Publications

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• Bhupinder Pal, Y. Chen, Francois Vaillant, Bianca D Capaldo, Rachel Joyce, Xiaoyu Song, Vanessa L Bryant, Jocelyn S Penington, Leon Di Stefano, Nina Tubau Ribera, Stephen Wilcox, Gregory B Mann, A. Papenfuss, Geoffrey J Lindeman, G. Smyth, Jane E Visvader, kConFab. A single?cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast. The EMBO journal, 40, e107333 (23pp), 2021. doi: 10.15252/embj.2020107333.

• Tom Sidwell, Yang Liao, Alexandra L Garnham, Ajithkumar Vasanthakumar, Renee Gloury, Jonas Blume, Peggy P Teh, David Chisanga, Christoph Thelemann, Fabian de Labastida Rivera, Christian R Engwerda, Lynn Corcoran, Kohei Kometani, Tomohiro Kurosaki, G. Smyth, Wei Shi, Axel Kallies. Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis.. Nature communications, 11, 252 (17pp), 2020. doi: 10.1038/s41467-019-14112-2.

• Caleb A Dawson, Bhupinder Pal, François Vaillant, Luke C Gandolfo, Zhaoyuan Liu, Camille Bleriot, Florent Ginhoux, G. Smyth, Geoffrey J Lindeman, Scott N Mueller, Anne C Rios, Jane E Visvader. Tissue-resident ductal macrophages survey the mammary epithelium and facilitate tissue remodelling.. Nature cell biology, 546-+, 2020. doi: 10.1038/s41556-020-0505-0.

• Andrew J Kueh, Samantha Eccles, Leonie Tang, Alexandra L Garnham, Rose E May, Marco J Herold, G. Smyth, Anne K Voss, Tim Thomas. 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, 2020. doi: 10.1128/MCB.00506-19.

• Ashley P Ng, Hannah D Coughlan, Soroor Hediyeh-Zadeh, Kira Behrens, Timothy M Johanson, Michael Sze Yuan Low, Charles C Bell, Omer Gilan, Y. Chan, Andrew J Kueh, Thomas Boudier, Rebecca Feltham, Anna Gabrielyan, Ladina DiRago, Craig D Hyland, Helen Ierino, Sandra Mifsud, Elizabeth Viney, Tracy Willson, Mark A Dawson, Rhys S Allan, Marco J Herold, Kelly Rogers, David M Tarlinton, G. Smyth, Melissa J Davis, Stephen L Nutt, Warren S Alexander. An Erg-driven transcriptional program controls B cell lymphopoiesis.. Nature communications, 11, 3013 (14pp), 2020. doi: 10.1038/s41467-020-16828-y.

• Stephane Chappaz, Charity W Law, Mark R Dowling, Kirstyn T Carey, Rachael M Lane, Linh H Ngo, Vihandha O Wickramasinghe, G. Smyth, M. Ritchie, Benjamin T Kile. Germline heterozygous mutations in Nxf1 perturb RNA metabolism and trigger thrombocytopenia and lymphopenia in mice.. Blood advances, 4, 1270-1283, 2020. doi: 10.1182/bloodadvances.2019001323.

• Najoua Lalaoui, Delphine Merino, Goknur Giner, Francois Vaillant, Diep Chau, Lin Liu, Tobias Kratina, Bhupinder Pal, James R Whittle, Nima Etemadi, Jean Berthelet, Julius Grasel, Cathrine Hall, M. Ritchie, Matthias Ernst, G. Smyth, David L Vaux, Jane E Visvader, Geoffrey J Lindeman, John Silke, Julius Gräsel. Targeting triple-negative breast cancers with the Smac-mimetic birinapant.. Cell death and differentiation, 27, 2768-2780, 2020. doi: 10.1038/s41418-020-0541-0.

• James R Whittle, François Vaillant, Elliot Surgenor, Antonia N Policheni, Göknur Giner, Bianca D Capaldo, Huei-Rong Chen, He K Liu, Johanna F Dekkers, Norman Sachs, Hans Clevers, Andrew Fellowes, Thomas Green, Huiling Xu, Stephen B Fox, Marco J Herold, G. Smyth, Daniel HD Gray, Jane E Visvader, Geoffrey J Lindeman. Dual Targeting of CDK4/6 and BCL2 Pathways Augments Tumor Response in Estrogen Receptor–Positive Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 26, 4120-4134, 2020. doi: 10.1158/1078-0432.CCR-19-1872.

• Andrew D Foers, Alexandra L Garnham, G. Smyth, Susanna M Proudman, Lesley Cheng, Andrew F Hill, Ken C Pang, Ian P Wicks. Circulating Small Noncoding RNA Biomarkers of Response to Triple Disease-modifying Antirheumatic Drug Therapy in White Women With Early Rheumatoid Arthritis.. The Journal of rheumatology, 1746-1751, 2020. doi: 10.3899/jrheum.191012.

• Charity W Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, G. Smyth, M. Ritchie. A guide to creating design matrices for gene expression experiments.. F1000Research, 9, 1444, 2020. doi: 10.12688/f1000research.27893.1.

• Charity W Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, G. Smyth, M. Ritchie. A guide to creating design matrices for gene expression experiments.. F1000Research, 9, 1444, 2020. doi: 10.12688/f1000research.27893.1.

• Helen M McRae, Alexandra L Garnham, Yifang Hu, Matthew T Witkowski, Mark A Corbett, Mathew P Dixon, Rose E May, Bilal N Sheikh, William Chiang, Andrew J Kueh, Tan A Nguyen, Kevin Man, Renee Gloury, Brandon J Aubrey, Antonia Policheni, Ladina Di Rago, Warren S Alexander, Daniel HD Gray, Andreas Strasser, Edwin D Hawkins, Stephen Wilcox, Jozef Gécz, Axel Kallies, Matthew P McCormack, G. Smyth, Anne K Voss, Tim Thomas. PHF6 regulates hematopoietic stem and progenitor cells and its loss synergizes with expression of TLX3 to cause leukemia.. Blood, 1729-1741, 2019. doi: 10.1182/blood-2018-07-860726.

• D Merino, TS Weber, A Serrano, F Vaillant, K Liu, B Pal, L Di Stefano, J Schreuder, D Lin, Y. Chen, ML Asselin-Labat, TN Schumacher, D. Cameron, G. Smyth, A. Papenfuss, GJ Lindeman, JE Visvader, SH Naik. Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer.. Nature communications, 10, 766 (12pp), 2019. doi: 10.1038/s41467-019-08595-2.

• Michael Chopin, Aaron T Lun, Yifan Zhan, Jaring Schreuder, Hannah Coughlan, Lisa A Mielke, Francisca F Almeida, Andrew J Kueh, Ross A Dickins, Gabrielle T Belz, Shalin H Naik, Andrew M Lew, Phillipe Bouillet, Marco J Herold, G. Smyth, Lynn M Corcoran, Stephen L Nutt. Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT.. Immunity, 50, 77-+, 2019. doi: 10.1016/j.immuni.2018.11.010.

• Yang Liao, G. Smyth, Wei Shi. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.. Nucleic acids research, e47 (9pp), 2019. doi: 10.1093/nar/gkz114.

• AC Rios, BD Capaldo, F Vaillant, B Pal, R van Ineveld, CA Dawson, Y. Chen, E Nolan, NY Fu, FC Jackling, S Devi, D Clouston, L Whitehead, G. Smyth, SN Mueller, GJ Lindeman, JE Visvader, 3DTCLSM Group. Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging.. Cancer cell, 35, 618-+, 2019. doi: 10.1016/j.ccell.2019.02.010.

• D Merino, TS Weber, A Serrano, F Vaillant, K Liu, B Pal, L Di Stefano, J Schreuder, D Lin, Y. Chen, ML Asselin-Labat, TN Schumacher, D. Cameron, G. Smyth, A. Papenfuss, GJ Lindeman, JE Visvader, SH Naik. Publisher Correction: Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer.. Nature communications, 10, 1945 (2pp), 2019. doi: 10.1038/s41467-019-09916-1.

• Alex RD Delbridge, Andrew J Kueh, Francine Ke, Natasha M Zamudio, Farrah El-Saafin, Natasha Jansz, Gao-Yuan Wang, Megan Iminitoff, Tamara Beck, Sue Haupt, Yifang Hu, Rose E May, Lachlan Whitehead, Lin Tai, William Chiang, Marco J Herold, G. Smyth, Tim Thomas, Marnie E Blewitt, Andreas Strasser, Anne K Voss. Loss of p53 Causes Stochastic Aberrant X-Chromosome Inactivation and Female-Specific Neural Tube Defects.. Cell reports, 27, 442-+, 2019. doi: 10.1016/j.celrep.2019.03.048.

• Angus T Stock, Nicholas Collins, G. Smyth, Yifang Hu, Jacinta A Hansen, Hamdi A Jama, Andrew M Lew, Thomas Gebhardt, Catriona A McLean, Ian P Wicks, Damian B D’Silva. The Selective Expansion and Targeted Accumulation of Bone Marrow–Derived Macrophages Drive Cardiac Vasculitis. The Journal of Immunology, 3282-3296, 2019. doi: 10.4049/jimmunol.1900071.

• Anne C Rios, Bianca D Capaldo, François Vaillant, Bhupinder Pal, Ravian van Ineveld, Caleb A Dawson, Y. Chen, Emma Nolan, Nai Yang Fu, 3DTCLSM Group, Felicity C Jackling, Sapna Devi, David Clouston, Lachlan Whitehead, G. Smyth, Scott N Mueller, Geoffrey J Lindeman, Jane E Visvader. Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging.. Cancer cell, 35, 953, 2019. doi: 10.1016/j.ccell.2019.05.011.

• Necla Kochan, G Yazgi Tutuncu, G. Smyth, Luke C Gandoffo, Goeknur Giner, Necla Koçhan, Luke C Gandolfo. qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data.. PeerJ, 7, e8260 (13pp), 2019. doi: 10.7717/peerj.8260.

• Cyril Seillet, Kylie Luong, Julie Tellier, Nicolas Jacquelot, Rui Dong Shen, Peter Hickey, Verena C Wimmer, Lachlan Whitehead, Kelly Rogers, G. Smyth, Alexandra L Garnham, M. Ritchie, Gabrielle T Belz. The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity.. Nature immunology, 21, 168-+, 2019. doi: 10.1038/s41590-019-0567-y.

• Ashley Ng, Hannah Coughlan, Soroor Hediyeh-zadeh, Kira Behrens, Timothy Johanson, Michael Sze Yuan Low, Charles Bell, Omer Gilan, Y. Chan, Andrew Kueh, Thomas Boudier, Ladina DiRago, Craig Hyland, Helen Ierino, Sandra Mifsud, Elizabeth Viney, Tracy Willson, Mark Dawson, Rhys Allan, Marco Herold, Kelly Rogers, David Tarlinton, G. Smyth, Melissa Davis, Stephen Nutt, Warren Alexander. An Erg driven transcriptional program controls B-lymphopoiesis. 861542, Cold Spring Harbor Laboratory, 2019. doi: 10.1101/861542.

• A Xin, M. Lee, Y. Hu, V Ignjatovic, WY Shi, A Shipp, S Praporski, A Kallies, RG Weintraub, PT Monagle, G. Smyth, IE Konstantinov. Identifying low-grade cellular rejection after heart transplantation in children by using gene expression profiling. Physiological Genomics, 50, 190-196, 2018. doi: 10.1152/physiolgenomics.00046.2017.

• TL Putoczki, LA Mielke, JT Low, A. Lin, A Preaudet, MJ Herold, K Yaprianto, L Tai, A Kueh, G Pacini, RL Ferrero, R Gugasyan, Y. Hu, M Christie, S Wilcox, R Grumont, MDW Griffin, G. Smyth, M Ernst, P Waring, S Gerondakis, A Strasser. Loss of NF-κB1 Causes Gastric Cancer with Aberrant Inflammation and Expression of Immune Checkpoint Regulators in a STAT-1-Dependent Manner. Immunity, 48, 570-+, 2018. doi: 10.1016/j.immuni.2018.03.003.

• Timothy M Johanson, Hannah D Coughlan, Aaron TL Lun, Naiara G Bediaga, Gaetano Naselli, Alexandra L Garnham, Leonard C Harrison, G. Smyth, Rhys S Allan. Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development.. PLoS genetics, 14, e1007431 (14pp), 2018. doi: 10.1371/journal.pgen.1007431.

• JB Baell, DJ Leaver, SJ Hermans, GL Kelly, MS Brennan, NL Downer, N Nguyen, J Wichmann, HM McRae, B Cleary, HR Lagiakos, S Mieruszynski, G Pacini, HK Vanyai, MI Bergamasco, RE May, BK Davey, KJ Morgan, AJ Sealey, B Wang, N Zamudio, S Wilcox, AL Garnham, BN Sheikh, BJ Aubrey, K Doggett, MC Chung, M de Silva, J Bentley, P Pilling, M Hattarki, O Dolezal, ML Dennis, H Falk, B Ren, SA Charman, KL White, J Rautela, A Newbold, ED Hawkins, RW Johnstone, ND Huntington, TS Peat, JK Heath, A Strasser, MW Parker, G. Smyth, IP Street, BJ Monahan, AK Voss, T Thomas. Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth.. Nature, 560, 253-+, 2018. doi: 10.1038/s41586-018-0387-5.

• Ewa M Michalak, Michael JG Milevskiy, Rachel M Joyce, Johanna F Dekkers, Paul R Jamieson, Bhupinder Pal, Caleb A Dawson, Yifang Hu, Stuart H Orkin, Warren S Alexander, Geoffrey J Lindeman, G. Smyth, Jane E Visvader. Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids.. PLoS biology, 16, e2004986 (21pp), 2018. doi: 10.1371/journal.pbio.2004986.

• Y. Chen, Bhupinder Pal, Jane Visvader, G. Smyth. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. 2055, 2018. doi: 10.12688/f1000research.13196.2.

• Timothy M Johanson, Aaron TL Lun, Hannah D Coughlan, Tania Tan, G. Smyth, Stephen L Nutt, Rhys S Allan. Transcription-factor-mediated supervision of global genome architecture maintains B cell identity.. Nature immunology, 1257-+, 2018. doi: 10.1038/s41590-018-0234-8.

• Wen C Aw, Samuel G Towarnicki, Richard G Melvin, Neil A Youngson, Michael R Garvin, Yifang Hu, Shaun Nielsen, Torsten Thomas, Russell Pickford, Sonia Bustamante, Antón Vila-Sanjurjo, G. Smyth, J William O Ballard. Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness.. PLoS genetics, 14, e1007735 (57pp), 2018. doi: 10.1371/journal.pgen.1007735.

• BJ Aubrey, A Janic, Y. Chen, C Chang, EC Lieschke, ST Diepstraten, AJ Kueh, JP Bernardini, G Dewson, L Whitehead, AK Voss, G. Smyth, A Strasser, GL Kelly. Mutant TRP53 exerts a target gene-selective dominant-negative effect to drive tumor development.. Genes Dev, 32, 1420-1429, 2018. doi: 10.1101/gad.314286.118.

• Geoffrey J Lindeman, Sheau Wen Lok, James R Whittle, Francois Vaillant, Charis E Teh, Louisa L Lo, Antonia N Policheni, Alice RT Bergin, Jayesh Desai, Sarah Ftouni, Luke C Gandolfo, Danny Liew, He K Liu, G Bruce Mann, Kate Moodie, Anand Murugasu, Bhupinder Pal, Andrew W Roberts, Mark A Rosenthal, Kylie Shackleton, Maria J Silva, Zhen R Siow, G. Smyth, Leanne Taylor, Avraham Travers, Belinda Yeo, Miriam M Yeung, Andjelija Zivanovic Bujak, Sarah-Jane Dawson, Daniel HD Gray, Jane E Visvader. 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, 354-369, 2018. doi: 10.1158/2159-8290.CD-18-1151.

• Nai Yang Fu, Bhupinder Pal, Y. Chen, Felicity C Jackling, Michael Milevskiy, Francois Vaillant, Bianca D Capaldo, Fusheng Guo, Kevin H Liu, Anne C Rios, Nicholas Lim, Andrew J Kueh, David M Virshup, Marco J Herold, Haley O Tucker, G. Smyth, Geoffrey J Lindeman, Jane E Visvader. Foxp1 Is Indispensable for Ductal Morphogenesis and Controls the Exit of Mammary Stem Cells from Quiescence.. Developmental cell, 47, 629-+, 2018. doi: 10.1016/j.devcel.2018.10.001.

• Man Lyang Kim, William J Martin, Gabriela Minigo, Joanne L Keeble, Alexandra L Garnham, Guido Pacini, G. Smyth, Terence P Speed, Jonathan Carapetis, Ian P Wicks. Dysregulated IL-1β-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine.. Circulation, 138, 2648-2661, 2018. doi: 10.1161/CIRCULATIONAHA.118.033891.

• Vrahnas Christina, Toby Dite, Yifang Hu, Nguyen Huynh, Mark R Forwood, Keith R Bambery, Mark J Tobin, G. Smyth, T John Martin, Natalie A Sims. Bone strength and mineralization are regulated independently of bone mass by ephrinB2-dependent autophagic processes in osteocytes. JOURNAL OF BONE AND MINERAL RESEARCH, 33, 64 (1pp), 2018.

• Charity Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, G. Smyth, M. Ritchie. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. 1408, 2018. doi: 10.12688/f1000research.9005.3.

• Julia L Gregory, Anne Walter, Yannick O Alexandre, Jyh Liang Hor, Ruijie Liu, Joel Z Ma, Sapna Devi, Nobuko Tokuda, Yuji Owada, Laura K Mackay, G. Smyth, William R Heath, Scott N Mueller. Infection Programs Sustained Lymphoid Stromal Cell Responses and Shapes Lymph Node Remodeling upon Secondary Challenge. Cell Reports, 18, 406-418, 2017. doi: 10.1016/j.celrep.2016.12.038.

• Steven P Williams, Adam F Odell, Tara Karnezis, Rae H Farnsworth, Cathryn M Gould, Jason Li, Sophie Paquet-Fifield, Nicole C Harris, Anne Walter, Julia L Gregory, Sara F Lamont, Ruofei Liu, Elena A Takano, Cameron J Nowell, Neil I Bower, Daniel Resnick, G. Smyth, Leigh Coultas, Benjamin M Hogan, Stephen B Fox, Scott N Mueller, Kaylene J Simpson, Marc G Achen, Steven A Stacker. Genome-wide functional analysis reveals central signaling regulators of lymphatic endothelial cell migration and remodeling. Science Signaling, 10, eaal2987 (19pp), 2017. doi: 10.1126/scisignal.aal2987.

• Sheila Dias, Erika Cretney, Yang Liao, Julie Tellier, Christine Bruggeman, Francisca F Almeida, Jamie Leahy, Gabrielle T Belz, G. Smyth, Wei Shi, Stephen L Nutt, Angela D’Amico. Effector Regulatory T Cell Differentiation and Immune Homeostasis Depend on the Transcription Factor Myb. Immunity, 46, 78-91, 2017. doi: 10.1016/j.immuni.2016.12.017.

• Delphine Merino, James R Whittle, Francois Vaillant, Antonin Serrano, Jia-Nan Gong, Goknur Giner, Ana Leticia Maragno, Maia Chanrion, Emilie Schneider, Bhupinder Pal, Xiang Li, Grant Dewson, Julius Grasel, Kevin Liu, Najoua Lalaoui, David Segal, Marco J Herold, David CS Huang, G. Smyth, Olivier Geneste, Guillaume Lessene, Jane E Visvader, Geoffrey J Lindeman, J Gräsel. 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, 2017. doi: 10.1126/scitranslmed.aam7049.

• Andrew J Kueh, Martin Pal, Lin Tai, Yang Liao, G. Smyth, Wei Shi, Marco J Herold. An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles. Cell Death and Differentiation, 24, 1821-1822, 2017. doi: 10.1038/cdd.2017.122.

• Bhupinder Pal, Yunshun Chen, Francois Vaillant, Paul Jamieson, Lavinia Gordon, Anne C Rios, Stephen Wilcox, Naiyang Fu, Kevin He Liu, Felicity C Jackling, Melissa J Davis, Geoffrey J Lindeman, G. Smyth, Jane E Visvader. Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling. Nature Communications, 8, 1627 (14pp), 2017. doi: 10.1038/s41467-017-01560-x.

• JM Wentworth, J-G Zhang, JG Zhang, E Bandala-Sanchez, G Naselli, R Liu, M Ritchie, G. Smyth, LC Harrison. 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, 1782-1789, 2017. doi: 10.1038/ijo.2017.180.

• Clare E Weeden, Yunshun Chen, Stephen B Ma, Yifang Hu, Georg Ramm, Kate D Sutherland, G. Smyth, Marie-Liesse Asselin-Labat. Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway. PLoS Biology, 15, e2000731 (27pp), 2017. doi: 10.1371/journal.pbio.2000731.

• Reema Jain, R Jain, Julie M Sheridan, JM Sheridan, Antonia Policheni, A Policheni, Melanie Heinlein, M Heinlein, Luke C Gandolfo, LC Gandolfo, Grant Dewson, G Dewson, G. Smyth, Stephen N Sansom, SN Sansom, Nai Yang Fu, NY Fu, Jane E Visvader, JE Visvader, Georg A Hollander, GA Holländer, Andreas Strasser, A Strasser, Daniel HD Gray, DHD Gray. A critical epithelial survival axis regulated by MCL-1 maintains thymic function in mice. Blood, 130, 2504-2515, 2017. doi: 10.1182/blood-2017-03-771576.

• Matthew T Witkowski, Y. Hu, Kathryn G Roberts, Judith M Boer, Mark D McKenzie, Grace J Liu, Oliver D Le Grice, Cedric S Tremblay, Margherita Ghisi, Tracy A Willson, Martin A Horstmann, Iannis Aifantis, Luisa Cimmino, Seth Frietze, Monique L den Boer, Charles G Mullighan, G. Smyth, Ross A Dickins. Conserved IKAROS-regulated genes associated with B-progenitor acute lymphoblastic leukemia outcome. Journal of Experimental Medicine, 214, 773-791, 2017. doi: 10.1084/jem.20160048.

• G. Smyth, Y. Chen, B Pal, JE Visvader. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research, 6, 2055, 2017. doi: 10.12688/f1000research.13196.1.

• Aliaksei Z Holik, C. Law, Ruijie Liu, Z. Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, G. Smyth, M. Ritchie. RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods. Nucleic Acids Research, 45, e30 (18pp), 2017. doi: 10.1093/nar/gkw1063.

• Dana Piovesan, Jessica Tempany, Andrea Di Pietro, Inge Baas, Callisthenis Yiannis, Y. Chen, Victor Peperzak, Gabrielle T Belz, Charles R Mackay, G. Smyth, Joanna R Groom, David M Tarlinton, Kim L Good-Jacobson, Kristy O’Donnell. c-Myb Regulates the T-Bet-Dependent Differentiation Program in B Cells to Coordinate Antibody Responses. Cell Reports, 19, 461-470, 2017. doi: 10.1016/j.celrep.2017.03.060.

• Ajithkumar Vasanthakumar, Dakang Xu, Aaron TL Lun, Andrew J Kueh, Klaas PJM van Gisbergen, Nadia Iannarella, X. Li, L. Yu, D. Wang, Bryan RG Williams, Stanley CW Lee, Ian J Majewski, Dale I Godfrey, G. Smyth, Warren S Alexander, Marco J Herold, Axel Kallies, Stephen L Nutt, Rhys S Allan. A non-canonical function of Ezh2 preserves immune homeostasis. EMBO Reports, 18, 619-631, 2017. doi: 10.15252/embr.201643237.

• Nai Yang Fu, Anne C Rios, Bhupinder Pal, C. Law, Paul Jamieson, Ruijie Liu, Francois Vaillant, Felicity Jackling, G. Smyth, Geoffrey J Lindeman, M. Ritchie, Jane E Visvader. Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive. Nature Cell Biology, 19, 164-176, 2017. doi: 10.1038/ncb3471.

• T. Nguyen, Blake RC Smith, Michelle D Tate, Gabrielle T Belz, Marilou H Barrios, Kirstin D Elgass, Alexandra S Weisman, P. Baker, Simon P Preston, Lachlan Whitehead, Alexandra Garnham, Rachel J Lundie, G. Smyth, Marc Pellegrini, Ian P Wicks, Seth L Masters, Craig P Hunter, Ken C Pang, A Weissman, Meredith O’Keeffe. SIDT2 Transports Extracellular dsRNA into the Cytoplasm for Innate Immune Recognition. Immunity, 47, 498-+, 2017. doi: 10.1016/j.immuni.2017.08.007.

• Aaron TL Lun, G. Smyth. 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, 84-94, 2017. doi: 10.1515/sagmb-2017-0010.

• Lisa A Mielke, Qiutong Huang, Matthew A Firth, Francisca F Almeida, Hesham Abdulla, Jai Rautela, Swee Heng Milon Pang, Waruni Abeysekera, Hai-Hui Xue, Nicholas D Huntington, G. Smyth, Alexandra L Garnham, Matthew P McCormack, Eric Vivier, Cyril Seillet, Gabrielle Belz T Belz. T cell factor-1 is a Critical Factor in Determining Natural Killer and Group 1 Innate Lymphoid Cell Fate Decisions. Cytokine, 100, 60 (1pp), 2017.

• Ajithkumar Vasanthakumar, Yang Liao, Peggy Teh, Maria F Pascutti, Anna E Oja, Alexandra L Garnham, Renee Gloury, Jessica C Tempany, Tom Sidwell, Eloy Cuadrado, Paul Tuijnenburg, Taco W Kuijpers, Najoua Lalaoui, Lisa A Mielke, Vanessa L Bryant, Philip D Hodgkin, John Silke, G. Smyth, Martijn A Nolte, Wei Shi, Axel Kallies. The TNF Receptor Superfamily-NF-kappa B Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues. Cell Reports, 20, 2906-2920, 2017. doi: 10.1016/j.celrep.2017.08.068.

• GJ Lindeman, E Nolan, F Vaillant, D Branstetter, B Pal, G Giner, L Whitehead, SW Lok, GB Mann, K Rohrbach, L-Y Huang, R Soriano, G. Smyth, WC Dougall, JE Visvader, Consortium kConFab. RANK ligand as a target for breast cancer prevention in BRCA1 mutation carriers. Cancer Research, 77, 2017. doi: 10.1158/1538-7445.SABCS16-S2-04.

• Nima Etemadi, Michael Chopin, Holly Anderton, Maria C Tanzer, James A Rickard, Waruni Abeysekera, Cathrine Hall, Sukhdeep K Spall, Bing Wang, Yuquan Xiong, Timothy Hla, Stuart M Pitson, Claudine S Bonder, Wendy Wei-Lynn Wong, Matthias Ernst, G. Smyth, David L Vaux, Stephen L Nutt, Ueli Nachbur, John Silke. Correction: TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1.. eLife, 6, 2017. doi: 10.7554/eLife.29849.

• Lucille C Rankin, Mathilde JH Girard-Madoux, Cyril Seillet, Lisa A Mielke, Yann Kerdiles, Aurore Fenis, Elisabeth Wieduwild, Tracy Putoczki, Stanislas Mondot, Olivier Lantz, Dieter Demon, A. Papenfuss, G. Smyth, Mohamed Lamkanfi, Sebastian Carotta, Jean-Christophe Renauld, Wei Shi, Sabrina Carpentier, Tim Soos, Christopher Arendt, Sophie Ugolini, Nicholas D Huntington, Gabrielle T Bez, Eric Vivier, GT Belz. Complementarity and redundancy of IL-22-producing innate lymphoid cells. Nature Immunology, 17, 179-186, 2016. doi: 10.1038/ni.3332.

• Annie Xin, Frederick Masson, Yang Liao, Simon Preston, Tianxia Guan, Renee Gloury, Moshe Olshansky, Jian-Xin Lin, Peng Li, T. Speed, G. Smyth, Matthias Ernst, Warren J Leonard, Marc Pellegrini, Susan M Kaech, Stephen L Nutt, Wei Shi, Gabrielle T Belz, Axel Kallies. A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet. Nature Immunology, 17, 422-+, 2016. doi: 10.1038/ni.3410.

• Benjamin J Shields, Jacob T Jackson, Donald Metcalf, Wei Shi, Qiutong Huang, Alexandra L Garnham, Stefan P Glaser, Dominik Beck, John E Pimanda, Clifford W Bogue, G. Smyth, Warren S Alexander, Matthew P McCormack. Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a. Genes & Development, 30, 78-91, 2016. doi: 10.1101/gad.268425.115.

• Dane M Newman, Shinya Sakaguchi, Aaron Lun, Simon Preston, Marc Pellegrini, Kseniya Khamina, Andreas Bergthaler, Stephen L Nutt, G. Smyth, Anne K Voss, Tim Thomas, Wilfried Ellmeier, Gabrielle T Belz, Rhys S Allan. Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity. Cell Reports, 16, 3311-3321, 2016. doi: 10.1016/j.celrep.2016.08.056.

• B. Phipson, Stanley Lee, Ian J Majewski, Warren S Alexander, G. Smyth. Robust Hyperparameter Estimation Protects Against Hypervariable Genes and Improves Power to Detect Differential Expression. Annals of Applied Statistics, 10, 946-963, 2016. doi: 10.1214/16-AOAS920.

• Emma Nolan, Francois Vaillant, Daniel Branstetter, Bhupinder Pal, Goeknur Giner, Lachlan Whitehead, Sheau W Lok, Gregory B Mann, Kathy Rohrbach, Li-Ya Huang, Rosalia Soriano, G. Smyth, William C Dougall, Jane E Visvader, Geoffrey J Lindeman, Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab). RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers. Nature Medicine, 22, 933-+, 2016. doi: 10.1038/nm.4118.

• Julie Tellier, Wei Shi, Martina Minnich, Yang Liao, Simon Crawford, G. Smyth, Axel Kallies, Meinrad Busslinger, Stephen L Nutt. Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response. Nature Immunology, 17, 323-330, 2016. doi: 10.1038/ni.3348.

• Carolyn A De Graaf, Jarny Choi, Tracey M Baldwin, Jessica E Bolden, Kirsten A Fairfax, A. Robinson, Christine Biben, Clare Morgan, Kerry Ramsay, A. Ng, Maria Kauppi, Elizabeth A Kruse, Tobias J Sargeant, Nick Seidenman, Erin C Lucas, Sandra Koernig, Adriana Baz Morelli, Michael J Wilson, Steven K Dower, Brenda Williams, Shen Y Heazlewood, Y. Hu, Susan K Nilsson, Li Wu, G. Smyth, Warren S Alexander, Douglas J Hilton, Carolyn A de Graaf, Adriana Baz Morelli. Haemopedia: An Expression Atlas of Murine Hematopoietic Cells. Stem Cell Reports, 7, 571-582, 2016. doi: 10.1016/j.stemcr.2016.07.007.

• Emma C Walker, Rachelle W Johnson, Y. Hu, Holly J Brennan, Ingrid J Poulton, J. Zhang, Brendan J Jenkins, G. Smyth, Nicos A Nicola, Natalie A Sims. Murine Oncostatin M Acts via Leukemia Inhibitory Factor Receptor to Phosphorylate Signal Transducer and Activator of Transcription 3 (STAT3) but Not STAT1, an Effect That Protects Bone Mass. Journal of Biological Chemistry, 291, 21703-21716, 2016. doi: 10.1074/jbc.M116.748483.

• G. Smyth, C. Law, M Alhamdoosh, S. Su, M. Ritchie. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research, 5, 1408, 2016. doi: 10.12688/f1000research.9005.2.

• C Teh, N Lalaoui, R Jain, A Policheni, M Heinlein, S Alvarez-Diaz, E Rieser, S Deuser, H-F Koay, Y. Hu, F Kupresanin, D Godfrey, G. Smyth, P Bouillet, A Strasser, H Walczak, J Silke, D Gray, JM Sheridan, M Darding. The linear ubiquitin chain assembly complex: a new function in thymic T cell differentiation and regulatory T cell homeostasis. European Journal of Immunology, 46, 259-260, 2016. doi: 10.1038/ncomms13353.

• Michael Chopin, Simon P Preston, Aaron TL Lun, Julie Tellier, G. Smyth, Marc Pellegrini, Gabrielle T Belz, Lynn M Corcoran, Jane E Visvader, Li Wu, Stephen L Nutt. RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity. Cell Reports, 15, 866-878, 2016. doi: 10.1016/j.celrep.2016.03.066.

• Y. Chen, ATL Lun, G. Smyth. From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 1; referees: 5 approved]. F1000Research, 5, 1438, 2016. doi: 10.12688/F1000RESEARCH.8987.1.

• Y. Chen, ATL Lun, G. Smyth. From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; referees: 5 approved]. F1000Research, 5, 1438, 2016. doi: 10.12688/F1000RESEARCH.8987.2.

• Goeknur Giner, G. Smyth. statmod: Probability Calculations for the Inverse Gaussian Distribution. R Journal, 8, 339-351, 2016.

• ATL Lun, G. Smyth. From reads to regions: A Bioconductor workflow to detect differential binding in ChIP-seq data. F1000Research, 4, 1080, 2016. doi: 10.12688/f1000research.7016.2.

• Aaron TL Lun, G. Smyth. csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Research, 44, e45 (10pp), 2016. doi: 10.1093/nar/gkv1191.

• BM Barea, S White, E Dunne, G. Smyth, R Power. Clinical pathways and patient characteristics five years after the establishment of the rapid access prostate clinics at Beaumont Hospital. BJU International, 118, 38 (1pp), 2016.

• WJ Martin, G Minigo, ML Kim, J Keeble, MC Pitman, P Tipping, G Pacini, G. Smyth, J Carapetis, IP Wicks. Aboriginal Australians with acute rheumatic fever have enhanced Th17 responses to group A streptococcus that can be inhibited in vitro by repurposed clinical drugs. European Journal of Immunology, 46, 503 (1pp), 2016.

• GJ Lindeman, E Nolan, B Pal, F Vaillant, G Giner, L Whitehead, GB Mann, SW Lok, K Shackleton, G. Smyth, JE Visvader. RANK ligand is a target for breast cancer prevention in BRCA1 mutation carriers. Cancer Research, 76, P3-11-05 (2pp), 2016. doi: 10.1158/1538-7445.SABCS15-P3-11-05.

• Phillippa C Taberlay, Joanna Achinger-Kawecka, Aaron TL Lun, Fabian A Buske, Kenneth Sabir, Cathryn M Gould, Elena Zotenko, Saul A Bert, Katherine A Giles, Denis C Bauer, G. Smyth, Clare Stirzaker, Susan J Clark. Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Research, 26, 719-731, 2016. doi: 10.1101/gr.201517.115.

• Charis E Teh, Najoua Lalaoui, Reema Jain, Antonia N Policheni, Melanie Heinlein, Silvia Alvarez-Diaz, Julie M Sheridan, Eva Rieser, Stefanie Deuser, Maurice Darding, Hui-Fern Koay, Y. Hu, Fiona Kupresanin, Dale I Godfrey, G. Smyth, Philippe Bouillet, Andreas Strasser, Henning Walczak, John Silke, Daniel HD Gray, Lorraine A O’Reilly. Linear ubiquitin chain assembly complex coordinates late thymic T-cell differentiation and regulatory T-cell homeostasis. Nature Communications, 7, 13353 (15pp), 2016. doi: 10.1038/ncomms13353.

• JM Wentworth, G Naselli, K Ngui, G. Smyth, R Liu, C Bruce, J Weir, M Cinel, PJ Meikle, LC Harrison. G(M3) ganglioside and phosphatidylethanolamine-containing lipids are adipose tissue markers of insulin resistance in obese women. International Journal of Obesity, 40, 706-713, 2016. doi: 10.1038/ijo.2015.223.

• F Masson, A Xin, Y Liao, S Preston, T Guan, R Gloury, M Olshansky, J-X Lin, P Li, T. Speed, G. Smyth, M Ernst, WJ Leonard, M Pellegrini, S Kaech, SL Nutt, W Shi, GT Belz, A Kallies. A combinatorial threshold model for effector differentiation of CD8(+) T cells mediated by Blimp-1 and T-bet. European Journal of Immunology, 46, 5 (1pp), 2016.

• EM Bolton, S White, M Skally, M Broe, M Hegazy, G. Smyth, I Cheema, M Morrin, F Keeling, R Power. The changing microbiological trends in TRUS sepsis following the implementation of a prospective surveillance programme. BJU International, 118, 35 (1pp), 2016.

• Aaron TL Lun, Y. Chen, G. Smyth. It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR. 1418, 391-416, HUMANA PRESS INC, 2016. doi: 10.1007/978-1-4939-3578-9_19.

• E Nolan, F Vaillant, D Branstetter, B Pal, G Giner, L Whitehead, SW Lok, GB Mann, K ConFab, K Rohrbach, LY Huang, R Soriano, G. Smyth, WC Dougall, JE Visvader, Geoffrey Lindeman. RANK LIGAND AS A TARGET FOR BREAST CANCER PREVENTION IN BRCA1 MUTATION CARRIERS. ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, 12, 97 (1pp), 2016.

• G Goldberg, S Chatfield, J Murphy, ES Pang, S Tadros, K Grebe, Y. Chen, G. Smyth, M. Ng, M Inouye, S Busfield, M Wilson, A Andrews, I Wicks. Evidence for a key role for neutrophils in rheumatoid arthritis. EUROPEAN JOURNAL OF IMMUNOLOGY, 46, 411 (1pp), 2016.

• Julie M Sheridan, M. Ritchie, Sarah A Best, Kun Jiang, Tamara J Beck, Francois Vaillant, Kevin Liu, Ross A Dickins, G. Smyth, Geoffrey J Lindeman, Jane E Visvader. A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1. BMC Cancer, 15, 221 (13pp), 2015. doi: 10.1186/s12885-015-1187-z.

• Nai Yang Fu, Anne C Rios, Bhupinder Pal, Rina Soetanto, Aaron TL Lun, Kevin Liu, Tamara Beck, Sarah A Best, Francois Vaillant, Philippe Bouillet, Andreas Strasser, Thomas Preiss, G. Smyth, Rey J Lindeman, Jane E Visvader. EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival. Nature Cell Biology, 17, 365-+, 2015. doi: 10.1038/ncb3117.

• MT Witkowski, L Cimmino, Y. Hu, T Trimarchi, H Tagoh, MD McKenzie, SA Best, L Tuohey, TA Willson, SL Nutt, M Busslinger, I Aifantis, G. Smyth, RA Dickins. Activated Notch counteracts Ikaros tumor suppression in mouse and human T-cell acute lymphoblastic leukemia. Leukemia, 29, 1301-1311, 2015. doi: 10.1038/leu.2015.27.

• Ruijie Liu, Aliaksei Z Holik, S. Su, Natasha Jansz, K. Chen, Huei San Leong, Marnie E Blewitt, Marie-Liesse Asselin-Labat, G. Smyth, M. Ritchie. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research, 43, E97-U28, 2015. doi: 10.1093/nar/gkv412.

• X Liu, BA Croker, KE Lawlor, G. Smyth, IP Wicks. 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, 2015. doi: 10.1016/j.joca.2015.05.011.

• A. Ng, Y. Hu, Donald Metcalf, Craig D Hyland, Helen Ierino, B. Phipson, Di Wu, Tracey M Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J Hilton, G. Smyth, Warren S Alexander. Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model. PLOS Genetics, 11, e1005211-19, 2015. doi: 10.1371/journal.pgen.1005211.

• Jwu Jin Khong, L. Wang, G. Smyth, Alan A McNab, Thomas G Hardy, Dinesh Selva, Bastien Llamas, Chol-Hee Jung, Shiwani Sharma, Kathryn P Burdon, Peter R Ebeling, Jamie E Craig. Differential Gene Expression Profiling of Orbital Adipose Tissue in Thyroid Orbitopathy. Investigative Ophthalmology & Visual Science, 56, 6438-6447, 2015. doi: 10.1167/iovs.15-17185.

• Jwu Jin Khong, L. Wang, G. Smyth, Alan A Mcnab, Thomas Hardy, Dinesh Selva, Shiwani Sharma, Kathryn P Burdon, Ebeling Peter, Jamie E Craig. Gene expression profiling of orbital adipose tissue in thyroid orbitopathy. Investigative Ophthalmology & Visual Science, 56, 2015.

• Bhupinder Pal, Y. Chen, Andrew Bert, Y. Hu, Julie M Sheridan, Tamara Beck, Wei Shi, Keith Satterley, Paul Jamieson, Gregory J Goodall, Geoffrey J Lindeman, G. Smyth, Jane E Visvader. Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits. Breast Cancer Research, 17, 85 (16pp), 2015. doi: 10.1186/s13058-015-0585-0.

• M. Ritchie, B. Phipson, Di Wu, Y. Hu, C. Law, Wei Shi, G. Smyth. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43, e47 (13pp), 2015. doi: 10.1093/nar/gkv007.

• Ajithkumar Vasanthakumar, Kazuyo Moro, Annie Xin, Yang Liao, Renee Gloury, Shimpei Kawamoto, Sidonia Fagarasan, Lisa A Mielke, Shoukat Afshar-Sterle, Seth L Masters, Susumu Nakae, Hirohisa Saito, John M Wentworth, Peng Li, Warren J Leonard, G. Smyth, Wei Shi, Stephen L Nutt, Shigeo Koyasu, Axel Kallies. The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells. Nature Immunology, 16, 276-U239, 2015. doi: 10.1038/ni.3085.

• Wei Shi, Yang Liao, Simon N Willis, Nadine Taubenheim, Michael Inouye, David M Tarlinton, G. Smyth, Philip D Hodgkin, Stephen L Nutt, Lynn M Corcoran. Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells. Nature Immunology, 16, 663-+, 2015. doi: 10.1038/ni.3154.

• BN Sheikh, B. Phipson, F El-Saafin, HK Vanyai, NL Downer, MJ Bird, AJ Kueh, RE May, G. Smyth, AK Voss, T Thomas. MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway. Oncogene, 34, 5807-5820, 2015. doi: 10.1038/onc.2015.33.

• Bilal N Sheikh, Natalie L Downer, B. Phipson, Hannah K Vanyai, Andrew J Kueh, D. McCarthy, G. Smyth, Tim Thomas, Anne K Voss. 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, 2015. doi: 10.1073/pnas.1422872112.

• Bilal N Sheikh, Stanley CW Lee, Farrah El-Saafin, Hannah K Vanyai, Y. Hu, Swee Heng Milon Pang, Stephanie Grabow, Andreas Strasser, Stephen L Nutt, Warren S Alexander, G. Smyth, Anne K Voss, Tim Thomas. MOZ regulates B-cell progenitors and, consequently, Moz haploinsufficiency dramatically retards MYC-induced lymphoma development. Blood, 125, 1910-1921, 2015. doi: 10.1182/blood-2014-08-594655.

• Aaron TL Lun, G. Smyth. diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics, 16, 258 (11pp), 2015. doi: 10.1186/s12859-015-0683-0.

• Michael J Coffey, Brad E Sleebs, Alessandro D Uboldi, Alexandra Garnham, Magdalena Franco, Nicole D Marino, Michael W Panas, David JP Ferguson, Marta Enciso, Sash Lopaticki, Rebecca J Stewart, Grant Dewson, G. Smyth, Brian J Smith, Seth L Masters, John C Boothroyd, Justin A Boddey, Christopher J Tonkin, MT O Neill. An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell. ELIFE, 4, 2015. doi: 10.7554/eLife.10809.

• Nima Etemadi, Michael Chopin, Holly Anderton, Maria C Tanzer, James A Rickard, Waruni Abeysekera, Cathrine Hall, Sukhdeep K Spall, Bing Wang, Yuquan Xiong, Timothy Hla, Stuart M Pitson, Claudine S Bonder, Wendy Wei-Lynn Wong, Matthias Ernst, G. Smyth, David L Vaux, Stephen L Nutt, Ueli Nachbur, John Silke. TRAF2 regulates TNF and NF-kappa B signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1. ELIFE, 4, 2015. doi: 10.7554/eLife.10592.

• Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, S. Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D Hansen, Rafael A Irizarry, Michael Lawrence, Michael I Love, James MacDonald, Valerie Obenchain, Andrzej K Oles, Herve Pages, Alejandro Reyes, Paul Shannon, G. Smyth, Dan Tenenbaum, Levi Waldron, Martin Morgan, AK Oles̈, H Pagès, Andrzej K OleÅ›. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods, 12, 115-121, 2015. doi: 10.1038/NMETH.3252.

• A Vasanthakumar, K Moro, A Xin, Y Liao, R Gloury, S Kawamoto, S Fagarasan, LA Mielke, S Afshar-Sterle, SL Masters, S Nakae, H Saito, JM Wentworth, P Li, WJ Leonard, G. Smyth, W Shi, SL Nutt, S Koyasu, A Kallies. Erratum: The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells (Nature Immunology (2015) 16 (276-285)). Nature Immunology, 16, 544, 2015. doi: 10.1038/ni0515-544d.

• Jwu Jin Khong, L. Wang, G. Smyth, Alan McNab, Thomas Hardy, Dinesh Selva, Bastien Llamas, Chol-Hee Jung, Shiwani Sharma, Kathryn Burdons, Peter Ebeling, Jamie Craig. Gene expression profiling of orbital adipose tissue in thyroid orbitopathy. Clinical and Experimental Ophthalmology, 43, 69-70, 2015.

• Aaron Tin Long Lun, G. Smyth. Statistical analyses of high-throughput sequencing data to study chromatin structure and organisation. 2015.

• Kathryn S Potts, Tobias J Sargeant, John F Markham, Wei Shi, Christine Biben, Emma C Josefsson, Lachlan W Whitehead, Kelly L Rogers, Anna Liakhovitskaia, G. Smyth, Benjamin T Kile, Alexander Medvinsky, Warren S Alexander, Douglas J Hilton, Samir Taoudi. A lineage of diploid platelet-forming cells precedes polyploid megakaryocyte formation in the mouse embryo. Blood, 124, 2725-2729, 2014. doi: 10.1182/blood-2014-02-559468.

• M. Holmes, Nicholas D Huntington, Rebecca PL Thong, Jason Brady, Yoshihiro Hayakawa, Christopher E Andoniou, Peter Fleming, Wei Shi, G. Smyth, Mariapia A Degli-Esposti, Gabrielle T Belz, Axel Kallies, Sebastian Carotta, Stephen L Nutt. Peripheral natural killer cell maturation depends on the transcription factor Aiolos. EMBO Journal, 33, 2721-2734, 2014. doi: 10.15252/embj.201487900.

• Sarah A Munro, Steven P Lund, P Scott Pine, Hans Binder, Djork-Arne Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nadereh Jafari, David P Kreil, Pawel P Labaj, Sheng Li, Yang Liao, S. Lin, Joseph Meehan, Christopher E Mason, Javier Santoyo-Lopez, Robert A Setterquist, L. Shi, G. Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Weida Tong, Charles Wang, J. Xu, Zhan Ye, Y. Yang, Y. Yu, Marc Salit, PP Łabaj. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature Communications, 5, 5125 (10pp), 2014. doi: 10.1038/ncomms6125.

• Grace J Liu, Luisa Cimmino, Julian G Jude, Y. Hu, Matthew T Witkowski, Mark D McKenzie, Mutlu Kartal-Kaess, Sarah A Best, Laura Tuohey, Yang Liao, Wei Shi, Charles G Mullighan, Michael A Farrar, Stephen L Nutt, G. Smyth, Johannes Zuber, Ross A Dickins. Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia. Genes & Development, 28, 1337-1350, 2014. doi: 10.1101/gad.240416.114.

• W Shi, K Man, G. Smyth, SL Nutt, A Kallies. Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells. Genomics Data, 2, 396-398, 2014. doi: 10.1016/j.gdata.2014.10.019.

• King-Hwa Ling, Chelsee A Hewitt, Kai-Leng Tan, Pike-See Cheah, Sharmili Vidyadaran, Mei-I Lai, H. Lee, Ken Simpson, Lavinia Hyde, Melanie A Pritchard, G. Smyth, Tim Thomas, Hamish S Scott. 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 (19pp), 2014. doi: 10.1186/1471-2164-15-624.

• KL Tan, KH Ling, CA Hewitt, PS Cheah, K Simpson, L Gordon, MA Pritchard, G. Smyth, T Thomas, HS Scott. Transcriptional profiling of the postnatal brain of the Ts1Cje mouse model of Down syndrome. Genomics Data, 2, 314-317, 2014. doi: 10.1016/j.gdata.2014.09.009.

• K Man, M Miasari, W Shi, A Xin, DC Henstridge, S Preston, M Pellegrini, GT Belz, G. Smyth, MA Febbraio, SL Nutt, A Kallies. Erratum: The transcription factor IRF4 is essential for TCR affinity-mediated metabolic programming and clonal expansion of T cells (Nature Immunology (2013) 14 (1155-1165 )). Nature Immunology, 15, 894, 2014. doi: 10.1038/ni0914-894b.

• L Dagley, CA White, Y Liao, W Shi, G. Smyth, JM Orian, A Emili, A Purcell. Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain. Proteomics, 14, 241-261, 2014. doi: 10.1002/pmic.201300196.

• SN Willis, K Jacobson, curtis, A Light, J Tellier, W Shi, G. Smyth, DM Tarlinton, GT Belz, LM Corcoran, A Kallies, SL Nutt, Kim L Good-Jacobson, Joan Curtis. Transcription Factor IRF4 Regulates Germinal Center Cell Formation through a B Cell-Intrinsic Mechanism. Journal of Immunology, 192, 3200-3206, 2014. doi: 10.4049/jimmunol.1303216.

• S Chevrier, D Emslie, W Shi, T Kratina, C Wellard, A Karnowski, E Erikci, G. Smyth, K Chowdhury, D Tarlinton, LM Corcoran. The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity. Journal of Experimental Medicine, 211, 827-840, 2014. doi: 10.1084/jem.20131831.

• KL Good-Jacobson, Y. Chen, AK Voss, G. Smyth, T Thomas, D Tarlinton. Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ. Proceedings of the National Academy of Sciences of the United States of America, 111, 9585-9590, 2014. doi: 10.1073/pnas.1402485111.

• Y Liao, G. Smyth, W Shi. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923-930, 2014. doi: 10.1093/bioinformatics/btt656.

• C. Law, Y. Chen, W Shi, G. Smyth. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology, 15, R29 (17pp), 2014. doi: 10.1186/gb-2014-15-2-r29.

• ATL Lun, G. Smyth. De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly. Nucleic Acids Research, 42, e95 (11pp), 2014. doi: 10.1093/nar/gku351.

• Zhenqiang Su, Pawel P Labaj, Sheng Li, Jean Thierry-Mieg, Wei Shi, Charles Wang, Gary P Schroth, Robert A Setterquist, John F Thompson, Wendell D Jones, Wenzhong Xiao, Weihong Xu, Roderick V Jensen, Reagan Kelly, Ana Conesa, Cesare Furlanello, Hanlin Gao, Huixiao Hong, Nadereh Jafari, Stan Letovsky, Yang Liao, Fei Lu, Edward J Oakeley, Zhiyu Peng, Craig A Praul, Javier Santoyo-Lopez, Andreas Scherer, G. Smyth, Frank Staedtler, Peter Sykacek, Xin-Xing Tan, Jo Vandesompele, Russell D Wolfinger, Jiri Zavadil, Scott S Auerbach, Wenjun Bao, Hans Binder, Thomas Blomquist, Murray H Brilliant, Pierre R Bushel, Weimin Cain, Jennifer G Catalano, C. Chang, Tao Chen, Marco Chierici, Djork-Arne Clevert, Youping Deng, Adnan Derti, Viswanath Devanarayan, Zirui Dong, Joaquin Dopazo, Tingting Du, Hong Fang, Mario Fasold, Anita Fernandez, Matthias Fischer, Pedro Furio-Tari, James C Fuscoe, Florian Caiment, Stan Gaj, Jorge Gandara, Weigong Ge, Yoichi Gondo, Binsheng Gong, Bridgett Green, Chao Guo, James Hadfield, Jan Hellemans,. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology, 32, 903-914, 2014. doi: 10.1038/nbt.2957.

• Y. Chen, Aaron TL Lun, G. Smyth. Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR. 51-74, SPRINGER INT PUBLISHING AG, 2014. doi: 10.1007/978-3-319-07212-8_3.

• Matthew Witkowski, Y. Hu, Priyanka Sathe, Mark McKenzie, Luisa Cimmino, Grace Liu, Andrew Keniry, G. Smyth, Nicholas Huntington, Ross Dickins. Probing Ikaros functions in B-All using novel mouse models. Experimental Hematology, 42, S66 (1pp), 2014. doi: 10.1016/j.exphem.2014.07.252.

• Matthew T Witkowski, Y. Hu, Luisa Cimmino, Mark D McKenzie, Grace J Liu, G. Smyth, Ross A Dickins. Reversible Tumor Suppression By Ikzf1/Ikaros in Mouse Models of BCR-ABL1+B-ALL. Blood, 124, 2014.

• Penelope A Bryant, G. Smyth, Travis Gooding, Alicia Oshlack, Zinta Harrington, Bart Currie, Jonathan R Carapetis, Roy Robins-Browne, Nigel Curtis. Susceptibility to acute rheumatic fever based on differential expression of genes involved in cytotoxicity, chemotaxis, and apoptosis.. Infection and immunity, 82, 753-761, 2014. doi: 10.1128/IAI.01152-13.

• Grace Liu, Luisa Cimmino, Julian Jude, Yifang Hu, Mutlu Kartal, Matthew Witkowski, Mark McKenzie, Sarah Best, Laura Tuohey, Charles Mullighan, Michael Farrar, Stephen Nutt, G. Smyth, Johannes Zuber, Ross Dickins. PAX5 loss imposes a reversible differentiation block in b-progenitor acute lymphoblastic leukemia. Experimental Hematology, 42, S46 (1pp), 2014. doi: 10.1016/j.exphem.2014.07.171.

• JE Bolden, W Shi, K Jankowski, CY Kan, L Cluse, BP Martin, KL MacKenzie, G. Smyth, RW Johnstone. HDAC inhibitors induce tumor-cell-selective pro-apoptotic transcriptional responses. Cell Death & Disease, 4, e519 (15pp), 2013. doi: 10.1038/cddis.2013.9.

• J George, K Alsop, D Etemadmoghadam, H Hondow, T Mikeska, A Dobrovic, A deFazio, G. Smyth, DA Levine, G Mitchell, DD Bowtell, Australian Ovarian Cancer Study Group. Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations . Clinical Cancer Research, 19, 3474-3484, 2013. doi: 10.1158/1078-0432.CCR-13-0066.

• Y Liao, G. Smyth, W Shi. The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41, e108 (17pp), 2013. doi: 10.1093/nar/gkt214.

• B Pal, T Bouras, W Shi, F Vaillant, JM Sheridan, NY Fu, K Breslin, K Jiang, M. Ritchie, M. Young, GJ Lindeman, G. Smyth, J Visvader. Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2. Cell Reports, 3, 411-426, 2013. doi: 10.1016/j.celrep.2012.12.020.

• F Vaillant, D Merino, L Lee, K Breslin, B Pal, M. Ritchie, G. Smyth, M Christie, LJ Phillipson, CJ Burns, GB Mann, JE Visvader, GJ Lindeman. Targeting BCL-2 with the BH3 Mimetic ABT-199 in Estrogen Receptor-Positive Breast Cancer. Cancer Cell, 24, 120-129, 2013. doi: 10.1016/j.ccr.2013.06.002.

• J. Tang, CL Carmichael, W Shi, D Metcalf, A. Ng, CD Hyland, NA Jenkins, NG Copeland, VM Howell, ZJ Zhao, G. Smyth, BT Kile, WS Alexander. 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, 2013. doi: 10.1073/pnas.1304234110.

• H Leong, K. Chen, Y. Hu, SC Lee, J Corbin, M Pakusch, JM Murphy, IJ Majewski, G. Smyth, WS Alexander, DJ Hilton, ME Blewitt. Epigenetic Regulator Smchd1 Functions as a Tumor Suppressor. Cancer Research, 73, 1591-1599, 2013. doi: 10.1158/0008-5472.CAN-12-3019.

• D Wu, Y. Hu, S Tong, BRG Williams, G. Smyth, MP Gantier. The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease. RNA, 19, 876-888, 2013. doi: 10.1261/rna.035055.112.

• G. Smyth, NS Altman. Separate-channel analysis of two-channel microarrays: recovering inter-spot information. BMC Bioinformatics, 14, 165 (15pp), 2013. doi: 10.1186/1471-2105-14-165.

• S Anders, D. McCarthy, Y. Chen, M Okoniewski, G. Smyth, W Huber, MD Robinson. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols, 8, 1765-1786, 2013. doi: 10.1038/nprot.2013.099.

• KK Man, M Miasari, W Shi, A Xin, DC Henstridge, SP Preston, M Pellegrini, GT Belz, G. Smyth, MA Febbraio, SL Nutt, A Kallies. The transcription factor IRF4 is essential for TCR affinity-mediated metabolic programming and clonal expansion of T cells. Nature Immunology, 14, 1155-1165, 2013. doi: 10.1038/ni.2710.

• S Lee, B. Phipson, CD Hyland, H Leong, R Allan, ATL Lun, DJ Hilton, SL Nutt, ME Blewitt, G. Smyth, WS Alexander, IJ Majewski. Polycomb repressive complex 2 (PRC2) suppresses E mμ-myc lymphoma. Blood, 122, 2654-2663, 2013. doi: 10.1182/blood-2013-02-484055.

• S Pasricha, M. Payne, D Canovas Lopez, LB Pase, P Ngaosuwankul, SA Beard, A Oshlack, G. Smyth, SC Chaiyaroj, KJ Boyce, A Andrianopoulos, David Canovas. 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, 2013. doi: 10.1534/g3.113.006809.

• J George, KL Gorringe, G. Smyth, DD Bowtell. Identifying associations between genomic alterations in tumors. 1049, 9-19, Springer, 2013. doi: 10.1007/978-1-62703-547-7_2.

• Kevin Y Lee, S. Russell, Siegfried Ussar, Jeremie Boucher, Cecile Vernochet, Marcelo A Mori, G. Smyth, Michael Rourk, Carly Cederquist, Evan D Rosen, Barbara B Kahn. Lessons on Conditional Gene Targeting in Mouse Adipose Tissue. Diabetes, 62, 864-874, 2013. doi: 10.2337/db12-1089.

• James L Bedford, Michael DR Thomas, G. Smyth. Beam modeling and VMAT performance with the Agility 160-leaf multileaf collimator. Journal of Applied Clinical Medical Physics, 14, 172-185, 2013. doi: 10.1120/jacmp.v14i2.4136.

• GJ Lindeman, F Vaillant, D Merino, L Lee, K Breslin, B Pal, M. Ritchie, G. Smyth, M Christie, LJ Phillipson, CJ Burns, GB Mann, JE Visvader. Targeting BCL-2 with the BH3 mimetic ABT-199 in ER-positive breast cancer. Cancer Research, 73, P2-09-01 (2pp), 2013. doi: 10.1158/0008-5472.SABCS13-P2-09-01.

• Bilal Sheikh, B. Phipson, Stanley Lee, Farrah El-Saafin, Natalie Downer, Stephanie Grabow, G. Smyth, Andreas Strasser, Warren Alexander, Anne Voss, Tim Thomas. The monocytic leukaemia zinc finger (MOZ) protein is a repressor of cellular senescence, and haploinsufficiency for MOZ increases survival 3-fold in the Es-MYC Lymphoma model. Experimental Hematology, 41, S54 (1pp), 2013. doi: 10.1016/j.exphem.2013.05.211.

• Ross Dickins, Grace Liu, Luisa Cimmino, Y. Hu, Sarah Best, Laura Tuohey, Michael Farrar, Stephen Nutt, G. Smyth. Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia. Experimental Hematology, 41, S16 (1pp), 2013. doi: 10.1016/j.exphem.2013.05.059.

• Charity Wai Man Law, G. Smyth. Precision weights for gene expression analysis. 2013.

• BELINDA PHIPSON, G. Smyth. Empirical bayes modelling of expression profiles and their associations. 2013.

• Y. Chen, G. Smyth. Differential expression analysis of complex RNA-seq experiments. 2013.

• Steven P Lund, Dan Nettleton, D. McCarthy, G. Smyth. Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates. Statistical Applications in Genetics and Molecular Biology, 11, 2012. doi: 10.1515/1544-6115.1826.

• D Young, J McCarthy, MJ Wakefield, G. Smyth, A Oshlack, D Robinson. Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design. 169-190, Springer, 2012. doi: 10.1007/9781461407829_10.

• LM Wakim, A Woodward-Davis, R Liu, Y. Hu, JA Villadangos, G. Smyth, MJ Bevan. The Molecular Signature of Tissue Resident Memory CD8 T Cells Isolated from the Brain. Journal of Immunology, 189, 3462-3471, 2012. doi: 10.4049/jimmunol.1201305.

• L Happo, B. Phipson, G. Smyth, A Strasser, CL Scott. 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 & Disease, 3, e306 (10pp), 2012. doi: 10.1038/cddis.2012.42.

• D. McCarthy, Y. Chen, G. Smyth. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research, 40, 4288-4297, 2012. doi: 10.1093/nar/gks042.

• WC Leong, JC Komen, CA Hewitt, E Arnaud, M McKenzie, B. Phipson, M. Bahlo, A Laskowski, SA Kinkel, G Davey, WR Heath, AK Voss, RI Zahedi, JJ Pitt, R Chrast, A Sickmann, MT Ryan, G. Smyth, DR Thorburn, HS Scott. Proteomic and Metabolomic Analyses of Mitochondrial Complex I-deficient Mouse Model Generated by Spontaneous B2 Short Interspersed Nuclear Element (SINE) Insertion into NADH Dehydrogenase (Ubiquinone) Fe-S Protein 4 (Ndufs4) Gene. Journal of Biological Chemistry, 287, 20652-20663, 2012. doi: 10.1074/jbc.M111.327601.

• D Wu, G. Smyth. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research, 40, e133 (12pp), 2012. doi: 10.1093/nar/gks461.

• AH Achtman, S Pilat, C. Law, J Lynn, Janot, L Mayer, Ma, Kindrachuk, B Finlay, SL Brinkman, G. Smyth, EW Hancock, D Schofield. Effective Adjunctive Therapy by an Innate Defense Regulatory Peptide in a Preclinical Model of Severe Malaria. Science Translational Medicine, 4, 135ra64 (10pp), 2012. doi: 10.1126/scitranslmed.3003515.

• S Oakes, F Vaillant, E Lim, LX Lee, K Breslin, F Feleppa, S Deb, M. Ritchie, E Takano, T Ward, S Fox, D Generali, G. Smyth, A Strasser, DC Huang, J Visvader, GJ Lindeman. 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, 2012. doi: 10.1073/pnas.1104778108.

• G. Smyth, P Frost. Ensuring safe occupational therapy practice with medicines: legal and practice issues. British Journal of Occupational Therapy, 75, 56 (1pp), 2012.

• Jeremie Boucher, Marcelo A Mori, Kevin Y Lee, G. Smyth, Chong Wee Liew, Yazmin Macotela, Michael Rourk, Matthias Bluher, S. Russell, C Ronald Kahn. Impaired thermogenesis and adipose tissue development in mice with fat-specific disruption of insulin and IGF-1 signalling. Nature Communications, 3, 2012. doi: 10.1038/ncomms1905.

• Cecile Vernochet, Arnaud Mourier, Olivier Bezy, Yazmin Macotela, Jeremie Boucher, Matthew J Rardin, Ding An, Kevin Y Lee, Olga R Ilkayeva, Cristina M Zingaretti, Brice Emanuelli, G. Smyth, Saverio Cinti, Christopher B Newgard, Bradford W Gibson, Nils-Goeran Larsson, Ronald Kahn. Adipose-Specific Deletion of TFAM Increases Mitochondrial Oxidation and Protects Mice against Obesity and Insulin Resistance. Cell Metabolism, 16, 765-776, 2012. doi: 10.1016/j.cmet.2012.10.016.

• Ariel H Achtman, Sandra Pilat, C. Law, David J Lynn, Laure Janot, Matt L Mayer, Shuhua Ma, Jason Kindrachuk, B Brett Finlay, Fiona SL Brinkman, G. Smyth, Robert EW Hancock, Louis Schofield. A Screening Room for Cerebral Malaria Drugs. Science Translational Medicine, 4, 2012.

• M. Young, D. McCarthy, Matthew J Wakefield, G. Smyth, Alicia Oshlack, Mark D Robinson. Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design. 169-190, SPRINGER, 2012. doi: 10.1007/978-1-4614-0782-9_10.

• Iris Tan, Leanne Mackin, Nancy Wang, A. Papenfuss, Colleen Elso, Michelle Ashton, Fiona Quirk, B. Phipson, M. Bahlo, T. Speed, G. Smyth, Grant Morahan, Thomas Brodnicki. Congenic mouse strains identify a novel gene for which allelic variation affects susceptibility to type 1 diabetes. Journal of Immunology, 186, 2011.

• A Helland, M Anglesio, J George, PA Cowin, C Johnstone, CM House, KE Sheppard, D Etemadmoghadam, N Melnyk, A Rustgi, WA Phillips, H Johnsen, R Holm, G Kristensen, M Birrer, RB Pearson, A Borresen-Dale, D Huntsman, A deFazio, C Creighton, G. Smyth, DD Bowtell, AL Børresen-Dale, Australian Ovarian Cancer Study Group. Deregulation of MYCN, LIN28B and LET7 in a Molecular Subtype of Aggressive High-Grade Serous Ovarian Cancers. PLoS One, 6, e18064 (9pp), 2011. doi: 10.1371/journal.pone.0018064.

• Lavinia Gordon, Ji-Hoon E Joo, Roberta Andronikos, Miina Ollikainen, Euan M Wallace, Mark P Umstad, Michael Permezel, Alicia Oshlack, Ruth Morley, J. Carlin, Richard Saffery, G. Smyth, Jeffrey M Craig. Expression discordance of monozygotic twins at birth Effect of intrauterine environment and a possible mechanism for fetal programming. Epigenetics, 6, 579-592, 2011. doi: 10.4161/epi.6.5.15072.

• K Ling, C Hewitt, T Beissbarth, L Hyde, P Cheah, G. Smyth, S. Tan, C Hahn, T Thomas, H Scott. Spatiotemporal 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, 2011. doi: 10.1093/cercor/bhq141.

• DJ Campbell, Y. Zhang, D Kelly, RE Gilbert, D. McCarthy, W Shi, G. Smyth. Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart. Clinical and Experimental Pharmacology and Physiology, 38, 623-631, 2011. doi: 10.1111/j.1440-1681.2011.05572.x.

• F Hubert, S Kinkel, G Davey, B. Phipson, S Mueller, A Liston, A Proietto, P Cannon, S Forehan, G. Smyth, L Wu, C Goodnow, F Carbone, H Scott, W Heath. Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance. Blood, 118, 2462-2472, 2011. doi: 10.1182/blood-2010-06-286393.

• N Zamudio, H Scott, K Wolski, C Lo, C. Law, D Leong, S Kinkel, S Chong, D Jolley, G. Smyth, D de Kretser, E Whitelaw. DNMT3L Is a Regulator of X Chromosome Compaction and Post-Meiotic Gene Transcription. PLoS One, 6, e18276 (12pp), 2011. doi: 10.1371/journal.pone.0018276.

• E Cretney, A Xin, W Shi, M Minnich, F Masson, M Miasari, G Belz, G. Smyth, M Busslinger, S Nutt, A Kallies. The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells. Nature Immunology, 12, 304-311, 2011. doi: 10.1038/ni.2006.

• PA Bryant, G. Smyth, RM Robins-Browne, RN Curtis. Technical Variability Is Greater than Biological Variability in a Microarray Experiment but Both Are Outweighed by Changes Induced by Stimulation. PLoS One, 6, e19556 (8pp), 2011. doi: 10.1371/journal.pone.0019556.

• M Kraft, I Cirstea, AK Voss, TJ Thomas, I Goehring, B Sheikh, L Gordon, H Scott, G. Smyth, M Ahmadian, U Trautmann, M Zenker, M Tartaglia, A Ekici, A Reis, H Doerr, A Rauch, C Thiel, HG Dörr. Disruption of the histone acetyltransferase MYST4 leads to a Noonan syndrome-like phenotype and hyperactivated MAPK signaling in humans and mice. Journal of Clinical Investigation, 121, 3479-3491, 2011. doi: 10.1172/JCI43428.

• A. Ng, SJ Loughran, D Metcalf, C Hyland, CA De Graaf, Y. Hu, G. Smyth, D Hilton, B Kile, W Alexander. Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice. Blood, 118, 2454-2461, 2011. doi: 10.1182/blood-2011-03-344739.

• J Jackson, Y. Hu, R Liu, F Masson, S Carotta, A Xin, M Camilleri, A Mount, A Kallies, L Wu, G. Smyth, S Nutt, G Belz. Id2 expression delineates differential checkpoints in the genetic program of CD8α+ and CD103+ dendritic cell lineages. EMBO Journal, 30, 2690-2704, 2011. doi: 10.1038/emboj.2011.163.

• M Asselin-Labat, K Sutherland, F Vaillant, DE Gyorki, D Wu, S Holroyd, K Breslin, T Ward, W Shi, M Bath, S Deb, S Fox, G. Smyth, G Lindeman, J Visvader. 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, 2011. doi: 10.1128/MCB.05766-11.

• BA Croker, C Nowell, D Metcalf, G Dewson, K Campbell, K Rogers, Y. Hu, G. Smyth, J. Zhang, M White, K Lackovic, L Cengia, P Bouillet, S Cory, A Strasser, AW Roberts. 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, 2011. doi: 10.1073/pnas.1110358108.

• MH Lahoud, F Ahmet, S Kitsoulis, SS Wan, D Vremec, C. Lee, B. Phipson, W Shi, G. Smyth, AM Lew, Y Kato, GM Davey, WR Heath, KD Shortman, I Caminschi, Scott N Mueller. 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, 2011. doi: 10.4049/jimmunol.1101176.

• DI WU, G. Smyth. Finding hidden relationships between gene expression profiles with application to breast cancer biology. 2011.

• Wei Shi, Alicia Oshlack, G. Smyth. Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips. Nucleic Acids Research, 38, e204 (11pp), 2010. doi: 10.1093/nar/gkq871.

• B. Phipson, G. Smyth. Permutation P-values should never be zero: Calculating exact P-values when permutations are randomly drawn. Statistical Applications in Genetics and Molecular Biology, 9, Article39, 2010. doi: 10.2202/1544-6115.1585.

• JM Wentworth, G Naselli, WA Brown, L Doyle, B. Phipson, G. Smyth, M Wabitsch, LC Harrison. Pro-inflammatory CD11c⁺CD206⁺ adipose tissue macrophages are associated with insulin resistance in human obesity. Diabetes, 59, 1648-1656, 2010. doi: 10.2337/db09-0287.

• I Majewski, M. Ritchie, B. Phipson, J Corbin, M Pakusch, A Ebert, M Busslinger, H Koseki, Y. Hu, G. Smyth, W Alexander, D Hilton, M Blewitt. Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells. Blood, 116, 731-739, 2010. doi: 10.1182/blood-2009-12-260760.

• Guipponi, Q. Li, Hyde, Beissbarth, G. Smyth, L Masters, S Scott. SAGE Analysis of Genes Differentially Expressed in Presymptomatic TgSOD1G93A Transgenic Mice Identified Cellular Processes Involved in Early Stage of ALS Pathology.. Journal of Molecular Neuroscience, 41, 172-182, 2010. doi: 10.1007/s12031-009-9317-1.

• C Hewitt, K Ling, T Merson, K Simpson, M. Ritchie, S King, M Pritchard, G. Smyth, T THOMAS, H Scott, A Voss. Gene Network Disruptions and Neurogenesis Defects in the Adult Ts1Cje Mouse Model of Down Syndrome. PLoS One, 5, e11561 (15pp), 2010. doi: 10.1371/journal.pone.0011561.

• A Sakthianandeswaren, J Curtis, C Elso, B Kumar, T Baldwin, S Lopaticki, L Kedzierski, G. Smyth, S Foote, E Handman. 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, 2010. doi: 10.1128/IAI.00126-10.

• D Etemadmoghadam, J George, P Cowin, C Cullinane, M Kansara, K Gorringe, G. Smyth, D Bowtell, Australian Ovarian Cancer Study Group. Amplicon-Dependent CCNE1 Expression Is Critical for Clonogenic Survival after Cisplatin Treatment and Is Correlated with 20q11 Gain in Ovarian Cancer. PLoS One, 5, e15498 (14pp), 2010. doi: 10.1371/journal.pone.0015498.

• K Gorringe, J George, M Anglesio, M Ramakrishna, D Etemadmoghadam, P Cowin, A Sridhar, L Williams, S Boyle, N Yanaihara, A Okamoto, M Urashima, G. Smyth, I Campbell, D Bowtell, Australian Ovarian Cancer Study. Copy Number Analysis Identifies Novel Interactions Between Genomic Loci in Ovarian Cancer. PLoS One, 5, 1-13, 2010. doi: 10.1371/journal.pone.0011408.

• KT Tan, L Mackin, NW Wang, A. Papenfuss, C Elso, MPA Ashton, F Quirk, B. Phipson, M. Bahlo, T. Speed, G. Smyth, G Morahan, T Brodnicki. A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. Genome Research, 20, 1629-1638, 2010. doi: 10.1101/gr.101881.109.

• M. Young, Matthew J Wakefield, G. Smyth, Alicia Oshlack. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology, 11, R14 (12pp), 2010. doi: 10.1186/gb-2010-11-2-r14.

• M Asselin-Labat, F Vaillant, J Sheridan, B Pal, D Wu, E Simpson, H Yasuda, G. Smyth, T Martin, J Visvader, G Lindeman. Control of mammary stem cell function by steroid hormone signalling. Nature, 465, 798-802, 2010. doi: 10.1038/nature09027.

• E Lim, D Wu, B Pal, T Bouras, M Asselin-Labat, F Vaillant, H Yagita, G Lindeman, G. Smyth, J Visvader. Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways. Breast Cancer Research, 12, R21 (14pp), 2010. doi: 10.1186/bcr2560.

• D Wu, E Lim, F Vaillant, M Asselin-Labat, J Visvader, G. Smyth. ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics, 26, 2176-2182, 2010. doi: 10.1093/bioinformatics/btq401.

• L Happo, M Cragg, B. Phipson, JM HAGA, E Jansen, M Herold, GD Dewson, EMM Michalak, CV Vandenberg, G. Smyth, AS Strasser, SC Cory, CLS Scott. Maximal killing of lymphoma cells by DNA damage-inducing therapy requires not only the p53 targets Puma and Noxa, but also Bim. Blood, 117, 5256-5267, 2010. doi: 10.1182/blood-2010-04-280818.

• C de Graaf, M Kauppi, T Baldwin, C Hyland, D Metcalf, T Willson, M Carpinelli, G. Smyth, WSA Alexander, DJH Hilton, C D. Hyland. Regulation of hematopoietic stem cells by their mature progeny. Proceedings of the National Academy of Sciences of the United States of America, 107, 21689-21694, 2010. doi: 10.1073/pnas.1016166108.

• W Shi, C de Graaf, S Kinkel, A Achtman, T Baldwin, DS Schofield, H Scott, D Hilton, G. Smyth. Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Research, 38, 2168-2176, 2010. doi: 10.1093/nar/gkp1204.

• CA de Graaf, M Kauppi, T Baldwin, C Hyland, M Carpinelli, D Metcalf, G. Smyth, WS Alexander, DJ Hilton. Regulation of hematopoietic stem cells by their mature progeny. Experimental Hematology, 38, S118 (1pp), 2010.

• Mark D Robinson, D. McCarthy, G. Smyth. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.. Bioinformatics (Oxford, England), 26, 139-140, 2010. doi: 10.1093/bioinformatics/btp616.

• Robert C Karn, Janet M Young, Christina M Laukaitis, G. Smyth. A candidate subspecies discrimination system involving a vomeronasal receptor gene with different alleles fixed in M. m. domesticus and M. m. musculus. GENOME BIOLOGY, 11, 2010. doi: 10.1186/gb-2010-11-S1-P22.

• Y Lim, E Hurley, P Riley, G. Smyth. Screening MRI in patients at high risk of breast carcinoma from the Manchester family history clinic: our initial 2-year experience. BREAST CANCER RESEARCH, 12, 2010. doi: 10.1186/bcr2685.

• MD Robinson, D. McCarthy, G. Smyth. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140, 2009. doi: 10.1093/bioinformatics/btp616.

• Y. Hu, G. Smyth. ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. Journal of Immunological Methods, 347, 70-78, 2009. doi: 10.1016/j.jim.2009.06.008.

• D. McCarthy, G. Smyth. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics, 25, 765-771, 2009. doi: 10.1093/bioinformatics/btp053.

• P Bryant, G. Smyth, R Robins-Browne, R Curtis, Nigel Curtis. Detection of gene expression in an individual cell type within a cell mixture using microarray analysis. PLoS One, 4, 1-10, 2009. doi: 10.1371/journal.pone.0004427.

• King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, G. Smyth, S. Tan, Hamish S Scott. Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Genome Biology, 10, R104 (31pp), 2009. doi: 10.1186/gb-2009-10-10-r104.

• D Liang, A Wong, M Singh, CA Beveridge, B. Phipson, G. Smyth, P Bhalla, C. Wong. Molecular Dissection of Pea Shoot Apical Meristem. Journal of Experimental Botany, 60, 4201-4213, 2009. doi: 10.1093/jxb/erp254.

• Wei Shi, Ashish Banerjee, M. Ritchie, Steve Gerondakis, G. Smyth. Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics, 10, 372 (12pp), 2009. doi: 10.1186/1471-2105-10-372.

• J. Silver, M. Ritchie, G. Smyth. Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics, 10, 352-363, 2009. doi: 10.1093/biostatistics/kxn042.

• IA Parish, S Rao, G. Smyth, T Juelich, GS Denyer, G Davey, A Strasser, W Heath. The Molecular signature of CD8+ T cells undergoing deletional tolerance. Blood, 118, 4575-4585, 2009. doi: 10.1182/blood-2008-10-185223.

• D Metcalf, A. Ng, S Loughran, B. Phipson, G. Smyth, L Di Rago, S Mifsud. 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, 2009. doi: 10.1073/pnas.0910354106.

• B McMorran, V Marshall, C de Graaf, K Drysdale, M Shabbar, G. Smyth, J Corbin, W Alexander, S Foote. Platelets Kill Intraerythrocytic Malarial Parasites and Mediate Survival to Infection. Science, 323, 797-800, 2009. doi: 10.1126/science.1166296.

• FX Hubert, S Kinkel, PE Crewther, PZF Cannon, KE Webster, M Link, R Uibo, A Meager, SP Forehan, G. Smyth, L Mittaz, SE Antonarakis, P Peterson, W Heath, HS Scott. Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype. Journal of Immunology, 182, 3902-3918, 2009. doi: 10.4049/jimmunol.0802124.

• E Michalak, E Jansen, L Happo, M Cragg, L Tai, G. Smyth, A Strasser, J Adams, C Scott. Puma and to a lesser extent Noxa are suppressors of Myc-induced lymphomagenesis. Cell Death & Differentiation, 16, 684-696, 2009. doi: 10.1038/cdd.2008.195.

• G. Smyth, AP Verbyla. Leverage adjustments for dispersion modelling in generalized nonlinear models. Australian and New Zealand Journal of Statistics, 51, 433-448, 2009. doi: 10.1111/j.1467-842X.2009.00556.x.

• E Lim, F Vaillant, D Wu, NC Forrest, B Pal, AH Hart, M Asselin-Labat, DE Gyorki, T Ward, A Partanen, F Feleppa, LI Huschtscha, HJ Thorne, SB Fox, M Yan, JD French, MA Brown, G. Smyth, J Visvader, G Lindeman, kConFab. Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nature Medicine, 15, 907-913, 2009. doi: 10.1038/nm.2000.

• D Emslie, D Metcalf, G. Smyth, A Karnowski, A Kallies, SL Nutt, LM Corcoran. Blimp1 is limiting for transformation in a mouse plasmacytoma model. Blood, 113, 5911-5919, 2009. doi: 10.1182/blood-2008-08-172866.

• E Lim, F Vaillant, D Wu, N Forrest, B Pal, D Gyorki, G. Smyth, J Visvader, G Lindeman. Investigation of human mammary stem and progenitor subpopulations from BRCA1 mutation carriers and noncarriers. Journal of Clinical Oncology, 27, 2009.

• Simon J Foote, Brendan J McMorran, Karen E Drysdale, Carolyn de Graaf, G. Smyth, Warren S Alexander. Platelets Play a Protective Role in Erythrocytic Stage Malaria Infection. Blood, 114, 1586-1587, 2009.

• L Robb, S Glaser, Y. Hu, G. Smyth, D Izon. Leukaemic transformation in murine AML induced by overexpression of the MIXL1 homeobox gene. Experimental Hematology, 37, S16 (1pp), 2009.

• Y Gao, S Lim, J Ng, Y Phoon, C Tham, R Quek, M Tao, G. Smyth. Analyzing white blood cell subpopulation for quick and simple predictors for autologous stem cell collection. JOURNAL OF CLINICAL ONCOLOGY, 27, 2009.

• Ran Blekhman, Alicia Oshlack, Adrien E Chabot, G. Smyth, Yoav Gilad. Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures. PLOS Genetics, 4, e1000271 (13pp), 2008. doi: 10.1371/journal.pgen.1000271.

• Ellis, Pan, G. Smyth, George, McCormack, Williams-Truax, Mita, Beck, Burris, G Ryan, Atadja, Butterfoss, Dugan, Culver, R Johnstone, H Prince. 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, 2008. doi: 10.1158/1078-0432.CCR-07-4262.

• Joelle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, M. Ritchie, Frederic Schuetz, Ping Cannon, M. Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner, T. Speed, Maria Kavallaris, G. Smyth, Hamish S Scott, F Schütz. Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics, 9, 363 (17pp), 2008. doi: 10.1186/1471-2164-9-363.

• Holly E Barker, G. Smyth, James Wettenhall, Teresa A Ward, Mary L Bath, Geoffrey J Lindeman, Jane E Visvader. Deaf-I regulates epithelial cell proliferation and side-branching in the mammary gland. BMC Developmental Biology, 8, 94 (14pp), 2008. doi: 10.1186/1471-213X-8-94.

• Samuel E Berkovic, Leanne M Dibbens, Alicia Oshlack, J. Silver, Marina Katerelos, Danya F Vears, Renate Luellmann-Rauch, Judith Blanz, Ke Wei Zhang, Jim Stankovich, Renate M Kalnins, John P Dowling, Eva Andermann, Enrico Faldini, Lata Vadlamudi, Richard A Macdonell, Bree L Hodgson, Marta A Bayly, Judy Savige, John C Mulley, G. Smyth, David A Power, Paul Saftig, M. Bahlo, R Lüllmann-Rauch. Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis. American Journal of Human Genetics, 82, 673-684, 2008. doi: 10.1016/j.ajhg.2007.12.019.

• JP Dwyer, M. Ritchie, G. Smyth, S Harrap, L Delbridge, A Domenighetti, R di Nicolantonio. Myocardial gene expression associated with genetic cardiac hypertrophy in the absence of hypertension. Hypertension Research, 31, 941-955, 2008. doi: 10.1291/hypres.31.941.

• Ian J Majewski, Marnie E Blewitt, Carolyn A de Graaf, Edward J McManus, M. Bahlo, Adrienne A Hilton, Craig D Hyland, G. Smyth, Jason E Corbin, Donald Metcalf, Warren S Alexander. Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activity. PLoS Biology, 6, 796-809, 2008. doi: 10.1371/journal.pbio.0060093.

• MD Robinson, G. Smyth. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332, 2008. doi: 10.1093/biostatistics/kxm030.

• PK Dunn, G. Smyth. Evaluation of Tweedie exponential dispersion model densities by Fourier inversion. Statistics and Computing, 18, 73-86, 2008. doi: 10.1007/s11222-007-9039-6.

• C Huggins, A Domenighetti, M. Ritchie, N Khalil, J Favaloro, J Proietto, G. Smyth, S Pepe, L Delbridge. Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention. Journal of Molecular and Cellular Cardiology, 44, 270-280, 2008. doi: 10.1016/j.yjmcc.2007.11.020.

• C Pridans, M. Holmes, M Polli, JM Wettenhall, A Dakic, LM Corcoran, G. Smyth, SL Nutt. Identification of Pax5 target genes in early B cell differentiation. Journal of Immunology, 180, 1719-1728, 2008. doi: 10.4049/jimmunol.180.3.1719.

• JE Bolden, W Shi, G. Smyth, LA Cluse, RW Johnstone. Mechanisms of tumour-selective apoptosis induced by the histone deacetylase inhibitor vorinostat. EJC Supplements, 6, 86 (1pp), 2008. doi: 10.1016/S1359-6349(08)71509-X.

• Francois Rozet, Guillaume Lesur, Xavier Cathelineau, Eric Barret, G. Smyth, Rafael Sanchez-Salas, Ali Kasraeian, Guy Vallancien. Oncological evaluation of the prostate-sparing cystectomy: Long-term results. Journal of Urology, 179, 292 (1pp), 2008. doi: 10.1016/S0022-5347(08)60850-2.

• Olga G Skibina, Victoria M Petreau, Helmut Butzkueven, G. Smyth, Yifang Hu, Trevor Kilpatrick. Gene expression profiling from T cells in patients with a first demyelinating episode. MULTIPLE SCLEROSIS, 14, S200 (1pp), 2008.

• Alicia Oshlack, Adrien E Chabot, G. Smyth, Yoav Gilad. Using DNA microarrays to study gene expression in closely related species. Bioinformatics, 23, 1235-1242, 2007. doi: 10.1093/bioinformatics/btm111.

• Alicia Oshlack, Dianne Emslie, Lynn M Corcoran, G. Smyth. Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biology, 8, R2 (8pp), 2007. doi: 10.1186/gb-2007-8-1-r2.

• M. Ritchie, J. Silver, Alicia Oshlack, M. Holmes, Dileepa Diyagama, Andrew Holloway, G. Smyth. A comparison of background correction methods for two-colour microarrays. Bioinformatics, 23, 2700-2707, 2007. doi: 10.1093/bioinformatics/btm412.

• T Baldwin, A Sakthianandeswaren, JM Curtis, B Kumar, G. Smyth, SJ Foote, E Handman. Wound healing response is a major contributor to the severityof cutaneous leishmaniasis in the ear model of infection. Parasite Immunology, 29, 501-513, 2007. doi: 10.1111/j.1365-3024.2007.00969.x.

• MD Robinson, G. Smyth. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics, 23, 2881-2887, 2007. doi: 10.1093/bioinformatics/btm453.

• Y. Pan, HM Prince, J George, RW Johnstone, L Ellis, C McCormack, G. Smyth, R Williams-Truax, P Atadja, D Butterfoss, M Dugan, K Culver. LBH589, a novel deacetylase inhibitor (DACI), in the treatment of cutaneous T-cell lymphoma (CTCL): Changes in tumor gene expression profiles related to clinical response after therapy. Haematologica - The Hematology Journal, 92, 55 (1pp), 2007.

• Samuel F Berkovic, LM Dibbens, A Oshlack, JD Silver, M Katerelos, DF Vears, J Stankovich, E Andermann, BL Hodgson, MA Bayly, JC Mulley, G. Smyth, DA Power, M. Bahlo. Identification of the gene for action myoclonus-renal failure syndrome. EPILEPSIA, 48, 386 (1pp), 2007.

• Danielle M Greenawalt, Cuong Duong, G. Smyth, Marianne L Ciavarella, Natalie J Thompson, Thomas Tiang, William K Murray, Robert JS Thomas, Wayne A Phillips. Gene expression profiling of esophageal cancer: comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma.. International journal of cancer, 120, 1914-1921, 2007. doi: 10.1002/ijc.22501.

• Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell, G. Smyth. Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. BMC Bioinformatics, 7, 511 (20pp), 2006. doi: 10.1186/1471-2105-7-511.

• G de silva, M Hildebrand, Christopoulos, Newman, Bell, Ritchie, G. Smyth, H Dahl, Michelle G De Silva. Gene expression changes during step-wise differentiation of embyronic stem cells along the inner ear hair cell pathway.. Acta Oto-Laryngologica, 126, 1148-1157, 2006. doi: 10.1080/00016480600702118.

• Mireille H Lahoud, Anna I Proietto, Kate H Gartlan, Susie Kitsoulis, Joan Curtis, James Wettenhall, Mariam Sofi, Carmel Daunt, Irina Caminschi, Keith Satterley, Alexandra Rizzitelli, Petra Schnorrer, Atsushi Hinohara, Yasunori Yamaguchi, Li Wu, G. Smyth, Emanuela Handman, Ken Shortman, Mark D Wright. Signal regulatory protein molecules are differentially expressed by CD8(-) dendritic cells. Journal of Immunology, 177, 372-382, 2006. doi: 10.4049/jimmunol.177.1.372.

• Samuel Wormald, Douglas J Hilton, G. Smyth, T. Speed. Proximal genomic localization of STATI binding and regulated transcriptional activity. BMC Genomics, 7, 254 (13pp), 2006. doi: 10.1186/1471-2164/7/254.

• Y Gilad, A Oshlack, G. Smyth, T. Speed, K. White. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature, 440, 242-245, 2006. doi: 10.1038/nature04559.

• JM Wettenhall, KM Simpson, K Satterley, G. Smyth. affylmGUI: A graphical user interface for linear modeling of single channel microarray data. Bioinformatics, 22, 897-899, 2006. doi: 10.1093/bioinformatics/btl025.

• M. Ritchie, D Diyagama, J Neilson, R van Laar, A Dobrovic, A Holloway, G. Smyth. Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics, 7, 261, 2006. doi: 10.1186/1471-2105-7-261.

• M Shackleton, F Valliant, K Simpson, J Sting, G. Smyth, M Asselin-Labat, L Wu, GJ Lindeman, JE Visvader, F Vaillant, J Stingl. Generation of a functional mammary gland from a single stem cell. Nature, 439, 84-88, 2006. doi: 10.1038/nature04372.

• ME Cox, A Moss, G. Smyth. Water quality condition and trend in North Queensland waterways. Marine Pollution Bulletin, 51, 89-98, 2005. doi: 10.1016/j.marpolbul.2004.10.039.

• MJ Peart, G. Smyth, RK van Laar, DD Bowtell, VM Richon, PA Marks, AJ Holloway, RW Johnstone. Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 102, 3697-3702, 2005. doi: 10.1073/pnas.0500369102.

• JA Tye-Din, G. Smyth, T. Speed, RP Anderson, T Beissbarth. A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. Bioinformatics, 21, I29-I37, 2005. doi: 10.1093/bioinformatics/bti1013.

• PK Dunn, G. Smyth. Series evaluation of Tweedie exponential dispersion model densities. Statistics and Computing, 15, 267-280, 2005. doi: 10.1007/s11222-005-4070-y.

• G. Smyth, J Michaud, HS Scott. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics, 21, 2067-2075, 2005. doi: 10.1093/bioinformatics/bti270.

• M Shackleton, F Vaillant, KJ Simpson, J Singl, G. Smyth, L Wu, JE Visvader, GJ Lindeman. A single mammary stem cell can reconstitute a functional mammary gland. Breast Cancer Research and Treatment, 94, S26 (1pp), 2005.

• IA Parish, G. Smyth, S Rao, WR Heath. Defining the molecular signature of peripheral CD8(+) T cell tolerance. Tissue Antigens, 66, 509 (1pp), 2005.

• JP Dwyer, M. Ritchie, G. Smyth, LM Delbridge, AA Domenighetti, SB Harrap, R Di Nicolantonio. Differentially expressed genes in cardiac tissue from the hypertrophic heart rat. CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, 32, A13-A14, 2005.

• C Elso, B Kumar, G. Smyth, S Foote, E Handman. Dissociation of disease susceptibility, inflammation and cytokine profile in lmr1/2 congenic mice infected with Leishmania major. Genes and Immunity, 5, 188-196, 2004. doi: 10.1038/sj.gene.6364056.

• G. Smyth. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, 3, 2004.

• HM Podlich, MJ Faddy, G. Smyth. Semi-parametric extended Poisson process models for count data. Statistics and Computing, 14, 311-321, 2004. doi: 10.1023/B:STCO.0000039480.66002.5a.

• Tim Beissbarth, Lavinia Hyde, G. Smyth, Chris Job, Wee-Ming Boon, S. Tan, Hamish S Scott, T. Speed, T Beissbarth. Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics, 20, 31-39, 2004. doi: 10.1093/bioinformatics/bth924.

• Boon, T Beissbarth, L HYDE, G. Smyth, JM Gunnersen, DA Denton, HS Scott, S. Tan. 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, 2004. doi: 10.1073/pnas.0406296101.

• JM Wettenhall, G. Smyth. limmaGUI: A graphical user interface for linear modeling of microarray data. Bioinformatics, 20, 3705-3706, 2004. doi: 10.1093/bioinformatics/bth449.

• RC Gentleman, VJ Carey, DM Bates, B Bolstad, M Dettling, S Dudoit, B Ellis, L Gautier, Y Ge, J Gentry, K Hornik, T Hothorn, W Huber, S Iacus, R Irizarry, F Leisch, C. Li, M Maechler, AJ Rossini, G Sawitzki, C Smith, G. Smyth, L Tierney, JYH Yang, J. Zhang. Bioconductor: open software development for computational biology and bioinformatics.. Genome Biology, 5, R80, 2004. doi: 10.1186/gb-2004-5-10-r80.

• CM Elso, LJ Roberts, G. Smyth, RJ Thomson, TM Baldwin, SJ Foote, E Handman. Leishmaniasis host response loci (lmr1-3) modify disease severity through a Th1/Th2-independent pathway. Genes and Immunity, 5, 93-100, 2004. doi: 10.1038/sj.gene.6364042.

• AA Domenighetti, M. Ritchie, G. Smyth, T Pedrazzini, J Proietto, LMD Delbridge. Gene expression profiling reveals distinct sets of genes altered during hormonally and metabolically induced cardiac hypertrophies. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 37, 303-304, 2004.

• G. Smyth, T. Speed. Normalization of cDNA microarray data. Methods, 31, 265-273, 2003. doi: 10.1016/S1046-2023(03)00155-5.

• D Toomey, G. Smyth, C Condron, J Kelly, AM Byrne, E Kay, RM Conroy, P Broe, D Bouchier-Hayes. Infiltrating immune cells, but not tumour cells, express FasL in non-small cell lung cancer: No association with prognosis identified in 3-year follow-up. International Journal of Cancer, 103, 408-412, 2003. doi: 10.1002/ijc.10836.

• G. Smyth, HM Podlich. An improved saddlepoint approximation based on the negative binomial distribution for the general birth process. Computational Statistics, 17, 17-27, 2002. doi: 10.1007/s001800200088.

• HM Podlich, MJ Faddy, G. Smyth. A general approach to modeling and analysis of species abundance data with extra zones. Journal of Agricultural, Biological and Environmental Statistics, 7, 324-334, 2002. doi: 10.1198/108571102221.

• G. Smyth. An efficient algorithm for reml in heteroscedastic regression. Journal of Computational and Graphical Statistics, 11, 836-847, 2002. doi: 10.1198/106186002871.

• G. Smyth, B Jørgensen. Fitting Tweedie's Compound Poisson Model to Insurance Claims Data: Dispersion Modelling. ASTIN Bulletin, 32, 143-157, 2002. doi: 10.2143/AST.32.1.1020.

• G. Smyth, F Huele, A Verbyla. Exact and approximate REML for heteroscedastic regression. Statistical Modeling, 1, 161-175, 2001. doi: 10.1177/1471082X0100100301.

• D Toomey, G. Smyth, C Condron, E Kay, R Conroy, D Foley, C Hong, B Hogan, S Toner, P McCormick, P Broe, C Kelly, D Bouchier-Hayes. Immune function, telomerase, and angiogenesis in patients with primary, operable nonsmall cell lung carcinoma: Tumor size and lymph node status remain the most important prognostic features. Cancer, 92, 2648-2657, 2001. doi: 10.1002/1097-0142(20011115)92:10<2648::AID-CNCR1618>3.0.CO;2-7.

• D Toomey, G. Smyth, C Condron, E Kay, R Conroy, D Foley, C Hong, B Hogan, S Toner, P McCormick, P Broe, C Kelly, D Bouchier-Hayes, T Yano, S Takeo. Thymidine phosphorylase activity in nonsmall cell lung carcinoma tissues. Cancer, 92, 2658-2661, 2001. doi: 10.1002/1097-0142(20011115)92:10<2658::AID-CNCR1619>3.0.CO;2-3.

• G. Smyth, DM Hawkins. Robust Frequency Estimation Using Elemental Sets. Journal of Computational and Graphical Statistics, 9, 196-214, 2000. doi: 10.1080/10618600.2000.10474874.

• G. Smyth. Employing symmetry constraints for improved frequency estimation by eigenanalysis methods. Technometrics, 42, 277-289, 2000. doi: 10.1080/00401706.2000.10486048.

• G. Smyth, DM Hawkins. Robust frequency estimation using elemental sets. Journal of Computational and Graphical Statistics, 9, 196-214, 2000. doi: 10.2307/1390621.

• G. Smyth. Employing symmetry constraints for improved frequency estimation by eigenanalysis methods. Technometrics, 42, 277-289, 2000. doi: 10.2307/1271082.

• G. Smyth, AP Verbyla. Adjusted likelihood methods for modelling dispersion in generalized linear models. Environmetrics, 10, 695-709, 1999.

• W Dixon, G. Smyth, B Chiswell. Optimized selection of river sampling sites. Water Research, 33, 971-978, 1999. doi: 10.1016/S0043-1354(98)00289-9.

• G. Smyth. Partitioned algorithms for maximum likelihood and other non-linear estimation. Statistics and Computing, 6, 201-216, 1996. doi: 10.1007/BF00140865.

• PK Dunn, G. Smyth. Randomized Quantile Residuals. Journal of Computational and Graphical Statistics, 5, 236-244, 1996. doi: 10.1080/10618600.1996.10474708.

• G. Smyth, AP Verbyla. A conditional likelihood approach to residual maximum likelihood estimation in generalized linear models. Journal of the Royal Statistical Society Series B: Methodological, 58, 565-572, 1996.

• S CHAKRABORTY, G. Smyth. A stochastic-model incorporating the effect of weather conditions on anthracnose development in Stylosanthes Scabra. Journal of Phytopathology - Phytopathologische Zeitschrift, 143, 495-499, 1995. doi: 10.1111/j.1439-0434.1995.tb04561.x.

• MR OSBORNE, G. Smyth. A modified PRONY algorithm for exponential function fitting. SIAM Journal on Scientific Computing, 16, 119-138, 1995. doi: 10.1137/0916008.

• G. Smyth. A note on modelling cross-correlations: Hyperbolic secant regression. Biometrika, 81, 396-402, 1994. doi: 10.1093/biomet/81.2.396.

• G. Smyth. REML in generalized linear models - A conditional approach. Computing Science and Statistics, 26, 130-134, 1994.

• MS MACKISACK, MR OSBORNE, G. Smyth. A modified PRONY algorithm for estimating sinusoidal frequencies. Journal of Statistical Computation and Simulation, 49, 111-124, 1994. doi: 10.1080/00949659408811564.

• MS Mackisack, G. Smyth. Acuity through discolored lenses. Optometry and Vision Science, 70, 692-693, 1993. doi: 10.1097/00006324-199308000-00020.

• LK Nielsen, G. Smyth, PF Greenfield. Accuracy of the endpoint assay for virus titration. Cytotechnology, 8, 231-236, 1992. doi: 10.1007/BF02522040.

• MH Kahn, MS Mackisack, MR Osborne, G. Smyth. On the consistency of prony’s method and related algorithms. Journal of Computational and Graphical Statistics, 1, 329-349, 1992. doi: 10.1080/10618600.1992.10474589.

• G. Smyth, S Chakraborty, RG Clark, AN Pettitt. A stochastic model for anthracnose development in Stylosanthes scabra.. Phytopathology, 82, 1267-1272, 1992. doi: 10.1094/phyto-82-1267.

• LK Nielsen, G. Smyth, PF Greenfield, Lars Nielson. Hemacytometer Cell Count Distributions: Implications of Non‐Poisson Behavior. Biotechnology Progress, 7, 560-563, 1991. doi: 10.1021/bp00012a600.

• G. Smyth. Exponential Dispersion Models and the Gauss-Newton algorithm. Australian Journal of Statistics, 33, 57-64, 1991. doi: 10.1111/j.1467-842X.1991.tb00412.x.

• MR OSBORNE, G. Smyth. A modified PRONY algorithm for fitting functions defined by difference-equations. SIAM Journal on Scientific and Statistical Computing, 12, 362-382, 1991. doi: 10.1137/0912020.

• G. Smyth, MW KNUIMAN, ML THORNETT, H KIIVERI. Using the EM algorithm to predict 1st year university performance. Australian Journal of Education, 34, 204-224, 1990. doi: 10.1177/000494419003400210.

• G. Smyth. Generalized linear-models with varying dispersion. Journal of the Royal Statistical Society Series B: Methodological, 51, 47-60, 1989.

• RA Berk, G. Smyth, LW Sherman. When random assignment fails: Some lessons from the Minneapolis Spouse Abuse Experiment. Journal of Quantitative Criminology, 4, 209-223, 1988. doi: 10.1007/BF01072450.

• KH WYRWOLL, G. Smyth. On using the log-hyperbolic distribution to describe the textural characteristics of eolian sediments - Reply. Journal of Sedimentary Petrology, 58, 161-162, 1988.

• RK ZIMMERFAUST, G. Smyth. Difference thresholds for odor detection by an aquatic animal. Chemical Senses, 12, 713 (1pp), 1987.

• RM HART, D KEAST, G SMYTHE, G. Smyth. Metabolic Stability of Phytophthora-Cinnamomi rands in Western Australia. Canadian Journal of Microbiology, 32, 820-822, 1986. doi: 10.1139/m86-150.

• KH Wyrwoll, G. Smyth. On using the log-hyperbolic distribution to describe the textural characteristics of eolian sediments.. Journal of Sedimentary Petrology, 55, 471-478, 1985.