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List of works by Gordon K Smyth

A Note on Modelling Cross-Correlations: Hyperbolic Secant Regression

scholarly article by Gordon K Smyth published June 1994 in Biometrika

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

scientific article published on 05 December 2018

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

scholarly article

A comparison of background correction methods for two-colour microarrays

scientific article

A guide to creating design matrices for gene expression experiments

publication published on 10 December 2020

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

scientific article published on 25 July 2014

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

scientific article published on 7 March 2016

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

scientific article published on 4 November 2010

A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

scientific article published on 05 May 2021

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

scientific article published in June 2005

ACUITY THROUGH DISCOLORED LENSES

scientific article published on 01 August 1993

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

scientific article published on 2 August 2009

Accuracy of the endpoint assay for virus titration

scientific article published in January 1992

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

scientific article published on 6 February 2015

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

scientific article

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

scientific article published on 19 April 2011

Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype

scientific article

Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart

scientific article published in September 2011

Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer

scientific article

An Efficient Algorithm for REML in Heteroscedastic Regression

article

An Erg-driven transcriptional program controls B cell lymphopoiesis

scientific article published on 15 June 2020

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

scientific article published on 18 November 2015

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

scientific article

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

scientific article

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

scientific article

Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis

scientific article published on 14 January 2020

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

scientific article published on 04 November 2019

Author Correction: The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity

scientific article published on 01 March 2020

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

scientific article published in Nature Communications

Bioconductor: open software development for computational biology and bioinformatics

scientific article

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

scientific article published on 18 January 2016

Blimp1 is limiting for transformation in a mouse plasmacytoma model

scientific article published on 27 March 2009

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

scientific article

Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands

scientific article

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

scientific article

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

scientific article published on 11 February 2017

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

scientific article published on 20 November 2017

Copy number analysis identifies novel interactions between genomic loci in ovarian cancer

scientific article

Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures.

scientific article published on 5 March 2009

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

scientific article published on 27 June 2017

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

2013 scientific article

DNMT3L is a regulator of X chromosome compaction and post-meiotic gene transcription

scientific article

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

scientific article

Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland

scientific article

Deregulation of MYCN, LIN28B and LET7 in a molecular subtype of aggressive high-grade serous ovarian cancers

scientific article

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

scientific article

Detection of gene expression in an individual cell type within a cell mixture using microarray analysis

scientific article

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

scholarly article published 22 September 2011

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

scientific article

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

scientific article published on 28 November 2017

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

scientific article

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

article

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

scientific article published on 02 June 2015

Dual targeting of CDK4/6 and BCL2 pathways augments tumor response in estrogen receptor positive breast cancer

scientific article published on 03 April 2020

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

scientific article published on 28 June 2009

Early lineage priming by trisomy of Erg leads to myeloproliferation in a Down syndrome model

scientific article published on 14 May 2015

Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria

scientific article published in May 2012

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

scientific article

Empirical array quality weights in the analysis of microarray data

scientific article

Employing Symmetry Constraints for Improved Frequency Estimation by Eigenanalysis Methods

scholarly article by Gordon K Smyth published August 2000 in Technometrics

Epigenetic regulator Smchd1 functions as a tumor suppressor

scientific article published on 26 December 2012

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

scientific article published on 14 June 2011

Erratum: Corrigendum: The transcription factor IRF4 is essential for TCR affinity–mediated metabolic programming and clonal expansion of T cells

scholarly article published in Nature Immunology

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

article

Estimating the proportion of microarray probes expressed in an RNA sample

scientific article

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

scientific article published in May 2011

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

scientific article

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

scientific article

Fine mapping of Leishmania major susceptibility Locus lmr2 and evidence of a role for Fli1 in disease and wound healing

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Gata-3 negatively regulates the tumor-initiating capacity of mammary luminal progenitor cells and targets the putative tumor suppressor caspase-14.

scientific article published on 19 September 2011

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

scientific article

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

scientific article published on May 2007

Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of Down syndrome

scientific article

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

scientific article

Gene regulation in primates evolves under tissue-specific selection pressures

scientific article

Generation of a functional mammary gland from a single stem cell

scientific article (publication date: 5 January 2006)

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

scientific article

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

scientific article published on 3 October 2017

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

scientific article published on 06 November 2018

Haemopedia: An Expression Atlas of Murine Hematopoietic Cells

scientific article published on 3 August 2016

Hemacytometer Cell Count Distributions: Implications of Non-Poisson Behavior

article

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

scientific article

Id2 expression delineates differential checkpoints in the genetic program of CD8α+ and CD103+ dendritic cell lineages

scientific article

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

scientific article

Identification of Pax5 target genes in early B cell differentiation

scientific article published in February 2008

Identification of diploid platelet-forming cells prior to the emergence of polyploidy megakaryocyte in the mouse embryo

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

scientific article

Identifying Associations Between Genomic Alterations in Tumors

scientific article published on 01 January 2013

Illumina WG-6 BeadChip strips should be normalized separately

scientific article

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

scientific article published on 31 July 2019

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

scientific article published on January 2017

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

scientific article published in Nature

Integrative analysis of RUNX1 downstream pathways and target genes

scientific article

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

scientific article published on 3 August 2017

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

scientific article published on January 2016

LEVERAGE ADJUSTMENTS FOR DISPERSION MODELLING IN GENERALIZED NONLINEAR MODELS

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

article

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

scientific article (publication date: 2004)

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

scientific article published on 18 November 2016

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

scientific article (publication date: 2017)

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

scientific article published on 14 April 2015

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

scientific article published on 24 July 2019

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

scientific article published on 20 January 2015

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

scientific article

Moderated statistical tests for assessing differences in tag abundance

scientific article

Molecular dissection of the pea shoot apical meristem

scientific article

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

scientific article

Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria

scientific article published on 01 April 2022

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

scientific article published on 18 August 2016

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

scientific article published on 23 October 2009

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

scientific article published on 26 October 2018

Myocardial Gene Expression Associated with Genetic Cardiac Hypertrophy in the Absence of Hypertension

article

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

scientific article

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

scientific article

Nonequivalent gene expression and copy number alterations in high-grade serous ovarian cancers with BRCA1 and BRCA2 mutations

scientific article published on 30 April 2013

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

scientific article published on January 2007

Normalization of cDNA microarray data ⬇️

scientific article (publication date: December 2003)

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

scientific article published on 5 May 2010

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

scientific article

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

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

scientific article published on 12 February 2019

Partitioned algorithms for maximum likelihood and other non-linear estimation

scholarly article by Gordon K Smyth published September 1996 in Statistics and Computing

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

scientific article

Peripheral natural killer cell maturation depends on the transcription factor Aiolos

scientific article

Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn ⬇️

scientific article published on October 31, 2010

Platelets kill intraerythrocytic malarial parasites and mediate survival to infection

scientific article published in February 2009

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

scientific article

Pre-mitotic genome re-organisation bookends the B cell differentiation process

scientific article published on 26 February 2021

Pro-inflammatory CD11c+CD206+ adipose tissue macrophages are associated with insulin resistance in human obesity ⬇️

scientific article

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

scientific journal article

Proximal genomic localization of STAT1 binding and regulated transcriptional activity

scientific article published on 11 October 2006

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

scientific article published on 24 April 2019

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

scientific article published on 16 January 2009

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

scientific article published on 06 January 2014

R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue

publication published on 23 March 2022

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

scientific article published on 20 June 2016

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

scientific article published in 2016

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

scientific article published on 17 June 2016

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

scientific article

ROAST: rotation gene set tests for complex microarray experiments

scientific article

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

scientific article published on June 2016

Regulation of hematopoietic stem cells by their mature progeny

scientific article

Robust Frequency Estimation Using Elemental Sets

SAGE analysis of genes differentially expressed in presymptomatic TgSOD1G93A transgenic mice identified cellular processes involved in early stage of ALS pathology

scientific article

Semi-parametric extended Poisson process models for count data

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

scientific article published on 18 July 2011

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

scientific article published in July 2006

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

scientific article

Spatiotemporal regulation of multiple overlapping sense and novel natural antisense transcripts at the Nrgn and Camk2n1 gene loci during mouse cerebral corticogenesis.

scientific article published on 6 August 2010

Statistical Issues in cDNA Microarray Data Analysis

scientific article published on January 1, 2003

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

scientific article

Statistical modeling of sequencing errors in SAGE libraries

scientific article

Susceptibility to acute rheumatic fever based on differential expression of genes involved in cytotoxicity, chemotaxis, and apoptosis

scientific article

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

scientific article published in August 2017

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

scientific article published on 23 December 2015

Targeting antigen to mouse dendritic cells via Clec9A induces potent CD4 T cell responses biased toward a follicular helper phenotype

scientific article published on 15 June 2011

Targeting triple-negative breast cancers with the Smac-mimetic birinapant

scientific article published on 27 April 2020

Technical variability is greater than biological variability in a microarray experiment but both are outweighed by changes induced by stimulation

scientific article

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

scientific article

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

scientific article

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

article by Yang Liao et al published 20 February 2019 in Nucleic Acids Research

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

scientific article published on 19 April 2019

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

scientific article published on April 4, 2013

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

scientific article published on 4 September 2017

The concerted change in the distribution of cell cycle phases and zone composition in germinal centers is regulated by IL-21

scientific article published on 09 December 2021

The molecular signature of CD8+ T cells undergoing deletional tolerance

scientific article published on 09 February 2009

The molecular signature of tissue resident memory CD8 T cells isolated from the brain

scientific article published on 24 August 2012

The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity

scientific article published on 23 December 2019

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

scientific article published on 22 September 2013

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

scientific article

Tissue-resident ductal macrophages survey the mammary epithelium and facilitate tissue remodelling

scientific article published on 27 April 2020

Transcription factor IRF4 regulates germinal center cell formation through a B cell-intrinsic mechanism

scientific article published on 3 March 2014

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

article by Timothy M Johanson et al published 15 October 2018 in Nature Immunology

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

scientific article

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

scientific article

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

scholarly article published on 26 March 2013

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

scientific article published on 18 January 2005

Using DNA microarrays to study gene expression in closely related species

scientific article published on 23 March 2007

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

scientific article published on 2 February 2006

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

scientific article published on April 2017

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

scientific article

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

scientific article published on 19 August 2015

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

scientific article (publication date: 2010)

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

scientific article

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

scientific article (publication date: 20 April 2015)

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

scientific article published on 5 August 2004

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

scientific article published on 18 December 2019

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

scientific article

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