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 …

Abstract The oncometabolite (R)-2-hydroxyglutarate (R-2-HG) produced by isocitrate
dehydrogenase (IDH) mutations promotes gliomagenesis via DNA and histone methylation …

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 …

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) …

Objective Pneumonia accounts for more deaths than any other infectious disease
worldwide. The intestinal microbiota supports local mucosal immunity and is increasingly …

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 …

Over 100 genetic loci harbor schizophrenia-associated variants, yet how these variants
confer liability is uncertain. The CommonMind Consortium sequenced RNA from …

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 …

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 …

Animal cells harbour multiple innate effector mechanisms that inhibit virus replication. For
the pathogenic retrovirus human immunodeficiency virus type 1 (HIV-1), these include …