Genome-wide analysis of gene expression articles from across Nature Portfolio

Ribosome profiling faces issues with rRNA contamination and measurements of ribosome numbers on transcripts. Here, the authors develop Ribo-FilterOut and Ribo-Calibration, methods which can be used to estimate kinetic and stoichiometric parameters of translation under various conditions.

Single-cell RNA sequencing (scRNA-seq) is widely used to characterize cell types based on their average gene expression profiles, however most studies do not consider cell type-specific variation across individuals. Here the authors introduce a model to study cell type-specificity of inter-individual variation in scRNA-seq data and show that it can identify biologically meaningful signals missed by conventional differential expression tests.

Time-course swRNA-seq in C. elegans reveals a three-stage process in wound repair potentially controlled by a complex gene regulatory network containing autoregulatory loops and more than 200 TFs, such as crucial factors nhr-76 and daf-16.

Nascent transcription in genes and enhancers genome-wide at the single-cell level is quantified using global run-on and sequencing (GRO–seq) with click chemistry.

The cereal endosperm constitutes most of the grain by volume. Here the authors use single-cell analysis of maize developing endosperm to decode gene regulatory networks that likely control endosperm growth and offer a framework for crop improvement.

Here we report Droplet Paired-Tag, a rapid and robust method to simultaneously profile histone modifications and gene expression in single cells at scale. The new procedure provides researchers with a tool for studying the epigenome and gene regulation in complex tissues and disease pathogenesis.

Spatially resolved and single-cell transcriptomics provide insights into tumor heterogeneity and tumor–microbiome interactions.

Barkley and colleagues conducted single-cell RNA sequencing of almost 20,000 malignant cells and identified cancer cell states that are both common and different across tumour types, and revealed how these states interact with the tumour microenvironment.