RNA sequencing data: hitchhiker's guide to expression analysis
K Van den Berge, KM Hembach… - Annual Review of …, 2019 - annualreviews.org
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …
regulatory programs are observable. The measurement of transcriptome-wide gene …
High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …
SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas
Infection-related diabetes can arise as a result of virus-associated β-cell destruction. Clinical
data suggest that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) …
data suggest that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) …
eccDNAs are apoptotic products with high innate immunostimulatory activity
Extrachromosomal circular DNA elements (eccDNAs) have been described in the literature
for several decades, and are known for their broad existence across different species …
for several decades, and are known for their broad existence across different species …
Radiotherapy in combination with CD47 blockade elicits a macrophage-mediated abscopal effect
Radiation therapy is a mainstay of cancer treatment but does not always lead to complete
tumor regression. Here we combine radiotherapy with blockade of the 'don't-eat-me'cell …
tumor regression. Here we combine radiotherapy with blockade of the 'don't-eat-me'cell …
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
Motivation In RNA-seq differential expression analysis, investigators aim to detect those
genes with changes in expression level across conditions, despite technical and biological …
genes with changes in expression level across conditions, despite technical and biological …
Leveraging polygenic functional enrichment to improve GWAS power
Functional genomics data has the potential to increase GWAS power by identifying SNPs
that have a higher prior probability of association. Here, we introduce a method that …
that have a higher prior probability of association. Here, we introduce a method that …
Bias, robustness and scalability in single-cell differential expression analysis
C Soneson, MD Robinson - Nature methods, 2018 - nature.com
Many methods have been used to determine differential gene expression from single-cell
RNA (scRNA)-seq data. We evaluated 36 approaches using experimental and synthetic …
RNA (scRNA)-seq data. We evaluated 36 approaches using experimental and synthetic …
Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells
Exercise training is critical for the prevention and treatment of obesity, but its underlying
mechanisms remain incompletely understood given the challenge of profiling …
mechanisms remain incompletely understood given the challenge of profiling …
Histone H2AK119 mono-ubiquitination is essential for polycomb-mediated transcriptional repression
S Tamburri, E Lavarone, D Fernández-Pérez… - Molecular cell, 2020 - cell.com
Polycomb group proteins (PcGs) maintain transcriptional repression to preserve cellular
identity in two distinct repressive complexes, PRC1 and PRC2, that modify histones by …
identity in two distinct repressive complexes, PRC1 and PRC2, that modify histones by …