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Lista de obras de 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

artículo científico publicado en 2018

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

artículo científico

A comparison of background correction methods for two-colour microarrays

artículo científico publicado en 2007

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

artículo científico

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

artículo científico publicado en 2021

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

artículo científico publicado en 2005

ACUITY THROUGH DISCOLORED LENSES

artículo científico publicado en 1993

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

artículo científico publicado en 2009

Accuracy of the endpoint assay for virus titration

artículo científico publicado en 1992

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2011

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

artículo científico publicado en 2009

Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart

artículo científico publicado en 2011

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

artículo científico publicado en 2010

An Efficient Algorithm for REML in Heteroscedastic Regression

article

An Erg-driven transcriptional program controls B cell lymphopoiesis

artículo científico publicado en 2020

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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

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

artículo científico publicado en 2020

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

artículo científico publicado en 2019

Bioconductor: open software development for computational biology and bioinformatics

artículo científico publicado en 2004

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

artículo científico publicado en 2016

Blimp1 is limiting for transformation in a mouse plasmacytoma model

artículo científico publicado en 2009

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

artículo científico publicado en 2012

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2010

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

artículo científico publicado en 2009

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2009

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2011

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.

artículo científico

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

artículo científico publicado en 2020

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

artículo científico publicado en 2009

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

artículo científico publicado en 2015

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

Empirical array quality weights in the analysis of microarray data

artículo científico publicado en 2006

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

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2011

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

artículo científico publicado en 2006

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

artículo científico publicado en 2011

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2007

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

artículo científico publicado en 2014

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

artículo científico publicado en 2011

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

artículo científico publicado en 2006

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

artículo científico

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

artículo científico publicado en 2010

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

artículo científico publicado en 2010

Gene regulation in primates evolves under tissue-specific selection pressures

artículo científico publicado en 2008

Generation of a functional mammary gland from a single stem cell

artículo científico publicado en 2006

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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2008

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

artículo científico publicado en 2011

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

artículo científico publicado en 2005

Identification of Pax5 target genes in early B cell differentiation

artículo científico publicado en 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.

artículo científico publicado en 2017

Identifying Associations Between Genomic Alterations in Tumors

artículo científico publicado en 2013

Illumina WG-6 BeadChip strips should be normalized separately

artículo científico publicado en 2009

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

artículo científico publicado en 2019

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

artículo científico publicado en 2017

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

artículo científico publicado en 2018

Integrative analysis of RUNX1 downstream pathways and target genes

artículo científico publicado en 2008

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

artículo científico publicado en 2017

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

artículo científico

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

artículo científico publicado en 2004

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2019

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

Moderated statistical tests for assessing differences in tag abundance

artículo científico publicado en 2007

Molecular dissection of the pea shoot apical meristem

artículo científico publicado en 2009

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2007

Normalization of cDNA microarray data ⬇️

artículo científico publicado el 1 de diciembre de 2003

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

artículo científico publicado en 2010

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

artículo científico publicado en 2010

Orchestrating high-throughput genomic analysis with Bioconductor

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2014

Peripheral natural killer cell maturation depends on the transcription factor Aiolos

artículo científico publicado en 2014

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

artículo científico publicado el 31 de octubre de 2010

Platelets kill intraerythrocytic malarial parasites and mediate survival to infection

artículo científico publicado en 2009

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

artículo científico publicado en 2008

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

artículo científico publicado en 2021

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

artículo científico publicado en 2010

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

artículo científico publicado en 2006

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

artículo científico publicado en 2019

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

artículo científico publicado en 2009

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

artículo científico

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.

artículo científico publicado en 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.

artículo científico publicado en 2016

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

artículo científico publicado en 2016

ROAST: rotation gene set tests for complex microarray experiments

artículo científico publicado en 2010

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

artículo científico publicado en 2016

Regulation of hematopoietic stem cells by their mature progeny

artículo científico publicado en 2010

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

artículo científico publicado en 2009

Semi-parametric extended Poisson process models for count data

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

artículo científico publicado en 2011

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

artículo científico publicado en 2006

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

artículo científico publicado en 2007

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

artículo científico publicado en 2010

Statistical Issues in cDNA Microarray Data Analysis

artículo científico publicado el 1 de enero de 2003

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

artículo científico publicado en 2006

Statistical modeling of sequencing errors in SAGE libraries

artículo científico publicado en 2004

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

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

artículo científico publicado en 2020

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

artículo científico publicado en 2011

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

artículo científico publicado en 2009

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

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

artículo científico publicado el 4 de abril de 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 2021

The molecular signature of CD8+ T cells undergoing deletional tolerance

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2005

Using DNA microarrays to study gene expression in closely related species

artículo científico publicado en 2007

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

artículo científico publicado en 2006

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

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

artículo científico publicado en 2004

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

artículo científico publicado en 2019

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

artículo científico publicado en 2014

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