014)

2013

• Pasricha S, Payne M, Canovas D, Pase L, Ngaosuwankul P, Beard S, Oshlack A, Smyth GK, Chaiyaroj SC, Boyce KJ, Andrianopoulos A (2013). Cell type specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological and environmental demands. G3: Genes, Genomes, Genetics 3, 1997-2014. [PubMed] [Cover image] (Accepted 6 September 2013, Epub 23 September 2013, Published 6 November 2013)
• Man K, Miasari M, Shi W, Xin A, Henstridge DC, Preston S, Pellegrini M, Belz GT, Smyth GK, Febbraio MA, Nutt SL, Kallies A (2013). IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells. Nature Immunology 14, 1155-1165. [PubMed] [F1000] (Accepted 31 July, Epub 22 September 2013, Published 1 November 2013)
• Lee, SCW, Phipson, B, Hyland, CD, Leong, HS, Allan, RS, Lun, A, Hilton, DJ, Nutt, SL, Blewitt, ME, Smyth, GK, Alexander, WS, Majewski, IJ (2013). Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma. Blood 122, 2654-2663. [PubMed] (Accepted 13 August 2013, Epub 27 August 2013, Published 10 October 2013)
• Anders, S, McCarthy, DJ, Chen, Y, Okoniewski, M, Smyth, GK, Huber, W, and Robinson, MD (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols. 8, 1765-1786. [PubMed] [Preprint] (Accepted 23 May 2013, Published 1 September 2013)
• Vaillant, F, Merino, D, Lee, L, Breslin, K, Ritchie, ME, Smyth, GK, Christie, M, Phillipson, LJ, Burns, CJ, Mann, GB, Visvader, JE, and Lindeman, GJ (2013). Targeting BCL-2 with the BH3 mimetic ABT-199 in ER-positive breast cancer. Cancer Cell 24, 120-129. [PubMed] (Accepted 4 June 2013, Published 8 July 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, 876-888. [PubMed] [Full Text] (Accepted 6 April 2013, Epub 24 May 2013, Published 1 July 2013)
• Phipson, B, Lee, S, Majewski, IJ, Alexander, WS, and 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] [See arXiv:1602.08678 for a later version of this manuscript.]
• 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 19, 3474-3484. [PubMed] (Accepted 27 April 2013, Epub 30 April 2013, Published 1 July 2013)
• George J#, Gorringe KL#, Smyth GK, Bowtell DDL (2013). Identifying associations between genomic alterations in tumors. Methods in Molecular Biology 1049, 9-19. [PubMed] [Full Text] (Accepted 21 February 2012, published Spring 2013)
• Smyth, GK, and Altman, NS (2013). Separate-channel analysis of two-channel microarrays: recovering inter-spot information. BMC Bioinformatics 14, 165. [Full Text] (Accepted 10 May 2013, Published 26 May 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(10), e108. [PubMed] [Full Text] [Software] (Accepted 8 March 2013, Epub 4 April 2013, Published 1 May 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 110, 6091-6096. [PubMed] (Accepted 12 March 2013, Epub 26 March 2013, Published 9 April 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, Epub 26 December 2012, Published 1 March 2013)
• Bolden JE, Shi W, Jankowski K, Kan C-Y, Cluse L, MacKenzie KL, Smyth GK, 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)
• Pal B, Bouras T#, Shi W#, Vaillant F, Sheridan J, Fu N, Breslin K, Jiang K, Ritchie ME, Young M, Lindeman GJ*, Smyth GK*, 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, Epub 31 January 2013, Published 21 February 2013)

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. [PubMed] [Preprint PDF] (Accepted 31 July 2012, Published 22 October 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, Epub 24 Aug 2012, Published 1 October 2012)
• Wu, D, Smyth, GK (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 40, e133. [PubMed] (Accepted 1 May 2012, Epub 25 May 2012, Published 1 September 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, 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. Journal of Biological Chemistry 287, 20652-20663. [PubMed] (Accepted 23 April 2012, Epub 25 April 2012, Published 8 June 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. [PubMed] (Accepted 31 March 2012, Published 23 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. [PubMed] (Accepted 29 February 2012, Published 10 May 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. [PubMed] (Accepted 10 January 2012, Epub 28 January 2012, Published 10 May 2012)
• Smyth, GK (one of a panel of eight experts) (2012). Transcriptomics Technical Guide. Genome Technology Magazine, 1 April. (Accepted 25 February 2012, Published 1 April 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. [F1000] (Accepted 22 June 2012, Epub 18 July 2011, Published 21 Feb 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, Epub 25 October 2011, Copyright year 2012)

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, Epub 19 September 2011, Published 1 November 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. [PubMed] (Accepted 8 June 2011, Epub 1 August 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, Epub 7 July 2011, Published 1 September 2011)
• Ng AP, Loughran SJ, Metcalf D, Hyland CD, deGraaf CA, Hu Y, Smyth GK, Hilton DJ, Kile BT, 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, Epub 14 June 2011, Published 1 September 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, Epub 19 April 2011, Published 1 September 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, Epub 18 July 2011, Published 9 August 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, SN, 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, Epub 15 June 2011, Published 15 July 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. [PubMed] (Accepted 13 May 2011, Published 31 May 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)
• Gordon L, Joo, JHE, Andronikos, R, Ollikainen, M, Wallace, EM, Umstad, MP, Permezel, M, Oshlack, A, Morley, R, Carlin, JB, Saffery, R, Smyth, GK, 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. [PubMed] (Accepted 5 February 2011, Published 1 May 2011)
• Helland Å#, Anglesio MS#, George J#, Cowin PA, Johnstone CN, House CM, Sheppard KE, Etemadmoghadam D, Melnyk N, Rustgi AK, Phillips WA, Johnsen H, Holm R, Kristensen GB, Australian Ovarian Cancer Study Group, Pearson RB, Børresen-Dale AL, Huntsman DG, deFazio A, Creighton CJ, Smyth GK, Bowtell DDL (2011). Deregulation of MYCN, LIN28B and LET7 in a molecular subtype of aggressive high-grade serous ovarian cancers. PLoS ONE 6, e18064. (Accepted 25 February 2011, Published 13 April 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, Epub 6 March 2011, Published 1 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. [Full Text] (Accepted 1 March 2011, Published 31 March 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, Epub 6 August 2010, Published 1 March 2011)

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. [Full Text] (Epub 29 November 2010, Published 14 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, Epub 9 September 2010, Published 9 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, Epub 4 November 2010, Published 1 December 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. [PubMed] (Accepted 16 September 2010, Epub 6 October 2010, Published 1 December 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. [PubMed] (Published 12 November 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)
• 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, Issue 1, Article 39. [PubMed] [Reprint with Corrections] (Accepted 13 September 2010, Published 31 October 2010, Corrected 9 February 2011)
• 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. [PubMed] (Accepted 16 April 2010, Published 10 September 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. [PubMed] (Accepted 4 July 2010, Epub 7 July 2010, Published 1 September 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. [PubMed] (Accepted 21 April 2010, Epub 5 May 2010, Published 5 August 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. [PubMed] (Accepted 31 May 2010, Published 16 July 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. [PubMed] (Accepted 16 March 2010, Epub 31 March 2010, Published 1 July 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. [PubMed] [F1000] (Epub 11 April 2010, Published 10 June 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. [PubMed] (Accepted 30 March 2010, Epub 5 April 2010, Published 1 June 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. [Full Text] (Accepted 16 November 2009, Epub 2 December 2009, Published 1 May 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. [PubMed] (Accepted 12 December 2009, Epub 7 January 2010, Published 1 April 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. [Full Text] [F1000] (Published 26 March 2010)
• Young, MD, Wakefield, MJ, Smyth, GK, Oshlack, A (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11, R14. [Full Text] (Published 4 February 2010)
• Robinson, MD, McCarthy, DJ, Smyth, GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. [PubMed] (Accepted 23 October 2009, Epub 11 November 2009, Published 1 January 2010)

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. [Full Text] (Accepted 10 November 2008, Epub 28 September 2009, Published 1 December 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. [Full Text] (Accepted 19 October 2009, Published 11 November 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. [Full Text] (Accepted 24 September 2009, Epub 23 October 2009, Published 10 November 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, Epub 25 August 2009, Published 14 October 2009)
• 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. [Full Text] (Accepted 25 September 2009, Published 2 October 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.
• 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. [Full Text] [Preprint PDF] (Accepted 20 June 2009, Epub 27 June 2009, Published 15 August 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 carriers. Nature Medicine 15, 907-913. [Full Text] [F1000] (Published 2 August 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. [PubMed] (Epub 27 March 2009, Published 4 June 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. [PubMed] (Epub 9 February 2009, Published 7 May 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. [PubMed] (Epub 16 January 2009, Published May 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. [PubMed] (Published 1 April 2009)
• Silver, JD, Ritchie, ME, and Smyth, GK (2009). Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics 10, 352-363. [PubMed] (Epub 8 Dec 2008, Published 1 April 2009)
• McCarthy, DJ, and Smyth, GK (2009). Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25, 765-771. [PubMed] (Epub 28 January 2009, Published 15 March 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. [PubMed] (Published 12 February 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. [PubMed] [F1000] (Published 6 February 2009)

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. [PubMed] (Published 21 November 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. [Full Text] (Published 1 October 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. [PubMed] (Published 31 July 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. [Full Text] (Published 14 July 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. [Full Text] (Accepted 28 November 2007, Published May 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. [Full Text] (Accepted 4 March 2008, Published 15 April 2008)
• Robinson, MD, and Smyth, GK (2008). Small sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9, 321-332. [Full Text] [Preprint] (Accepted 19 July 2007, Epub 29 August 2007, Published 1 April 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. [Full Text] (Published 1 March 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, Epub 17 October 2007, Published 1 March 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. [PubMed] [Nature Review Genetics Research Highlight] (Accepted 28 December 2007, Published 28 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. [PubMed] (Accepted 5 December 2007, Published 1 February 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)

2007

• Robinson, MD, and Smyth, GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887. [PubMed] [Supplementary information] [Software] (Epub 19 September 2007, Published 1 November 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. [PubMed] [Supplementary Information] (Epub 25 August 2007, Published 15 October 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. [PubMed] (Accepted 25 July 2007, Published October 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. [PDF] (Published 2 April 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] (Published 23 March 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] (Published 1 May 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] (Published 4 Jan 2007)

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] [Data and Supplementary Information] (Published 22 Nov 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. [Full Text] (Published 11 October 2006)
• Smyth, G. K. (2006). Optimization. Encyclopedia of Environmetrics, DOI: 10.1002/9780470057339.vao011. (Originally published 15 January 2002, republished in the online edition 15 September 2006)
• Smyth, G. K. (2006). Nonlinear Regression. Encyclopedia of Environmetrics, DOI: 10.1002/9780470057339.van017. (Originally published 15 January 2002, republished in the online edition 15 September 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] (Published 1 July 2006)
• Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics 7, Article 261. [PubMed] [Full Text] [Supplementary Information] (Published 19 May 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. [PubMed] (Epub 12 May 2006, Published 1 Dec 2006)
• 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. [PubMed] (Published 1 April 2006)
• 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. [Full Text] [F1000] (Published 9 March 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. [Full Text] [F1000] (Published 5 January 2006)

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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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. [PubMed] [Supplementary Information] [Preprint PDF] [Errata] [Faculty1000Prime] (Epub 18 January 2005, Published 1 May 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)
• 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. [Full Text] (Published 8 March 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)
• Smyth, G. K. (2005). Polynomial approximation. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 4136-4140. [Preprint] (Published Feb 2005)
• Smyth, G. K. (2005). Optimization and nonlinear equations. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 3857-3863. (Published Feb 2005)
• Smyth, G. K. (2005). Numerical integration. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 3766-3773. (Published Feb 2005)
• Smyth, G. K. (2005). Numerical analysis. In: Encyclopedia of Biostatistics Second Edition, Volume 6, P. Armitage and T. Colton (eds.), Wiley, London, pages 3762-3766. (Published Feb 2005)
• Maindonald, J. H. and Smyth, G. K. 2005. Matrix computations. In: Encyclopedia of Biostatistics Second Edition, Volume 5, P. Armitage and T. Colton (eds.), Wiley, London, 8 pages. (Published Feb 2005)

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. [Full Text] (Published 12 Oct 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)
• 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, Y. H., and Zhang, J. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 5, R80. [Full Text] (Published 15 Sep 2004)
• Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706. [PubMed] (Published 5 Aug 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. [PubMed] (Published Aug 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)
• 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)
• 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. [PubMed] (Published 1 Mar 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. [PubMed] [Reprint PDF with corrections] (Published Feb 2004)

2003

• Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273. [PubMed] [Preprint PDF] (Published December 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., Yang, Y.-H., Speed, T. P. (2003). Statistical issues in cDNA microarray data analysis. Methods in Molecular Biology 224, 111-136. [PubMed] [Full Text PDF] [Preprint PDF] (Published March 2003)

Earlier Publications

• Publications up to 2002

Epub = Electronic Publication ahead of print (aka Advance Online Publication).
Publications on this page are in reverse chronological order of publication (starting from most recent).