Gordon Smyth Home
- Publications to 2002
- Publications 2003-2014
- Lun, ATL, and 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.
(Accepted 26 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.
(Accepted 19 October 2016, Epub 29 November 2016)
- 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, and 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.
(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.
(Accepted 23 January 2017, Epub 21 February 2017, Published 1 April 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.
(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.
(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.
(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.
(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, and Mueller, SN (2017).
Infection programs sustained lymphoid stromal cell responses and shapes lymph node remodeling upon secondary challenge.
Cell Reports 18(2), 406-418.
(Accepted 12 December 2016, Published 10 January 2017)
- 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, and Gray, D (2016).
The linear ubiquitin chain assembly complex coordinates late thymic T cell differentiation and regulatory T cell homeostasis.
Nature Communications 7, 13353.
(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.
(Accepted 17 August 2016, Epub 18 August 2016, Published 7 October 2016)
- Newman DM, Sakaguchi S, Lun A, 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.
(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.
(Accepted 10 July 2016, Epub 4 August 2016, Published 13 September 2016)
- Giner, G, and Smyth, GK (2016).
statmod: probability calculations for the inverse Gaussian distribution.
R Journal 8(1), 339-351.
(Accepted 28 April 2016, Published 31 August 2016)
- Nolan, E, Vaillant, F, Branstetter, D, Pal, B, Giner, G, Whitehead, L, Lok, SW, Mann, GB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (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.
(Accepted 6 May 2016, Epub 20 June 2016, Published 1 August 2016)
- Phipson, B, Lee, S, Majewski, IJ, Alexander, WS, and Smyth, GK (2016).
Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression.
Annals of Applied Statistics 10, 946-963.
(Accepted 25 February 2016, Published 31 June 2016)
- Chen Y, Lun ATL, and 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.
[Data and R code]
(Published 20 June 2016)
- Law, CW, Alhamdoosh, M, Su, S, Smyth, GK, Ritchie, ME (2016).
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.
F1000Research 5, 1408.
(Published 17 June 2016, Revised 1 January 2017)
- 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.
(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, and Nutt, SL (2016).
RUNX2 mediates plasmacytoid dendritic cell egress from the bone marrow and controls viral immunity.
Cell Reports 15, 866-878.
(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.
A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet.
Nature Immunology 17, 422-432.
(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.
(Epub 26 October 2015, Published 1 April 2016)
- Lun, ATL, Chen, Y, and 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.
[Preprint 8 April 2015]
(Accepted 9 October 2015, Published 24 March 2016)
- Lun, ATL, and Smyth, GK (2016).
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.
Nucleic Acids Research 44, e45.
(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.
(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.
(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.
(Accepted 24 November 2015, Published 1 January 2016)
- 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.
(Accepted 21 December 2015, Published 23 December 2015)
- Coffey, MJ, Sleebs, BE, Uboldi, AD, Garnham, A, 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.
(Accepted 18 November 2015, Published 18 November 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.
(Accepted 23 January 2015, Epub 16 March 2015, Published 19 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.
(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.
(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.
(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.
(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.
(Accepted 21 July 2015, Published 19 August 2015)
- Pal, B, Chen, Y, Bert, A, Yifang 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.
(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.
(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.
(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.
(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.
(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.
[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.
(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.
(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, 1-9.
[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.
(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.
(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.
(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)
Epub = Electronic Publication ahead of print (aka Advance Online Publication)