[HTML][HTML] limma powers differential expression analyses for RNA-sequencing and microarray studies
Abstract limma is an R/Bioconductor software package that provides an integrated solution
for analysing data from gene expression experiments. It contains rich features for handling …
for analysing data from gene expression experiments. It contains rich features for handling …
Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate
Abstract The oncometabolite (R)-2-hydroxyglutarate (R-2-HG) produced by isocitrate
dehydrogenase (IDH) mutations promotes gliomagenesis via DNA and histone methylation …
dehydrogenase (IDH) mutations promotes gliomagenesis via DNA and histone methylation …
Integrative approaches for large-scale transcriptome-wide association studies
Many genetic variants influence complex traits by modulating gene expression, thus altering
the abundance of one or multiple proteins. Here we introduce a powerful strategy that …
the abundance of one or multiple proteins. Here we introduce a powerful strategy that …
[HTML][HTML] Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression
One of the most common analysis tasks in genomic research is to identify genes that are
differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) …
differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) …
The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia
TJ Schuijt, JM Lankelma, BP Scicluna, FS e Melo… - Gut, 2016 - gut.bmj.com
Objective Pneumonia accounts for more deaths than any other infectious disease
worldwide. The intestinal microbiota supports local mucosal immunity and is increasingly …
worldwide. The intestinal microbiota supports local mucosal immunity and is increasingly …
Apoptotic caspases suppress mtDNA-induced STING-mediated type I IFN production
MJ White, K McArthur, D Metcalf, RM Lane, JC Cambier… - Cell, 2014 - cell.com
Activated caspases are a hallmark of apoptosis induced by the intrinsic pathway, but they
are dispensable for cell death and the apoptotic clearance of cells in vivo. This has led to the …
are dispensable for cell death and the apoptotic clearance of cells in vivo. This has led to the …
Gene expression elucidates functional impact of polygenic risk for schizophrenia
Over 100 genetic loci harbor schizophrenia-associated variants, yet how these variants
confer liability is uncertain. The CommonMind Consortium sequenced RNA from …
confer liability is uncertain. The CommonMind Consortium sequenced RNA from …
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
Read alignment is an ongoing challenge for the analysis of data from sequencing
technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and …
technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and …
Camera: a competitive gene set test accounting for inter-gene correlation
Competitive gene set tests are commonly used in molecular pathway analysis to test for
enrichment of a particular gene annotation category amongst the differential expression …
enrichment of a particular gene annotation category amongst the differential expression …
Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection
C Goujon, O Moncorgé, H Bauby, T Doyle, CC Ward… - Nature, 2013 - nature.com
Animal cells harbour multiple innate effector mechanisms that inhibit virus replication. For
the pathogenic retrovirus human immunodeficiency virus type 1 (HIV-1), these include …
the pathogenic retrovirus human immunodeficiency virus type 1 (HIV-1), these include …