Dr Gordon Smyth

Statistical Bioinformatics and Genomics: Modern genomic technologies produce huge amounts of data that allow us to examine gene activity on a genome-wide scale. We can observe which genes are turned on and how active they are in any type of cell at any time.

My research group develops advanced computational and statistical strategies to analyse and interpret these huge data sets. In collaboration with biomedical collaborators, we examine which genes play essential roles in normal cell development and which genes are disrupted or activated inappropriately in any particular disease. Our goal is to learn how diseases originate by examining how genetic disruption comes about and how it might be controlled. We analyse data from a number of genomic technologies, especially RNA sequencing (RNA-seq), but also DNA sequencing, gene expression microarrays, protein arrays, mass spectrometry and high-throughput PCR arrays. One of our key interests is the identification of genes, transcripts or molecular pathways that are differentially expressed between experimental conditions. We also analyse ChIP sequencing experiments to detect changes in the DNA epigenetic marks and DNA structure. We develop high performance algorithms to map short sequence reads to a reference genome. We use mathematical techniques such a linear modelling and empirical Bayes to borrow strength between genes and between experimental units, providing robust statistical conclusions even when the number of experimental units is relatively small.

Find out more about Gordon Smyth's experience

Gordon Smyth's highlights

FEATURED Journal article

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Gordon Smyth's selected work

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq d..

Journal article

Increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary..

Journal article

MOZ directs the distal-less homeobox gene expression program during craniofacial developme..

Journal article

The Selective Expansion and Targeted Accumulation of Bone Marrow-Derived Macrophages Drive..

Journal article

The R package Rsubread is easier, faster, cheaper and better for alignment and quantificat..

Journal article

PHF6 regulates hematopoietic stem and progenitor cells and its loss synergizes with expres..

Journal article

Scholarly Works

Displaying the 277 most recent scholarly works by Gordon Smyth.

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Dharmesh D Bhuva, Joseph Cursons, Gordon K Smyth, Melissa J Davis

Journal article | 2019 | Genome Biology

BACKGROUND: Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological c..

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data

Necla Koçhan, Gözde Tütüncü, Gordon Smyth, Luke Gandolfo, Göknur Giner

Journal article | 2019

Abstract Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern m..

Increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary mineralization and brittle bone

Christina Vrahnas, Martha Blank, Toby A Dite, Liliana Tatarczuch, Niloufar Ansari, Blessing Crimeen-Irwinl, Nguyen Huynh, Mark R Forwood, Yifang Hu, Mika Ikegame, Keith R Bambery, Cyril Petibois, Eleanor J Mackie, Mark J Tobin, Gordon K Smyth, Jonathan S Oakhill, T John Martin, Natalie A Sims

Journal article | 2019 | Nature Communications

Mineralized bone forms when collagen-containing osteoid accrues mineral crystals. This is initiated rapidly (primary mineralizatio..

MOZ directs the distal-less homeobox gene expression program during craniofacial development

Hannah K Vanyai, Alexandra Garnham, Rose E May, Helen M McRae, Caitlin Collin, Stephen Wilcox, Gordon K Smyth, Tim Thomas, Anne K Voss

Journal article | 2019 | Development

Oral clefts are common birth defects. Individuals with oral clefts who have identical genetic mutations regularly present with var..

The Selective Expansion and Targeted Accumulation of Bone Marrow-Derived Macrophages Drive Cardiac Vasculitis

Angus T Stock, Nicholas Collins, Gordon K Smyth, Yifang Hu, Jacinta A Hansen, Damian B D'Silva, Hamdi A Jama, Andrew M Lew, Thomas Gebhardt, Catriona A McLean, Ian P Wicks

Journal article | 2019 | The Journal of Immunology

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

Yang Liao, Gordon K Smyth, Wei Shi

Journal article | 2019 | Nucleic Acids Research

PHF6 regulates hematopoietic stem and progenitor cells and its loss synergizes with expression of TLX3 to cause leukemia

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, et al.

Journal article | 2019 | Blood

Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

Anne C Rios, Bianca D Capaldo, Francois Vaillant, Bhupinder Pal, Ravian van Ineveld, Caleb A Dawson, Yunshun Chen, Emma Nolan, Nai Yang Fu, Felicity C Jackling, Sapna Devi, David Clouston, Lachlan Whitehead, Gordon K Smyth, Scott N Mueller, Geoffrey J Lindeman, Jane E Visvader, Jamie R Flynn, William M Palmer, Antony P Martin, et al.

Journal article | 2019 | Cancer Cell

Loss of p53 Causes Stochastic Aberrant X-Chromosome Inactivation and Female-Specific Neural Tube Defects

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, Ygal Haupt, Gordon K Smyth, Tim Thomas, Marnie E Blewitt, et al.

Journal article | 2019 | Cell Reports

A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2-Positive Metastatic Breast Cancer

Sheau W 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 Joao Silva, et al.

Journal article | 2019 | Cancer Discovery

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

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, GK Smyth, AT Papenfuss, GJ Lindeman, JE Visvader, SH Naik

Journal article | 2019 | Nature Communications

Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT

Michael Chopin, Aaron T Lun, Yifan Zhan, Jaring Schreuder, Hannah Coughlan, Angela D'Amico, 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, Gordon K Smyth, Lynn M Corcoran, Stephen L Nutt

Journal article | 2019 | Immunity

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Charity Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon Smyth, Matthew Ritchie

Journal article | 2018 | F1000Research

The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with cou..

Dysregulated IL-1-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine

Man Lyang Kim, William J Martin, Gabriela Minigo, Joanne L Keeble, Alexandra L Garnham, Guido Pacini, Gordon K Smyth, Terence P Speed, Jonathan Carapetis, Ian P Wicks

Journal article | 2018 | Circulation

Foxp1 Is Indispensable for Ductal Morphogenesis and Controls the Exit of Mammary Stem Cells from Quiescence

Nai Yang Fu, Bhupinder Pal, Yunshun 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, Gordon K Smyth, Geoffrey J Lindeman, Jane E Visvader

Journal article | 2018 | Developmental Cell

Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness

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, Anton Vila-Sanjurjo, Gordon K Smyth, J William O Ballard

Journal article | 2018 | PLOS Genetics

Transcription-factor-mediated supervision of global genome architecture maintains B cell identity

Timothy M Johanson, Aaron TL Lun, Hannah D Coughlan, Tania Tan, Gordon K Smyth, Stephen L Nutt, Rhys S Allan

Journal article | 2018 | Nature Immunology

Mutant TRP53 exerts a target gene-selective dominant-negative effect to drive tumor development

Brandon J Aubrey, Ana Janic, Yunshun Chen, Catherine Chang, Elizabeth C Lieschke, Sarah T Diepstraten, Andrew J Kueh, Jonathan P Bernardini, Grant Dewson, Lorraine A O'Reilly, Lachlan Whitehead, Anne K Voss, Gordon K Smyth, Andreas Strasser, Gemma L Kelly

Journal article | 2018 | Genes & Development

Bone strength and mineralization are regulated independently of bone mass by ephrinB2-dependent autophagic processes in osteocytes

Vrahnas Christina, Toby Dite, Yifang Hu, Nguyen Huynh, Mark R Forwood, Keith R Bambery, Mark J Tobin, Gordon K Smyth, T John Martin, Natalie A Sims

Conference Proceedings | 2018 | JOURNAL OF BONE AND MINERAL RESEARCH

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

Yunshun Chen, Bhupinder Pal, Jane Visvader, Gordon Smyth

Journal article | 2018 | F1000Research

Cytosine methylation is an important DNA epigenetic modification. In vertebrates, methylation occurs at CpG sites, which are dinuc..

Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth

Jonathan B Baell, David J Leaver, Stefan J Hermans, Gemma L Kelly, Margs S Brennan, Natalie L Downer, Nghi Nguyen, Johannes Wichmann, Helen M Mcrae, Yuqing Yang, Ben Cleary, H Rachel Lagiakos, Stephen Mieruszynski, Guido Pacini, Hannah K Vanyai, Maria I Bergamasco, Rose E May, Bethany K Davey, Kimberly J Morgan, Andrew J Sealey, et al.

Journal article | 2018 | Nature

Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids

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, Gordon K Smyth, Jane E Visvader

Journal article | 2018 | PLOS Biology

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

Timothy M Johanson, Hannah D Coughlan, Aaron TL Lun, Naiara G Bediaga, Gaetano Naselli, Alexandra L Garnham, Leonard C Harrison, Gordon K Smyth, Rhys S Allan

Journal article | 2018 | PLOS Genetics

Loss of NF-kappa B1 Causes Gastric Cancer with Aberrant Inflammation and Expression of Immune Checkpoint Regulators in a STAT-1-Dependent Manner

Lorraine A O'Reilly, Tracy L Putoczki, Lisa A Mielke, Jun T Low, Ann Lin, Adele Preaudet, Marco J Herold, Kelvin Yaprianto, Lin Tai, Andrew Kueh, Guido Pacini, Richard L Ferrero, Raffi Gugasyan, Yifang Hu, Michael Christie, Stephen Wilcox, Raelene Grumont, Michael DW Griffin, Liam O'Connor, Gordon K Smyth, et al.

Journal article | 2018 | Immunity

Identifying low-grade cellular rejection after heart transplantation in children by using gene expression profiling

Annie Xin, Melissa GY Lee, Yifang Hu, Vera Ignjatovic, William Y Shi, Anne Shipp, Slavica Praporski, Axel Kallies, Robert G Weintraub, Paul T Monagle, Gordon K Smyth, Igor E Konstantinov

Journal article | 2018 | Physiological Genomics

A critical epithelial survival axis regulated by MCL-1 maintains thymic function in mice

Reema Jain, Julie M Sheridan, Antonia Policheni, Melanie Heinlein, Luke C Gandolfo, Grant Dewson, Gordon K Smyth, Stephen N Sansom, Nai Yang Fu, Jane E Visvader, Georg A Hollander, Andreas Strasser, Daniel HD Gray

Journal article | 2017 | Blood

Interferon-gamma released from omental adipose tissue of insulin-resistant humans alters adipocyte phenotype and impairs response to insulin and adiponectin release

JM Wentworth, J-G Zhang, E Bandala-Sanchez, G Naselli, R Liu, M Ritchie, GK Smyth, PE O'Brien, LC Harrison

Journal article | 2017 | International Journal of Obesity

Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

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, Gordon K Smyth, Jane E Visvader

Journal article | 2017 | Nature Communications

Genome-wide functional analysis reveals central signaling regulators of lymphatic endothelial cell migration and remodeling

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, Gordon K Smyth, Leigh Coultas, Benjamin M Hogan, Stephen B Fox, et al.

Journal article | 2017 | Science Signaling

An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles

Andrew J Kueh, Martin Pal, Lin Tai, Yang Liao, Gordon K Smyth, Wei Shi, Marco J Herold

Journal article | 2017 | Cell Death & Differentiation

The TNF Receptor Superfamily-NF-kappa B Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues

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, Gordon K Smyth, Martijn A Nolte, Wei Shi, et al.

Journal article | 2017 | Cell Reports

SIDT2 Transports Extracellular dsRNA into the Cytoplasm for Innate Immune Recognition

Tan A Nguyen, Blake RC Smith, Michelle D Tate, Gabrielle T Belz, Marilou H Barrios, Kirstin D Elgass, Alexandra S Weisman, Paul J Baker, Simon P Preston, Lachlan Whitehead, Alexandra Garnham, Rachel J Lundie, Gordon K Smyth, Marc Pellegrini, Meredith O'Keeffe, Ian P Wicks, Seth L Masters, Craig P Hunter, Ken C Pang

Journal article | 2017 | Immunity

Synergistic action of the MCL-1 inhibitor S63845 with current therapies in preclinical models of triple-negative and HER2-amplified breast cancer

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, Gordon K Smyth, Olivier Geneste, et al.

Journal article | 2017 | Science Translational Medicine

Correction: TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1.

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, Gordon K Smyth, David L Vaux, Stephen L Nutt, Ueli Nachbur, John Silke

Journal article | 2017 | eLife

c-Myb Regulates the T-Bet-Dependent Differentiation Program in B Cells to Coordinate Antibody Responses

Dana Piovesan, Jessica Tempany, Andrea Di Pietro, Inge Baas, Callisthenis Yiannis, Kristy O'Donnell, Yunshun Chen, Victor Peperzak, Gabrielle T Belz, Charles R Mackay, Gordon K Smyth, Joanna R Groom, David M Tarlinton, Kim L Good-Jacobson

Journal article | 2017 | Cell Reports

A non-canonical function of Ezh2 preserves immune homeostasis

Ajithkumar Vasanthakumar, Dakang Xu, Aaron TL Lun, Andrew J Kueh, Klaas PJM van Gisbergen, Nadia Iannarella, Xiaofang Li, Liang Yu, Die Wang, Bryan RG Williams, Stanley CW Lee, Ian J Majewski, Dale I Godfrey, Gordon K Smyth, Warren S Alexander, Marco J Herold, Axel Kallies, Stephen L Nutt, Rhys S Allan

Journal article | 2017 | EMBO reports

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data

Aaron TL Lun, Gordon K Smyth

Journal article | 2017 | Statistical Applications in Genetics and Molecular Biology

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie

Journal article | 2017 | Nucleic Acids Research

Conserved IKAROS-regulated genes associated with B-progenitor acute lymphoblastic leukemia outcome

Matthew T Witkowski, Yifang 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, Gordon K Smyth, Ross A Dickins

Journal article | 2017 | The Journal of Experimental Medicine

Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive

Nai Yang Fu, Anne C Rios, Bhupinder Pal, Charity W Law, Paul Jamieson, Ruijie Liu, Francois Vaillant, Felicity Jackling, Kevin He Liu, Gordon K Smyth, Geoffrey J Lindeman, Matthew E Ritchie, Jane E Visvader

Journal article | 2017 | Nature Cell Biology

RANK ligand as a target for breast cancer prevention in BRCA1 mutation carriers

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, GK Smyth, WC Dougall, JE Visvader

Conference Proceedings | 2017 | General Session Abstracts

Effector Regulatory T Cell Differentiation and Immune Homeostasis Depend on the Transcription Factor Myb

Sheila Dias, Angela D'Amico, Erika Cretney, Yang Liao, Julie Tellier, Christine Bruggeman, Francisca F Almeida, Jamie Leahy, Gabrielle T Belz, Gordon K Smyth, Wei Shi, Stephen L Nutt

Journal article | 2017 | Immunity

Infection Programs Sustained Lymphoid Stromal Cell Responses and Shapes Lymph Node Remodeling upon Secondary Challenge

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, Gordon K Smyth, William R Heath, Scott N Mueller

Journal article | 2017 | Cell Reports

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.

Yunshun Chen, Bhupinder Pal, Jane E Visvader, Gordon K Smyth

Journal article | 2017 | F1000Research

Cytosine methylation is an important DNA epigenetic modification. In vertebrates, methylation occurs at CpG sites, which are dinuc..

Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway

Clare E Weeden, Yunshun Chen, Stephen B Ma, Yifang Hu, Georg Ramm, Kate D Sutherland, Gordon K Smyth, Marie-Liesse Asselin-Labat

Journal article | 2017 | PLOS Biology

Linear ubiquitin chain assembly complex coordinates late thymic T-cell differentiation and regulatory T-cell homeostasis

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, Yifang Hu, Fiona Kupresanin, Lorraine A O'Reilly, Dale I Godfrey, Gordon K Smyth, Philippe Bouillet, Andreas Strasser, Henning Walczak, John Silke, et al.

Journal article | 2016 | Nature Communications

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

Emma C Walker, Rachelle W Johnson, Yifang Hu, Holly J Brennan, Ingrid J Poulton, Jian-Guo Zhang, Brendan J Jenkins, Gordon K Smyth, Nicos A Nicola, Natalie A Sims

Journal article | 2016 | Journal of Biological Chemistry

Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity

Dane M Newman, Shinya Sakaguchi, Aaron Lun, Simon Preston, Marc Pellegrini, Kseniya Khamina, Andreas Bergthaler, Stephen L Nutt, Gordon K Smyth, Anne K Voss, Tim Thomas, Wilfried Ellmeier, Gabrielle T Belz, Rhys S Allan

Journal article | 2016 | Cell Reports

Haemopedia: An Expression Atlas of Murine Hematopoietic Cells

Carolyn A De Graaf, Jarny Choi, Tracey M Baldwin, Jessica E Bolden, Kirsten A Fairfax, Aaron J Robinson, Christine Biben, Clare Morgan, Kerry Ramsay, Ashley P Ng, Maria Kauppi, Elizabeth A Kruse, Tobias J Sargeant, Nick Seidenman, Angela D'Amico, Marthe C D'Ombrain, Erin C Lucas, Sandra Koernig, Adriana Baz Morelli, Michael J Wilson, et al.

Journal article | 2016 | Stem Cell Reports

Clinical pathways and patient characteristics five years after the establishment of the rapid access prostate clinics at Beaumont Hospital

BM Barea, F O'Kelly, S White, E Dunne, G Smyth, R Power

Conference Proceedings | 2016 | BJU INTERNATIONAL

The changing microbiological trends in TRUS sepsis following the implementation of a prospective surveillance programme

EM Bolton, S White, M Skally, M Broe, M Hegazy, G Smyth, I Cheema, M Morrin, F Keeling, R Power

Conference Proceedings | 2016 | BJU INTERNATIONAL

RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers

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, Gordon K Smyth, William C Dougall, Jane E Visvader, Geoffrey J Lindeman

Journal article | 2016 | Nature Medicine

Evidence for a key role for neutrophils in rheumatoid arthritis

G Goldberg, S Chatfield, J Murphy, D D'Silva, ES Pang, C O'Neill, S Tadros, K Grebe, Y Chen, G Smyth, M Ng, M Inouye, S Busfield, M Wilson, A Andrews, N Wilson, I Wicks

Conference Proceedings | 2016 | EUROPEAN JOURNAL OF IMMUNOLOGY

statmod: Probability Calculations for the Inverse Gaussian Distribution

Goeknur Giner, Gordon K Smyth

Journal article | 2016 | R Journal

A combinatorial threshold model for effector differentiation of CD8( ) T cells mediated by Blimp-1 and T-bet

F Masson, A Xin, Y Liao, S Preston, T Guan, R Gloury, M Olshansky, J-X Lin, P Li, TP Speed, GK Smyth, M Ernst, WJ Leonard, M Pellegrini, S Kaech, SL Nutt, W Shi, GT Belz, A Kallies

Conference Proceedings | 2016 | EUROPEAN JOURNAL OF IMMUNOLOGY

Aboriginal Australians with acute rheumatic fever have enhanced Th17 responses to group A streptococcus that can be inhibited in vitro by repurposed clinical drugs

WJ Martin, G Minigo, ML Kim, J Keeble, MC Pitman, P Tipping, G Pacini, GK Smyth, J Carapetis, IP Wicks

Conference Proceedings | 2016 | EUROPEAN JOURNAL OF IMMUNOLOGY

ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION

Belinda Phipson, Stanley Lee, Ian J Majewski, Warren S Alexander, Gordon K Smyth

Journal article | 2016 | The Annals of Applied Statistics

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

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, Gordon K Smyth, Clare Stirzaker, Sean I O'Donoghue, Susan J Clark

Journal article | 2016 | Genome Research

RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity

Michael Chopin, Simon P Preston, Aaron TL Lun, Julie Tellier, Gordon K Smyth, Marc Pellegrini, Gabrielle T Belz, Lynn M Corcoran, Jane E Visvader, Li Wu, Stephen L Nutt

Journal article | 2016 | Cell Reports

A molecular threshold for effector CD8( ) T cell differentiation controlled by transcription factors Blimp-1 and T-bet

Annie Xin, Frederick Masson, Yang Liao, Simon Preston, Tianxia Guan, Renee Gloury, Moshe Olshansky, Jian-Xin Lin, Peng Li, Terence P Speed, Gordon K Smyth, Matthias Ernst, Warren J Leonard, Marc Pellegrini, Susan M Kaech, Stephen L Nutt, Wei Shi, Gabrielle T Belz, Axel Kallies

Journal article | 2016 | Nature Immunology

G(M3) ganglioside and phosphatidylethanolamine-containing lipids are adipose tissue markers of insulin resistance in obese women

JM Wentworth, G Naselli, K Ngui, GK Smyth, R Liu, PE O'Brien, C Bruce, J Weir, M Cinel, PJ Meikle, LC Harrison

Journal article | 2016 | International Journal of Obesity

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

Aaron TL Lun, Gordon K Smyth

Journal article | 2016 | Nucleic Acids Research

Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response

Julie Tellier, Wei Shi, Martina Minnich, Yang Liao, Simon Crawford, Gordon K Smyth, Axel Kallies, Meinrad Busslinger, Stephen L Nutt

Journal article | 2016 | Nature Immunology

Complementarity and redundancy of IL-22-producing innate lymphoid cells

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, Anthony T Papenfuss, Gordon K Smyth, Mohamed Lamkanfi, Sebastian Carotta, Jean-Christophe Renauld, Wei Shi, Sabrina Carpentier, Tim Soos, Christopher Arendt, et al.

Journal article | 2016 | Nature Immunology

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]

Y Chen, ATL Lun, GK Smyth

Journal article | 2016 | F1000Research

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most ..

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR

Aaron TL Lun, Yunshun Chen, Gordon K Smyth

Book Chapter | 2016 | Methods in Molecular Biology

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

Charity W Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K Smyth, Matthew E Ritchie

Journal article | 2016 | F1000Research

The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with cou..

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

Yunshun Chen, Aaron TL Lun, Gordon K Smyth

Journal article | 2016 | F1000Research

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most ..

Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a

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, Gordon K Smyth, Warren S Alexander, Matthew P McCormack

Journal article | 2016 | Genes & Development

TRAF2 regulates TNF and NF-kappa B signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1

Journal article | 2015 | eLife

MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway

BN Sheikh, B Phipson, F El-Saafin, HK Vanyai, NL Downer, MJ Bird, AJ Kueh, RE May, GK Smyth, AK Voss, T Thomas

Journal article | 2015 | Oncogene

An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell

Michael J Coffey, Brad E Sleebs, Alessandro D Uboldi, Alexandra Garnham, Magdalena Franco, Nicole D Marino, Michael W Panas, David JP Ferguson, Marta Enciso, Matthew T O'Neill, Sash Lopaticki, Rebecca J Stewart, Grant Dewson, Gordon K Smyth, Brian J Smith, Seth L Masters, John C Boothroyd, Justin A Boddey, Christopher J Tonkin

Journal article | 2015 | eLife

Distinctive pro-inflammatory gene signatures induced in articular chondrocytes by oncostatin M and IL-6 are regulated by Suppressor of Cytokine Signaling-3

X Liu, R Liu, BA Croker, KE Lawlor, GK Smyth, IP Wicks

Journal article | 2015 | Osteoarthritis and Cartilage

Differential Gene Expression Profiling of Orbital Adipose Tissue in Thyroid Orbitopathy

Jwu Jin Khong, Lynn Yuning Wang, Gordon K 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

Journal article | 2015 | Investigative Opthalmology & Visual Science

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

Ruijie Liu, Aliaksei Z Holik, Shian Su, Natasha Jansz, Kelan Chen, Huei San Leong, Marnie E Blewitt, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie

Journal article | 2015 | Nucleic Acids Research

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

Aaron TL Lun, Gordon K Smyth

Journal article | 2015 | BMC Bioinformatics

Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits

Bhupinder Pal, Yunshun Chen, Andrew Bert, Yifang Hu, Julie M Sheridan, Tamara Beck, Wei Shi, Keith Satterley, Paul Jamieson, Gregory J Goodall, Geoffrey J Lindeman, Gordon K Smyth, Jane E Visvader

Journal article | 2015 | Breast Cancer Research

Activated Notch counteracts Ikaros tumor suppression in mouse and human T-cell acute lymphoblastic leukemia

MT Witkowski, L Cimmino, Y Hu, T Trimarchi, H Tagoh, MD McKenzie, SA Best, L Tuohey, TA Willson, SL Nutt, M Busslinger, I Aifantis, GK Smyth, RA Dickins

Journal article | 2015 | Leukemia

Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

Wei Shi, Yang Liao, Simon N Willis, Nadine Taubenheim, Michael Inouye, David M Tarlinton, Gordon K Smyth, Philip D Hodgkin, Stephen L Nutt, Lynn M Corcoran

Journal article | 2015 | Nature Immunology

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model

Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J Hilton, Gordon K Smyth, Warren S Alexander

Journal article | 2015 | PLoS genetics

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo

Bilal N Sheikh, Natalie L Downer, Belinda Phipson, Hannah K Vanyai, Andrew J Kueh, Davis J McCarthy, Gordon K Smyth, Tim Thomas, Anne K Voss

Journal article | 2015 | Proceedings of the National Academy of Sciences

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth

Journal article | 2015 | Nucleic Acids Research

A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1

Julie M Sheridan, Matthew E Ritchie, Sarah A Best, Kun Jiang, Tamara J Beck, Francois Vaillant, Kevin Liu, Ross A Dickins, Gordon K Smyth, Geoffrey J Lindeman, Jane E Visvader

Journal article | 2015 | BMC Cancer

EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival

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, Gordon K Smyth, Rey J Lindeman, Jane E Visvader

Journal article | 2015 | Nature Cell Biology

MOZ regulates B-cell progenitors and, consequently, Moz haploinsufficiency dramatically retards MYC-induced lymphoma development

Bilal N Sheikh, Stanley CW Lee, Farrah El-Saafin, Hannah K Vanyai, Yifang Hu, Swee Heng Milon Pang, Stephanie Grabow, Andreas Strasser, Stephen L Nutt, Warren S Alexander, Gordon K Smyth, Anne K Voss, Tim Thomas

Journal article | 2015 | Blood

The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells

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, Wei Liao, Warren J Leonard, Gordon K Smyth, Wei Shi, Stephen L Nutt, Shigeo Koyasu, et al.

Journal article | 2015 | Nature Immunology

Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean 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, et al.

Journal article | 2015 | Nature Methods

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data.

Aaron TL Lun, Gordon K Smyth

Journal article | 2015 | F1000Research

Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites f..

Reversible Tumor Suppression By Ikzf1/Ikaros in Mouse Models of BCR-ABL1 B-ALL

Matthew T Witkowski, Yifang Hu, Luisa Cimmino, Mark D McKenzie, Grace J Liu, Gordon K Smyth, Ross A Dickins

Conference Proceedings | 2014 | BLOOD

Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells.

Wei Shi, Kevin Man, Gordon K Smyth, Stephen L Nutt, Axel Kallies

Journal article | 2014 | Genomics Data

Clonal population expansion of T cells during an immune response is dependent on the affinity of the T cell receptor (TCR) for its..

Transcriptional profiling of the postnatal brain of the Ts1Cje mouse model of Down syndrome.

Kai-Leng Tan, King-Hwa Ling, Chelsee A Hewitt, Pike-See Cheah, Ken Simpson, Lavinia Gordon, Melanie A Pritchard, Gordon K Smyth, Tim Thomas, Hamish S Scott

Journal article | 2014 | Genomics Data

The Ts1Cje mouse model of Down syndrome (DS) has partial trisomy of mouse chromosome 16 (MMU16), which is syntenic to human chromo..

Peripheral natural killer cell maturation depends on the transcription factor Aiolos

Melissa L Holmes, Nicholas D Huntington, Rebecca PL Thong, Jason Brady, Yoshihiro Hayakawa, Christopher E Andoniou, Peter Fleming, Wei Shi, Gordon K Smyth, Mariapia A Degli-Esposti, Gabrielle T Belz, Axel Kallies, Sebastian Carotta, Mark J Smyth, Stephen L Nutt

Journal article | 2014 | The EMBO Journal

A lineage of diploid platelet-forming cells precedes polyploid megakaryocyte formation in the mouse embryo

Kathryn S Potts, Tobias J Sargeant, John F Markham, Wei Shi, Christine Biben, Emma C Josefsson, Lachlan W Whitehead, Kelly L Rogers, Anna Liakhovitskaia, Gordon K Smyth, Benjamin T Kile, Alexander Medvinsky, Warren S Alexander, Douglas J Hilton, Samir Taoudi

Journal article | 2014 | Blood

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

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, Simon M Lin, Joseph Meehan, Christopher E Mason, Javier Santoyo-Lopez, Robert A Setterquist, et al.

Journal article | 2014 | Nature Communications

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Zhenqiang Su, Pawel P Labaj, Sheng Li, Jean Thierry-Mieg, Danielle 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, Joshua Xu, Ana Conesa, Cesare Furlanello, Hanlin Gao, Huixiao Hong, et al.

Journal article | 2014 | Nature Biotechnology

PROBING IKAROS FUNCTIONS IN B-ALL USING NOVEL MOUSE MODELS

Matthew Witkowski, Yifang Hu, Priyanka Sathe, Mark McKenzie, Luisa Cimmino, Grace Liu, Andrew Keniry, Gordon K Smyth, Nicholas Huntington, Ross Dickins

Conference Proceedings | 2014 | Experimental Hematology

Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks

King-Hwa Ling, Chelsee A Hewitt, Kai-Leng Tan, Pike-See Cheah, Sharmili Vidyadaran, Mei-I Lai, Han-Chung Lee, Ken Simpson, Lavinia Hyde, Melanie A Pritchard, Gordon K Smyth, Tim Thomas, Hamish S Scott

Journal article | 2014 | BMC Genomics

Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ

Kim L Good-Jacobson, Yunshun Chen, Anne K Voss, Gordon K Smyth, Tim Thomas, David Tarlinton

Journal article | 2014 | Proceedings of the National Academy of Sciences of the United States of America

Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia

Grace J Liu, Luisa Cimmino, Julian G Jude, Yifang 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, Gordon K Smyth, Johannes Zuber, Ross A Dickins

Journal article | 2014 | Genes & Development

The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity

Stephane Chevrier, Dianne Emslie, Wei Shi, Tobias Kratina, Cameron Wellard, Alexander Karnowski, Erdem Erikci, Gordon K Smyth, Kamal Chowdhury, David Tarlinton, Lynn M Corcoran

Journal article | 2014 | Journal of Experimental Medicine

Transcription Factor IRF4 Regulates Germinal Center Cell Formation through a B Cell-Intrinsic Mechanism

Simon N Willis, Kim L Good-Jacobson, Joan Curtis, Amanda Light, Julie Tellier, Wei Shi, Gordon K Smyth, David M Tarlinton, Gabrielle T Belz, Lynn M Corcoran, Axel Kallies, Stephen L Nutt

Journal article | 2014 | Journal of Immunology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Yang Liao, Gordon K Smyth, Wei Shi

Journal article | 2014 | Bioinformatics

Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain

Laura F Dagley, Carl A White, Yang Liao, Wei Shi, Gordon K Smyth, Jacqueline M Orian, Andrew Emili, Anthony W Purcell

Journal article | 2014 | Proteomics

Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR

Yunshun Chen, Aaron TL Lun, Gordon K Smyth

Book Chapter | 2014

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

Aaron TL Lun, Gordon K Smyth

Journal article | 2014 | Nucleic Acids Research

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth

Journal article | 2014 | Genome Biology

The transcription factor IRF4 is essential for TCR affinity-mediated metabolic programming and clonal expansion of T cells

Kevin Man, Maria Miasari, Wei Shi, Annie Xin, Darren C Henstridge, Simon Preston, Marc Pellegrini, Gabrielle T Belz, Gordon K Smyth, Mark A Febbraio, Stephen L Nutt, Axel Kallies

Journal article | 2013 | Nature Immunology

Cell-Type-Specific Transcriptional Profiles of the Dimorphic Pathogen Penicillium marneffei Reflect Distinct Reproductive, Morphological, and Environmental Demands

Shivani Pasricha, Michael Payne, David Canovas, Luke Pase, Nathamon Ngaosuwankul, Sally Beard, Alicia Oshlack, Gordon K Smyth, Sansanee C Chaiyaroj, Kylie J Boyce, Alex Andrianopoulos

Journal article | 2013 | G3: Genes, Genomes, Genetics

Polycomb repressive complex 2 (PRC2) suppresses E mu-myc lymphoma

Stanley CW Lee, Belinda Phipson, Craig D Hyland, Huei San Leong, Rhys S Allan, Aaron Lun, Douglas J Hilton, Stephen L Nutt, Marnie E Blewitt, Gordon K Smyth, Warren S Alexander, Ian J Majewski

Journal article | 2013 | Blood

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Simon Anders, Davis J McCarthy, Yunshun Chen, Michal Okoniewski, Gordon K Smyth, Wolfgang Huber, Mark D Robinson

Journal article | 2013 | Nature Protocols

PAX5 LOSS IMPOSES A REVERSIBLE DIFFERENTIATION BLOCK IN B-PROGENITOR ACUTE LYMPHOBLASTIC LEUKEMIA

Ross Dickins, Grace Liu, Luisa Cimmino, Yifang Hu, Sarah Best, Laura Tuohey, Michael Farrar, Stephen Nutt, Gordon Smyth

Conference Proceedings | 2013 | Experimental Hematology

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

Bilal Sheikh, Belinda Phipson, Stanley Lee, Farrah El-Saafin, Natalie Downer, Stephanie Grabow, Gordon Smyth, Andreas Strasser, Warren Alexander, Anne Voss, Tim Thomas

Conference Proceedings | 2013 | Experimental Hematology

Targeting BCL-2 with the BH3 Mimetic ABT-199 in Estrogen Receptor-Positive Breast Cancer

Francois Vaillant, Delphine Merino, Lily Lee, Kelsey Breslin, Bhupinder Pal, Matthew E Ritchie, Gordon K Smyth, Michael Christie, Louisa J Phillipson, Christopher J Burns, G Bruce Mann, Jane E Visvader, Geoffrey J Lindeman

Journal article | 2013 | Cancer Cell

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

Di Wu, Yifang Hu, Stephen Tong, Bryan RG Williams, Gordon K Smyth, Michael P Gantier

Journal article | 2013 | RNA

Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations

Joshy George, Kathryn Alsop, Dariush Etemadmoghadam, Heather Hondow, Thomas Mikeska, Alexander Dobrovic, Anna DeFazio, Gordon K Smyth, Douglas A Levine, Gillian Mitchell, David D Bowtell

Journal article | 2013 | Clinical Cancer Research

Separate-channel analysis of two-channel microarrays: recovering inter-spot information

Gordon K Smyth, Naomi S Altman

Journal article | 2013 | BMC Bioinformatics

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Yang Liao, Gordon K Smyth, Wei Shi

Journal article | 2013 | Nucleic Acids Research

Transposon mutagenesis reveals cooperation of ETS family transcription factors with signaling pathways in erythro-megakaryocytic leukemia

Jian Zhong Tang, Catherine L Carmichael, Wei Shi, Donald Metcalf, Ashley P Ng, Craig D Hyland, Nancy A Jenkins, Neal G Copeland, Viive M Howell, Zhizhuang Joe Zhao, Gordon K Smyth, Benjamin T Kile, Warren S Alexander

Journal article | 2013 | Proceedings of the National Academy of Sciences of the United States of America

Lessons on Conditional Gene Targeting in Mouse Adipose Tissue

Kevin Y Lee, Steven J Russell, Siegfried Ussar, Jeremie Boucher, Cecile Vernochet, Marcelo A Mori, Graham Smyth, Michael Rourk, Carly Cederquist, Evan D Rosen, Barbara B Kahn, C Ronald Kahn

Journal article | 2013 | Diabetes

Epigenetic Regulator Smchd1 Functions as a Tumor Suppressor

Huei San Leong, Kelan Chen, Yifang Hu, Stanley Lee, Jason Corbin, Miha Pakusch, James M Murphy, Ian J Majewski, Gordon K Smyth, Warren S Alexander, Douglas J Hilton, Marnie E Blewitt

Journal article | 2013 | Cancer Research

Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2

Bhupinder Pal, Toula Bouras, Wei Shi, Francois Vaillant, Julie M Sheridan, Naiyang Fu, Kelsey Breslin, Kun Jiang, Matthew E Ritchie, Matthew Young, Geoffrey J Lindeman, Gordon K Smyth, Jane E Visvader

Journal article | 2013 | Cell Reports

HDAC inhibitors induce tumor-cell-selective pro-apoptotic transcriptional responses

JE Bolden, W Shi, K Jankowski, C-Y Kan, L Cluse, BP Martin, KL MacKenzie, GK Smyth, RW Johnstone

Journal article | 2013 | Cell Death & Disease

Identifying Associations Between Genomic Alterations in Tumors

Joshy George, Kylie L Gorringe, Gordon K Smyth, David DL Bowtell

Book Chapter | 2013 | Methods in Molecular Biology

Adipose-Specific Deletion of TFAM Increases Mitochondrial Oxidation and Protects Mice against Obesity and Insulin Resistance

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, Graham Smyth, Saverio Cinti, Christopher B Newgard, Bradford W Gibson, Nils-Goeran Larsson, Ronald Kahn

Journal article | 2012 | Cell Metabolism

The Molecular Signature of Tissue Resident Memory CD8 T Cells Isolated from the Brain

Linda M Wakim, Amanda Woodward-Davis, Ruijie Liu, Yifang Hu, Jose Villadangos, Gordon Smyth, Michael J Bevan

Journal article | 2012 | Journal of Immunology

Camera: a competitive gene set test accounting for inter-gene correlation

Di Wu, Gordon K Smyth

Journal article | 2012 | Nucleic Acids Research

Ensuring safe occupational therapy practice with medicines: legal and practice issues

GK Smyth, P Frost

Conference Proceedings | 2012 | BRITISH JOURNAL OF OCCUPATIONAL THERAPY

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

Dillon W Leong, Jasper C Komen, Chelsee A Hewitt, Estelle Arnaud, Matthew McKenzie, Belinda Phipson, Melanie Bahlo, Adrienne Laskowski, Sarah A Kinkel, Gayle M Davey, William R Heath, Anne K Voss, Rene P Zahedi, James J Pitt, Roman Chrast, Albert Sickmann, Michael T Ryan, Gordon K Smyth, David R Thorburn, Hamish S Scott

Journal article | 2012 | Journal of Biological Chemistry

Impaired thermogenesis and adipose tissue development in mice with fat-specific disruption of insulin and IGF-1 signalling

Jeremie Boucher, Marcelo A Mori, Kevin Y Lee, Graham Smyth, Chong Wee Liew, Yazmin Macotela, Michael Rourk, Matthias Bluher, Steven J Russell, C Ronald Kahn

Journal article | 2012 | Nature Communications

Effective Adjunctive Therapy by an Innate Defense Regulatory Peptide in a Preclinical Model of Severe Malaria

Ariel H Achtman, Sandra Pilat, Charity W Law, David J Lynn, Laure Janot, Matt L Mayer, Shuhua Ma, Jason Kindrachuk, B Brett Finlay, Fiona SL Brinkman, Gordon K Smyth, Robert EW Hancock, Louis Schofield

Journal article | 2012 | Science Translational Medicine

A Screening Room for Cerebral Malaria Drugs

Journal article | 2012 | SCIENCE TRANSLATIONAL MEDICINE

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

L Happo, B Phipson, GK Smyth, A Strasser, CL Scott

Journal article | 2012 | Cell Death & Disease

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

Davis J McCarthy, Yunshun Chen, Gordon K Smyth

Journal article | 2012 | Nucleic Acids Research

Sensitization of BCL-2-expressing breast tumors to chemotherapy by the BH3 mimetic ABT-737

Samantha R Oakes, Francois Vaillant, Elgene Lim, Lily Lee, Kelsey Breslin, Frank Feleppa, Siddhartha Deb, Matthew E Ritchie, Elena Takano, Teresa Ward, Stephen B Fox, Daniele Generali, Gordon K Smyth, Andreas Strasser, David CS Huang, Jane E Visvader, Geoffrey J Lindeman

Journal article | 2012 | Proceedings of the National Academy of Sciences of the United States of America

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

Matthew D Young, Davis J McCarthy, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack, Mark D Robinson

Book Chapter | 2012

Differential expression for RNA sequencing (RNA-Seq) data: Mapping, summarization, statistical analysis, and experimental design

MD Young, DJ McCarthy, MJ Wakefield, GK Smyth, A Oshlack, MD Robinson

Book Chapter | 2012

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

Steven P Lund, Dan Nettleton, Davis J McCarthy, Gordon K Smyth

Journal article | 2012 | Statistical Applications in Genetics and Molecular Biology

Gata-3 Negatively Regulates the Tumor-Initiating Capacity of Mammary Luminal Progenitor Cells and Targets the Putative Tumor Suppressor Caspase-14

Marie-Liesse Asselin-Labat, Kate D Sutherland, Francois Vaillant, David E Gyorki, Di Wu, Sheridan Holroyd, Kelsey Breslin, Teresa Ward, Wei Shi, Mary L Bath, Siddhartha Deb, Stephen B Fox, Gordon K Smyth, Geoffrey J Lindeman, Jane E Visvader

Journal article | 2011 | Molecular and Cellular Biology

Disruption of the histone acetyltransferase MYST4 leads to a Noonan syndrome-like phenotype and hyperactivated MAPK signaling in humans and mice

Michael Kraft, Ion Cristian Cirstea, Anne Kathrin Voss, Tim Thomas, Ina Goehring, Bilal N Sheikh, Lavinia Gordon, Hamish Scott, Gordon K Smyth, Mohammad Reza Ahmadian, Udo Trautmann, Martin Zenker, Marco Tartaglia, Arif Ekici, Andre Reis, Helmuth-Guenther Doerr, Anita Rauch, Christian Thomas Thiel

Journal article | 2011 | Journal of Clinical Investigation

Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart

Duncan J Campbell, Yuan Zhang, Darren J Kelly, Richard E Gilbert, Davis J McCarthy, Wei Shi, Gordon K Smyth

Journal article | 2011 | Clinical and Experimental Pharmacology and Physiology

Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance

Francois-Xavier Hubert, Sarah A Kinkel, Gayle M Davey, Belinda Phipson, Scott N Mueller, Adrian Liston, Anna I Proietto, Ping ZF Cannon, Simon Forehan, Gordon K Smyth, Li Wu, Christopher C Goodnow, Francis R Carbone, Hamish S Scott, William R Heath

Journal article | 2011 | Blood

Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice

Ashley P Ng, Stephen J Loughran, Donald Metcalf, Craig D Hyland, Carolyn A de Graaf, Yifang Hu, Gordon K Smyth, Douglas J Hilton, Benjamin T Kile, Warren S Alexander

Journal article | 2011 | Blood

Fas-mediated neutrophil apoptosis is accelerated by Bid, Bak, and Bax and inhibited by Bcl-2 and Mcl-1

Ben A Croker, Joanne A O'Donnell, Cameron J Nowell, Donald Metcalf, Grant Dewson, Kirsteen J Campbell, Kelly L Rogers, Yifang Hu, Gordon K Smyth, Jian-Guo Zhang, Michael White, Kurt Lackovic, Louise H Cengia, Lorraine A O'Reilly, Philippe Bouillet, Suzanne Cory, Andreas Strasser, Andrew W Roberts

Journal article | 2011 | Proceedings of the National Academy of Sciences of the United States of America

Targeting Antigen to Mouse Dendritic Cells via Clec9A Induces Potent CD4 T Cell Responses Biased toward a Follicular Helper Phenotype

Mireille H Lahoud, Fatma Ahmet, Susie Kitsoulis, Soo San Wan, David Vremec, Chin-Nien Lee, Belinda Phipson, Wei Shi, Gordon K Smyth, Andrew M Lew, Yu Kato, Scott N Mueller, Gayle M Davey, William R Heath, Ken Shortman, Irina Caminschi

Journal article | 2011 | Journal of Immunology

Id2 expression delineates differential checkpoints in the genetic program of CD8 alpha( ) and CD103( ) dendritic cell lineages

Jacob T Jackson, Yifang Hu, Ruijie Liu, Frederick Masson, Angela D'Amico, Sebastian Carotta, Annie Xin, Mary J Camilleri, Adele M Mount, Axel Kallies, Li Wu, Gordon K Smyth, Stephen L Nutt, Gabrielle T Belz

Journal article | 2011 | EMBO Journal

Technical Variability Is Greater than Biological Variability in a Microarray Experiment but Both Are Outweighed by Changes Induced by Stimulation

Penelope A Bryant, Gordon K Smyth, Roy Robins-Browne, Nigel Curtis

Journal article | 2011 | PLoS One

Expression discordance of monozygotic twins at birth Effect of intrauterine environment and a possible mechanism for fetal programming

Lavinia Gordon, Ji-Hoon E Joo, Roberta Andronikos, Miina Ollikainen, Euan M Wallace, Mark P Umstad, Michael Permezel, Alicia Oshlack, Ruth Morley, John B Carlin, Richard Saffery, Gordon K Smyth, Jeffrey M Craig

Journal article | 2011 | Epigenetics

Deregulation of MYCN, LIN28B and LET7 in a Molecular Subtype of Aggressive High-Grade Serous Ovarian Cancers

Aslaug Helland, Michael S Anglesio, Joshy George, Prue A Cowin, Cameron N Johnstone, Colin M House, Karen E Sheppard, Dariush Etemadmoghadam, Nataliya Melnyk, Anil K Rustgi, Wayne A Phillips, Hilde Johnsen, Ruth Holm, Gunnar B Kristensen, Michael J Birrer, Richard B Pearson, Anne-Lise Borresen-Dale, David G Huntsman, Anna deFazio, Chad J Creighton, et al.

Journal article | 2011 | PLoS One

The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells

Erika Cretney, Annie Xin, Wei Shi, Martina Minnich, Frederick Masson, Maria Miasari, Gabrielle T Belz, Gordon K Smyth, Meinrad Busslinger, Stephen L Nutt, Axel Kallies

Journal article | 2011 | Nature Immunology

DNMT3L Is a Regulator of X Chromosome Compaction and Post-Meiotic Gene Transcription

Natasha M Zamudio, Hamish S Scott, Katja Wolski, Chi-Yi Lo, Charity Law, Dillon Leong, Sarah A Kinkel, Suyinn Chong, Damien Jolley, Gordon K Smyth, David de Kretser, Emma Whitelaw, Moira K O'Bryan

Journal article | 2011 | PLoS One

Spatiotemporal Regulation of Multiple Overlapping Sense and Novel Natural Antisense Transcripts at the Nrgn and Camk2n1 Gene Loci during Mouse Cerebral Corticogenesis

King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Pike-See Cheah, Gordon K Smyth, Seong-Seng Tan, Christopher N Hahn, Tim Thomas, Paul Q Thomas, Hamish S Scott

Journal article | 2011 | Cerebral Cortex

Regulation of hematopoietic stem cells by their mature progeny

Carolyn A de Graaf, Maria Kauppi, Tracey Baldwin, Craig D Hyland, Donald Metcalf, Tracy A Willson, Marina R Carpinelli, Gordon K Smyth, Warren S Alexander, Douglas J Hilton

Journal article | 2010 | Proceedings of the National Academy of Sciences of the United States of America

Maximal killing of lymphoma cells by DNA damage-inducing therapy requires not only the p53 targets Puma and Noxa, but also Bim

Lina Happo, Mark S Cragg, Belinda Phipson, Jon M Haga, Elisa S Jansen, Marco J Herold, Grant Dewson, Ewa M Michalak, Cassandra J Vandenberg, Gordon K Smyth, Andreas Strasser, Suzanne Cory, Clare L Scott

Journal article | 2010 | Blood

A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility

Iris KL Tan, Leanne Mackin, Nancy Wang, Anthony T Papenfuss, Colleen M Elso, Michelle P Ashton, Fiona Quirk, Belinda Phipson, Melanie Bahlo, Terence P Speed, Gordon K Smyth, Grant Morahan, Thomas C Brodnicki

Journal article | 2010 | Genome Research

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

Wei Shi, Alicia Oshlack, Gordon K Smyth

Journal article | 2010 | Nucleic Acids Research

Amplicon-Dependent CCNE1 Expression Is Critical for Clonogenic Survival after Cisplatin Treatment and Is Correlated with 20q11 Gain in Ovarian Cancer

Dariush Etemadmoghadam, Joshy George, Prue A Cowin, Carleen Cullinane, Maya Kansara, Kylie L Gorringe, Gordon K Smyth, David DL Bowtell

Journal article | 2010 | PLoS One

Copy Number Analysis Identifies Novel Interactions Between Genomic Loci in Ovarian Cancer

Kylie L Gorringe, Joshy George, Michael S Anglesio, Manasa Ramakrishna, Dariush Etemadmoghadam, Prue Cowin, Anita Sridhar, Louise H Williams, Samantha E Boyle, Nozomu Yanaihara, Aikou Okamoto, Mitsuyoshi Urashima, Gordon K Smyth, Ian G Campbell, David DL Bowtell

Journal article | 2010 | PLoS One

ROAST: rotation gene set tests for complex microarray experiments

Di Wu, Elgene Lim, Francois Vaillant, Marie-Liesse Asselin-Labat, Jane E Visvader, Gordon K Smyth

Journal article | 2010 | Bioinformatics

REGULATION OF HEMATOPOIETIC STEM CELLS BY THEIR MATURE PROGENY

CA de Graaf, M Kauppi, T Baldwin, C Hyland, M Carpinelli, D Metcalf, GK Smyth, WS Alexander, DJ Hilton

Conference Proceedings | 2010 | EXPERIMENTAL HEMATOLOGY

Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells

Ian J Majewski, Matthew E Ritchie, Belinda Phipson, Jason Corbin, Miha Pakusch, Anja Ebert, Meinrad Busslinger, Haruhiko Koseki, Yifang Hu, Gordon K Smyth, Warren S Alexander, Douglas J Hilton, Marnie E Blewitt

Journal article | 2010 | Blood

Gene Network Disruptions and Neurogenesis Defects in the Adult Ts1Cje Mouse Model of Down Syndrome

Chelsee A Hewitt, King-Hwa Ling, Tobias D Merson, Ken M Simpson, Matthew E Ritchie, Sarah L King, Melanie A Pritchard, Gordon K Smyth, Tim Thomas, Hamish S Scott, Anne K Voss

Journal article | 2010 | PLoS One

Pro-Inflammatory CD11c( )CD206( ) Adipose Tissue Macrophages Are Associated With Insulin Resistance in Human Obesity

John M Wentworth, Gaetano Naselli, Wendy A Brovvn, Lisa Doyle, Belinda Phipson, Gordon K Smyth, Martin Wabitsch, Paul E O'Brien, Leonard C Harrison

Journal article | 2010 | Diabetes

Control of mammary stem cell function by steroid hormone signalling

Marie-Liesse Asselin-Labat, Francois Vaillant, Julie M Sheridan, Bhupinder Pal, Di Wu, Evan R Simpson, Hisataka Yasuda, Gordon K Smyth, T John Martin, Geoffrey J Lindeman, Jane E Visvader

Journal article | 2010 | Nature

Fine Mapping of Leishmania major Susceptibility Locus lmr2 and Evidence of a Role for Fli1 in Disease and Wound Healing

Anuratha Sakthianandeswaren, Joan M Curtis, Colleen Elso, Beena Kumar, Tracey M Baldwin, Sash Lopaticki, Lukasz Kedzierski, Gordon K Smyth, Simon J Foote, Emanuela Handman

Journal article | 2010 | Infection and Immunity

SAGE Analysis of Genes Differentially Expressed in Presymptomatic TgSOD1(G93A) Transgenic Mice Identified Cellular Processes Involved in Early Stage of ALS Pathology

Michel Guipponi, Qiao-Xin Li, Lavinia Hyde, Tim Beissbarth, Gordon K Smyth, Colin L Masters, Hamish S Scott

Journal article | 2010 | Journal of Molecular Neuroscience

Estimating the proportion of microarray probes expressed in an RNA sample

Wei Shi, Carolyn A de Graaf, Sarah A Kinkel, Ariel H Achtman, Tracey Baldwin, Louis Schofield, Hamish S Scott, Douglas J Hilton, Gordon K Smyth

Journal article | 2010 | Nucleic Acids Research

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack

Journal article | 2010 | Genome Biology

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

Belinda Phipson, Gordon K Smyth

Journal article | 2010 | Statistical Applications in Genetics and Molecular Biology

A candidate subspecies discrimination system involving a vomeronasal receptor gene with different alleles fixed in M. m. domesticus and M. m. musculus

Robert C Karn, Janet M Young, Christina M Laukaitis

Conference Proceedings | 2010 | Genome Biology

Screening MRI in patients at high risk of breast carcinoma from the Manchester family history clinic: our initial 2-year experience

Y Lim, E Hurley, P Riley

Conference Proceedings | 2010 | Breast Cancer Research

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D Robinson, Davis J McCarthy, Gordon K Smyth

Journal article | 2010 | Bioinformatics

Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways

Elgene Lim, Di Wu, Bhupinder Pal, Toula Bouras, Marie-Liesse Asselin-Labat, Francois Vaillant, Hideo Yagita, Geoffrey J Lindeman, Gordon K Smyth, Jane E Visvader

Journal article | 2010 | Breast Cancer Research

LEVERAGE ADJUSTMENTS FOR DISPERSION MODELLING IN GENERALIZED NONLINEAR MODELS

Gordon K Smyth, Arunas P Verbyla

Journal article | 2009 | Australian & New Zealand Journal of Statistics

Platelets Play a Protective Role in Erythrocytic Stage Malaria Infection

Simon J Foote, Brendan J McMorran, Karen E Drysdale, Carolyn de Graaf, Gordon K Smyth, Warren S Alexander

Conference Proceedings | 2009 | BLOOD

edgeR: A Bioconductor package for differential expression analysis of digital gene expression data

MD Robinson, DJ McCarthy, GK Smyth

Journal article | 2009 | Bioinformatics

Illumina WG-6 BeadChip strips should be normalized separately

Wei Shi, Ashish Banerjee, Matthew E Ritchie, Steve Gerondakis, Gordon K Smyth

Journal article | 2009 | BMC Bioinformatics

Murine hematopoietic blast colony-forming cells and their progeny have distinctive membrane marker profiles

Donald Metcalf, Ashley P Ng, Stephen JL Loughran, Belinda Phipson, Gordon K Smyth, Ladina Di Rago, Sandra Mifsud

Journal article | 2009 | Proceedings of the National Academy of Sciences of the United States of America

LEUKAEMIC TRANSFORMATION IN MURINE AML INDUCED BY OVEREXPRESSION OF THE MIXL1 HOMEOBOX GENE

L Robb, S Glaser, Y Hu, GK Smyth, D Izon

Conference Proceedings | 2009 | EXPERIMENTAL HEMATOLOGY

ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays

Yifang Hu, Gordon K Smyth

Journal article | 2009 | Journal of Immunological Methods

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

Elgene Lim, Francois Vaillant, Di Wu, Natasha C Forrest, Bhupinder Pal, Adam H Hart, Marie-Liesse Asselin-Labat, David E Gyorki, Teresa Ward, Audrey Partanen, Frank Feleppa, Lily I Huschtscha, Heather J Thorne, Stephen B Fox, Max Yan, Juliet D French, Melissa A Brown, Gordon K Smyth, Jane E Visvader, Geoffrey J Lindeman

Journal article | 2009 | Nature Medicine

Blimp1 is limiting for transformation in a mouse plasmacytoma model

Kathy D'Costa, Dianne Emslie, Donald Metcalf, Gordon K Smyth, Alexander Karnowski, Axel Kallies, Stephen L Nutt, Lynn M Corcoran

Journal article | 2009 | Blood

Analyzing white blood cell subpopulation for quick and simple predictors for autologous stem cell collection

Y Gao, S Lim, F Gao, J Ng, Y Phoon, C Tham, R Quek, M Tao

Conference Proceedings | 2009 | JOURNAL OF CLINICAL ONCOLOGY

Investigation of human mammary stem and progenitor subpopulations from BRCA1 mutation carriers and noncarriers

E Lim, F Vaillant, D Wu, N Forrest, B Pal, D Gyorki, GK Smyth, J Visvader, G Lindeman

Conference Proceedings | 2009 | JOURNAL OF CLINICAL ONCOLOGY

The molecular signature of CD8( ) T cells undergoing deletional tolerance

Ian A Parish, Sudha Rao, Gordon K Smyth, Torsten Juelich, Gareth S Denyer, Gayle M Davey, Andreas Strasser, William R Heath

Journal article | 2009 | Blood

Puma and to a lesser extent Noxa are suppressors of Myc-induced lymphomagenesis

EM Michalak, ES Jansen, L Happo, MS Cragg, L Tai, GK Smyth, A Strasser, JM Adams, CL Scott

Journal article | 2009 | Cell Death & Differentiation

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution

Jeremy D Silver, Matthew E Ritchie, Gordon K Smyth

Journal article | 2009 | Biostatistics

Testing significance relative to a fold-change threshold is a TREAT

Davis J McCarthy, Gordon K Smyth

Journal article | 2009 | Bioinformatics

Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype

Francois-Xavier Hubert, Sarah A Kinkel, Pauline E Crewther, Ping ZF Cannon, Kylie E Webster, Maire Link, Raivo Uibo, Moira K O'Bryan, Anthony Meager, Simon P Forehan, Gordon K Smyth, Laureane Mittaz, Stylianos E Antonarakis, Paert Peterson, William R Heath, Hamish S Scott

Journal article | 2009 | Journal of Immunology

Detection of Gene Expression in an Individual Cell Type within a Cell Mixture Using Microarray Analysis

Penelope A Bryant, Gordon K Smyth, Roy Robins-Browne, Nigel Curtis

Journal article | 2009 | PLoS One

Platelets Kill Intraerythrocytic Malarial Parasites and Mediate Survival to Infection

Brendan J McMorran, Vikki M Marshall, Carolyn de Graaf, Karen E Drysdale, Meriam Shabbar, Gordon K Smyth, Jason E Corbin, Warren S Alexander, Simon J Foote

Journal article | 2009 | Science

Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling

King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, Hamish S Scott

Journal article | 2009 | Genome Biology

Molecular dissection of the pea shoot apical meristem

Dacheng Liang, Chui E Wong, Mohan B Singh, Christine A Beveridge, Belinda Phipson, Gordon K Smyth, Prem L Bhalla

Journal article | 2009 | Journal of Experimental Botany

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

Ran Blekhman, Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad

Journal article | 2008 | PLoS Genetics

Deaf-I regulates epithelial cell proliferation and side-branching in the mammary gland

Holly E Barker, Gordon K Smyth, James Wettenhall, Teresa A Ward, Mary L Bath, Geoffrey J Lindeman, Jane E Visvader

Journal article | 2008 | BMC Developmental Biology

Gene expression profiling from T cells in patients with a first demyelinating episode

Olga G Skibina, Victoria M Petreau, Helmut Butzkueven, Gordon Smyth, Yifang Hu, Trevor Kilpatrick

Conference Proceedings | 2008 | MULTIPLE SCLEROSIS

Integrative analysis of RUNX1 downstream pathways and target genes

Joelle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, Matthew E Ritchie, Frederic Schuetz, Ping Cannon, Marjorie Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner, Terence P Speed, Maria Kavallaris, Gordon K Smyth, Hamish S Scott

Journal article | 2008 | BMC Genomics

Histone deacetylase inhibitor panobinostat induces clinical responses with associated alterations in gene expression profiles in cutaneous T-cell lymphoma

Leigh Ellis, Yan Pan, Gordon K Smyth, Daniel J George, Chris McCormack, Roxanne Williams-Truax, Monica Mita, Joachim Beck, Howard Burris, Gail Ryan, Peter Atadja, Dale Butterfoss, Margaret Dugan, Kenneth Culver, Ricky W Johnstone, H Miles Prince

Journal article | 2008 | Clinical Cancer Research

Mechanisms of tumour-selective apoptosis induced by the histone deacetylase inhibitor vorinostat

JE Bolden, W Shi, GK Smyth, LA Cluse, RW Johnstone

Conference Proceedings | 2008 | European Journal of Cancer Supplements

Myocardial gene expression associated with genetic cardiac hypertrophy in the absence of hypertension

Jeremy P Dwyer, Matthew E Ritchie, Gordon K Smyth, Stephen B Harrap, Lea MD Delbridge, Andrea A Domenighetti, Robert Di Nicolantonio

Journal article | 2008 | Hypertension Research

Oncological evaluation of the prostate-sparing cystectomy: Long-term results

Francois Rozet, Guillaume Lesur, Xavier Cathelineau, Eric Barret, Gordon P Smyth, Rafael Sanchez-Salas, Ali Kasraeian, Guy Vallancien

Conference Proceedings | 2008 | Journal of Urology

Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activity

Ian J Majewski, Marnie E Blewitt, Carolyn A de Graaf, Edward J McManus, Melanie Bahlo, Adrienne A Hilton, Craig D Hyland, Gordon K Smyth, Jason E Corbin, Donald Metcalf, Warren S Alexander, Douglas J Hilton

Journal article | 2008 | PLoS Biology

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

Mark D Robinson, Gordon K Smyth

Journal article | 2008 | Biostatistics

Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis

Samuel E Berkovic, Leanne M Dibbens, Alicia Oshlack, Jeremy D Silver, Marina Katerelos, Danya F Vears, Renate Luellmann-Rauch, Judith Blanz, Ke Wei Zhang, Jim Stankovich, Renate M Kalnins, John P Dowling, Eva Andermann, Frederick Andermann, Enrico Faldini, Rudi D'Hooge, Lata Vadlamudi, Richard A Macdonell, Bree L Hodgson, Marta A Bayly, et al.

Journal article | 2008 | American Journal of Human Genetics

Evaluation of Tweedie exponential dispersion model densities by Fourier inversion

Peter K Dunn, Gordon K Smyth

Journal article | 2008 | Statistics and Computing

Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention

CE Huggins, AA Domenighetti, ME Ritchie, N Khalil, JM Favaloro, J Proietto, GK Smyth, S Pepe, LMD Delbridge

Journal article | 2008 | Journal of Molecular and Cellular Cardiology

Identification of Pax5 target genes in early B cell differentiation

Clare Pridans, Melissa L Holmes, Matthew Polli, James M Wettenhall, Aleksandar Dakic, Lynn M Corcoran, Gordon K Smyth, Stephen L Nutt

Journal article | 2008 | Journal of Immunology

Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention

CE Huggins, AA Domenighetti, ME Ritchie, N Khalil, JM Favaloro, J Proletto, GK Smyth, S Pepe, LMD Delbridge

Journal article | 2008 | Journal of Molecular and Cellular Cardiology

Moderated statistical tests for assessing differences in tag abundance

Mark D Robinson, Gordon K Smyth

Journal article | 2007 | Bioinformatics

A comparison of background correction methods for two-colour microarrays

Matthew E Ritchie, Jeremy Silver, Alicia Oshlack, Melissa Holmes, Dileepa Diyagama, Andrew Holloway, Gordon K Smyth

Journal article | 2007 | BIOINFORMATICS

Wound healing response is a major contributor to the severity of cutaneous leishmaniasis in the ear model of infection

T Baldwin, A Sakthianandeswaren, JM Curtis, B Kumar, GK Smyth, SJ Foote, E Handman

Journal article | 2007 | Parasite Immunology

Identification of the gene for action myoclonus-renal failure syndrome

Samuel F Berkovic, LM Dibbens, A Oshlack, JD Silver, M Katerelos, DF Vears, J Stankovich, E Andermann, F Andermann, BL Hodgson, MA Bayly, JC Mulley, GK Smyth, DA Power, M Bahlo

Conference Proceedings | 2007 | EPILEPSIA

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

Y Pan, HM Prince, J George, RW Johnstone, L Ellis, C McCormack, GK Smyth, R Williams-Truax, P Atadja, D Butterfoss, M Dugan, K Culver

Conference Proceedings | 2007 | HAEMATOLOGICA-THE HEMATOLOGY JOURNAL

Using DNA microarrays to study gene expression in closely related species

Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad

Journal article | 2007 | Bioinformatics

Gene expression profiling of esophageal cancer: Comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma

Danielle M Greenawalt, Cuong Duong, Gordon K Smyth, Marianne L Ciavarella, Natalie J Thompson, Thomas Tiang, William K Murray, Robert JS Thomas, Wayne A Phillips

Journal article | 2007 | International Journal of Cancer

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

Alicia Oshlack, Dianne Emslie, Lynn M Corcoran, Gordon K Smyth

Journal article | 2007 | Genome Biology

Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway

Michelle G De Silva, Michael S Hildebrand, Helen Christopoulos, Michelle R Newman, Katrina Bell, Matthew Ritchie, Gordon K Smyth, Hans-Henrik M Dahl

Journal article | 2006 | Acta Oto-Laryngologica

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell, Gordon K Smyth

Journal article | 2006 | BMC BIOINFORMATICS

Proximal genomic localization of STATI binding and regulated transcriptional activity

Samuel Wormald, Douglas J Hilton, Gordon K Smyth, Terence P Speed

Journal article | 2006 | BMC Genomics

Signal regulatory protein molecules are differentially expressed by CD8(-) dendritic cells

Mireille H Lahoud, Anna I Proietto, Kate H Gartlan, Susie Kitsoulis, Joan Curtis, James Wettenhall, Mariam Sofi, Carmel Daunt, Meredith O'Keeffe, Irina Caminschi, Keith Satterley, Alexandra Rizzitelli, Petra Schnorrer, Atsushi Hinohara, Yasunori Yamaguchi, Li Wu, Gordon Smyth, Emanuela Handman, Ken Shortman, Mark D Wright

Journal article | 2006 | The Journal of Immunology

Empirical array quality weights in the analysis of microarray data

Matthew E Ritchie, Dileepa Diyagama, Jody Neilson, Ryan van Laar, Alexander Dobrovic, Andrew Holloway, Gordon K Smyth

Journal article | 2006 | BMC BIOINFORMATICS

affylmGUI: a graphical user interface for linear modeling of single channel microarray data

JM Wettenhall, KM Simpson, K Satterley, GK Smyth

Journal article | 2006 | Bioinformatics

Expression profiling in primates reveals a rapid evolution of human transcription factors

Y Gilad, A Oshlack, GK Smyth, TP Speed, KP White

Journal article | 2006 | Nature

Generation of a functional mammary gland from a single stem cell

M Shackleton, F Vaillant, KJ Simpson, J Stingl, GK Smyth, ML Asselin-Labat, L Wu, GJ Lindeman, JE Visvader

Journal article | 2006 | Nature

Defining the molecular signature of peripheral CD8( ) T cell tolerance

IA Parish, GK Smyth, S Rao, WR Heath

Conference Proceedings | 2005 | TISSUE ANTIGENS

Series evaluation of Tweedie exponential dispersion model densities

PK Dunn, KS Gordon

Journal article | 2005 | Statistics and Computing

Differentially expressed genes in cardiac tissue from the hypertrophic heart rat

JP Dwyer, ME Ritchie, GK Smyth, LM Delbridge, AA Domenighetti, SB Harrap, R Di Nicolantonio

Conference Proceedings | 2005 | CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY

A systematic approach for comprehensive T-cell epitope discovery using peptide libraries

T Beissbarth, JA Tye-Din, GK Smyth, TP Speed, RP Anderson

Journal article | 2005 | Bioinformatics

Use of within-array replicate spots for assessing differential expression in microarray experiments

GK Smyth, J Michaud, HS Scott

Journal article | 2005 | Bioinformatics

Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors

MJ Peart, GK Smyth, RK van Laar, DD Bowtell, VM Richon, PA Marks, AJ Holloway, RW Johnstone

Journal article | 2005 | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single mammary stem cell can reconstitute a functional mammary gland

M Shackleton, F Vaillant, KJ Simpson, J Singl, GK Smyth, L Wu, JE Visvader, GJ Lindeman

Conference Proceedings | 2005 | BREAST CANCER RESEARCH AND TREATMENT

Water quality condition and trend in North Queensland waterways

ME Cox, A Moss, GK Smyth

Conference Proceedings | 2005 | Marine Pollution Bulletin

limmaGUI: A graphical user interface for linear modeling of microarray data

JM Wettenhall, GK Smyth

Journal article | 2004 | Bioinformatics

A comparative analysis of transcribed genes in the mouse hypothalamus and neocortex reveals chromosomal clustering

WM Boon, T Beissbarth, L Hyde, G Smyth, J Gunnersen, DA Denton, H Scott, SS Tan

Journal article | 2004 | Proceedings of the National Academy of Sciences of the United States of America

Semi-parametric extended Poisson process models for count data

HM Podlich, MJ Faddy, GK Smyth

Journal article | 2004 | Statistics and Computing

Statistical modeling of sequencing errors in SAGE libraries

Tim Beissbarth, Lavinia Hyde, Gordon K Smyth, Chris Job, Wee-Ming Boon, Seong-Seng Tan, Hamish S Scott, Terence P Speed

Journal article | 2004 | Bioinformatics

Gene expression profiling reveals distinct sets of genes altered during hormonally and metabolically induced cardiac hypertrophies

AA Domenighetti, M Ritchie, G Smyth, T Pedrazzini, J Proietto, LMD Delbridge

Conference Proceedings | 2004 | JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Dissociation of disease susceptibility, inflammation and cytokine profile in lmr1/2 congenic mice infected with Leishmania major

C Elso, B Kumar, G Smyth, S Foote, E Handman

Journal article | 2004 | Genes & Immunity

Leishmaniasis host response loci (lmr1-3) modify disease severity through a Th1/Th2-independent pathway

CM Elso, LJ Roberts, GK Smyth, RJ Thomson, TM Baldwin, SJ Foote, E Handman

Journal article | 2004 | Genes & Immunity

Bioconductor: open software development for computational biology and bioinformatics

RC Gentleman, VJ Carey, DM Bates, B Bolstad, M Dettling, S Dudoit, B Ellis, L Gautier, YC Ge, J Gentry, K Hornik, T Hothorn, W Huber, S Iacus, R Irizarry, F Leisch, C Li, M Maechler, AJ Rossini, G Sawitzki, et al.

Journal article | 2004 | Genome Biology

Linear models and empirical bayes methods for assessing differential expression in microarray experiments.

Gordon K Smyth

Journal article | 2004 | Statistical Applications in Genetics and Molecular Biology

The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2..

Normalization of cDNA microarray data

GK Smyth, T Speed

Journal article | 2003 | Methods

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.

Deirdre Toomey, Gordon Smyth, Claire Condron, James Kelly, Ann-Marie Byrne, Elaine Kay, Ronan M Conroy, Patrick Broe, David Bouchier-Hayes

Journal article | 2003 | International Journal of Cancer

Non-small cell lung cancer (NSCLC) remains a difficult disease to treat and independent prognostic markers other than tumour stage..

An efficient algorithm for REML in heteroscedastic regression

GK Smyth

Journal article | 2002 | Journal of Computational and Graphical Statistics

A general approach to modeling and analysis of species abundance data with extra zeros

HM Podlich, MJ Faddy, GK Smyth

Journal article | 2002 | Journal of Agricultural, Biological, and Environmental Statistics

Fitting Tweedie's Compound Poisson Model to Insurance Claims Data: Dispersion Modelling

GK Smyth, B Jørgensen

Journal article | 2002 | ASTIN Bulletin

AbstractWe reconsider the problem of producing fair and accurate tariffs based on aggregated insurance data giving numbers of clai..

An improved saddlepoint approximation based on the negative binomial distribution for the general birth process

GK Smyth, HM Podlich

Journal article | 2002 | Computational Statistics

Thymidine phosphorylase activity in nonsmall cell lung carcinoma tissues.

T Yano, S Takeo

Journal article | 2001 | Cancer

BACKGROUND: This is the first study on the quantitative assessment of thymidine phosphorylase (TP) activity in patients with nonsm..

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.

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

Journal article | 2001 | Cancer

BACKGROUND: Lung carcinoma usually is advanced at the time of presentation and frequently shows metastatic spread. In recent times..

Exact and approximate REML for heteroscedastic regression

Gordon K Smyth, A Frederik Huele, Arunas P Verbyla

Journal article | 2001 | Statistical Modelling: An International Journal

Employing symmetry constraints for improved frequency estimation by eigenanalysis methods

GK Smyth

Journal article | 2000 | Technometrics

Robust frequency estimation using elemental sets

GK Smyth, DM Hawkins

Journal article | 2000 | Journal of Computational and Graphical Statistics

Employing symmetry constraints for improved frequency estimation by eigenanalysis methods

GK Smyth

Journal article | 2000 | Technometrics

Robust Frequency Estimation Using Elemental Sets

GK Smyth, DM Hawkins

Journal article | 2000 | Journal of Computational and Graphical Statistics

Adjusted likelihood methods for modelling dispersion in generalized linear models

GK Smyth, AP Verbyla

Journal article | 1999 | Environmetrics

Optimized selection of river sampling sites

W Dixon, GK Smyth, B Chiswell

Journal article | 1999 | Water Research

Partitioned algorithms for maximum likelihood and other non-linear estimation

GK Smyth

Journal article | 1996 | Statistics and Computing

A conditional likelihood approach to residual maximum likelihood estimation in generalized linear models

GK Smyth, AP Verbyla

Journal article | 1996 | JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-METHODOLOGICAL

Randomized Quantile Residuals

PK Dunn, GK Smyth

Journal article | 1996 | Journal of Computational and Graphical Statistics

A STOCHASTIC-MODEL INCORPORATING THE EFFECT OF WEATHER CONDITIONS ON ANTHRACNOSE DEVELOPMENT IN STYLOSANTHES SCABRA

S CHAKRABORTY, GK SMYTH

Journal article | 1995 | Journal of Phytopathology

A MODIFIED PRONY ALGORITHM FOR EXPONENTIAL FUNCTION FITTING

MR OSBORNE, GK SMYTH

Journal article | 1995 | SIAM Journal on Scientific Computing

A NOTE ON MODELING CROSS-CORRELATIONS - HYPERBOLIC SECANT REGRESSION

GK SMYTH

Journal article | 1994 | Biometrika

A MODIFIED PRONY ALGORITHM FOR ESTIMATING SINUSOIDAL FREQUENCIES

MS MACKISACK, MR OSBORNE, GK SMYTH

Journal article | 1994 | Journal of Statistical Computation and Simulation

REML IN GENERALIZED LINEAR MODELS - A CONDITIONAL APPROACH

GK SMYTH

Conference Proceedings | 1994 | COMPUTING SCIENCE AND STATISTICS, VOL 26

ACUITY THROUGH DISCOLORED LENSES

MS MACKISACK, GK SMYTH

Journal article | 1993 | Optometry and Vision Science

A STOCHASTIC-MODEL FOR ANTHRACNOSE DEVELOPMENT IN STYLOSANTHES-SCABRA

GK SMYTH, S CHAKRABORTY, RG CLARK, AN PETTITT

Journal article | 1992 | Phytopathology

ACCURACY OF THE END-POINT ASSAY FOR VIRUS TITRATION

LK NIELSEN, GK SMYTH, PF GREENFIELD

Journal article | 1992 | Cytotechnology

On the consistency of prony’s method and related algorithms

MH Kahn, MS Mackisack, MR Osborne, GK Smyth

Journal article | 1992 | Journal of Computational and Graphical Statistics

HEMACYTOMETER CELL COUNT DISTRIBUTIONS - IMPLICATIONS OF NON-POISSON BEHAVIOR

LK NIELSEN, GK SMYTH, PF GREENFIELD

Journal article | 1991 | Biotechnology Progress

A MODIFIED PRONY ALGORITHM FOR FITTING FUNCTIONS DEFINED BY DIFFERENCE-EQUATIONS

MR OSBORNE, GK SMYTH

Journal article | 1991 | SIAM Journal on Scientific and Statistical Computing

EXPONENTIAL DISPERSION MODELS AND THE GAUSS‐NEWTON ALGORITHM

GK Smyth

Journal article | 1991 | Australian Journal of Statistics

USING THE EM ALGORITHM TO PREDICT 1ST YEAR UNIVERSITY PERFORMANCE

GK SMYTH, MW KNUIMAN, ML THORNETT, H KIIVERI

Journal article | 1990 | Australian Journal of Education

GENERALIZED LINEAR-MODELS WITH VARYING DISPERSION

GK SMYTH

Journal article | 1989 | JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-METHODOLOGICAL

When random assignment fails: Some lessons from the Minneapolis Spouse Abuse Experiment

RA Berk, GK Smyth, LW Sherman

Journal article | 1988 | Journal of Quantitative Criminology

ON USING THE LOG-HYPERBOLIC DISTRIBUTION TO DESCRIBE THE TEXTURAL CHARACTERISTICS OF EOLIAN SEDIMENTS - REPLY

KH WYRWOLL, G SMYTH

Journal article | 1988 | JOURNAL OF SEDIMENTARY PETROLOGY

DIFFERENCE THRESHOLDS FOR ODOR DETECTION BY AN AQUATIC ANIMAL

RK ZIMMERFAUST, G SMYTH

Conference Proceedings | 1987 | CHEMICAL SENSES

METABOLIC STABILITY OF PHYTOPHTHORA-CINNAMOMI RANDS IN WESTERN AUSTRALIA

RM HART, D KEAST, G SMYTHE

Journal article | 1986 | Canadian Journal of Microbiology

ON USING THE LOG-HYPERBOLIC DISTRIBUTION TO DESCRIBE THE TEXTURAL CHARACTERISTICS OF EOLIAN SEDIMENTS

KH WYRWOLL, GK SMYTH

Journal article | 1985 | Journal of Sedimentary Petrology

277

Scholarly Works

Keyword Analysis

Clinical Health (organs, Diseases and Abnormal Conditions)

Expanding Knowledge

Oncology and Carcinogenesis

Genetics

Immunology

Biochemistry and Cell Biology

Clinical Sciences

Cardiovascular Medicine and Haematology

Clinical (organs, Diseases and Abnormal Conditions)

Neurosciences

Honours, Awards and Fellowships

2018

Clarivate Highly Cited Researcher

2019

NHMRCF - NHMRC Fellowship

2

Awards

Credentials

Positions

Visitor

Mathematics And Statistics

Honorary

Mathematics And Statistics

Education

PhD (Statistics) ANU

Australian National University

BSc Hon I (Mathematics) UWA

The University of Western Australia

Dr

Gordon Smyth

Dr

Gordon Smyth

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Statistics

Dr

Gordon Smyth

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Gordon Smyth's highlights

FEATURED Journal article

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Gordon Smyth's selected work

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Scholarly Works

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data

Increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary mineralization and brittle bone

MOZ directs the distal-less homeobox gene expression program during craniofacial development

The Selective Expansion and Targeted Accumulation of Bone Marrow-Derived Macrophages Drive Cardiac Vasculitis

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

PHF6 regulates hematopoietic stem and progenitor cells and its loss synergizes with expression of TLX3 to cause leukemia

Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

Loss of p53 Causes Stochastic Aberrant X-Chromosome Inactivation and Female-Specific Neural Tube Defects

A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2-Positive Metastatic Breast Cancer

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Dysregulated IL-1-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine

Foxp1 Is Indispensable for Ductal Morphogenesis and Controls the Exit of Mammary Stem Cells from Quiescence

Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness

Transcription-factor-mediated supervision of global genome architecture maintains B cell identity

Mutant TRP53 exerts a target gene-selective dominant-negative effect to drive tumor development

Bone strength and mineralization are regulated independently of bone mass by ephrinB2-dependent autophagic processes in osteocytes

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth

Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

Loss of NF-kappa B1 Causes Gastric Cancer with Aberrant Inflammation and Expression of Immune Checkpoint Regulators in a STAT-1-Dependent Manner

Identifying low-grade cellular rejection after heart transplantation in children by using gene expression profiling

A critical epithelial survival axis regulated by MCL-1 maintains thymic function in mice

Interferon-gamma released from omental adipose tissue of insulin-resistant humans alters adipocyte phenotype and impairs response to insulin and adiponectin release

Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

Genome-wide functional analysis reveals central signaling regulators of lymphatic endothelial cell migration and remodeling

An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles

The TNF Receptor Superfamily-NF-kappa B Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues

SIDT2 Transports Extracellular dsRNA into the Cytoplasm for Innate Immune Recognition

Synergistic action of the MCL-1 inhibitor S63845 with current therapies in preclinical models of triple-negative and HER2-amplified breast cancer

Correction: TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1.

c-Myb Regulates the T-Bet-Dependent Differentiation Program in B Cells to Coordinate Antibody Responses

A non-canonical function of Ezh2 preserves immune homeostasis

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

Conserved IKAROS-regulated genes associated with B-progenitor acute lymphoblastic leukemia outcome

Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive

RANK ligand as a target for breast cancer prevention in BRCA1 mutation carriers

Effector Regulatory T Cell Differentiation and Immune Homeostasis Depend on the Transcription Factor Myb

Infection Programs Sustained Lymphoid Stromal Cell Responses and Shapes Lymph Node Remodeling upon Secondary Challenge

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.

Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway

Linear ubiquitin chain assembly complex coordinates late thymic T-cell differentiation and regulatory T-cell homeostasis

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

Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity

Haemopedia: An Expression Atlas of Murine Hematopoietic Cells

Clinical pathways and patient characteristics five years after the establishment of the rapid access prostate clinics at Beaumont Hospital

The changing microbiological trends in TRUS sepsis following the implementation of a prospective surveillance programme

RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers

Evidence for a key role for neutrophils in rheumatoid arthritis

statmod: Probability Calculations for the Inverse Gaussian Distribution