Genome assembly projects get a boost from high-accuracy long-read sequencing.

This Review describes proximity labeling methods that make use of peroxidases (APEX) or biotin ligases (TurboID, BioID), and their applications to studying protein–protein and protein–nucleic acid interactions in living systems.

The Perspective reviews the computational methods for subclonal reconstruction and recommends best practices for analyses and quality assessments.

Commonly used organic dyes can photoconvert to blue-shifted fluorescent species, especially under intense illumination. The mechanism of this process and how to avoid unwanted artifacts in super-resolution microscopy are explored here.

G-GESS is a serotonin biosensor, derived from a tick serotonin-binding protein. The biosensor has been applied here in cell culture, primary neurons, mouse brain slices and in vivo in the mouse brain.

The DRACO algorithm deconvolutes coexisting RNA structures from mutational profiling experiments, and can be applied to bacterial regulatory structures and elements from the SARS-CoV-2 genome.

This Perspective describes technological advances for imaging-based screening of diverse cellular phenotypes.

Nuc-MS makes use of top–down mass spectrometry in ‘native’ mode to quantitatively interrogate histone proteoforms and their post-translational modifications in a single experiment.

Paired-Tag offers a multiomics assay for joint profiling of histone modifications and gene expression in single nuclei, and is applied to mouse frontal cortex and hippocampus for measuring cell-type-resolved chromatin state and transcriptome.

Beyond the well-known pantheon of model organisms are others. A shift is underway to level the playing field.

Global protein structure readouts help detect protein functional changes.

DeepLabCut-Live! performs pose estimation in real time and allows closed-loop feedback on behavior.

Loop-seq is a high-throughput sequencing assay that measures DNA looping and can help explain how DNA bendability contributes to nucleosome organization.

DNA-PAINT with left-handed DNA oligomers enables imaging of nuclear structures with reduced background.

New year, big changes: Nature Methods now offers authors the ability to publish research papers on an open access basis, including via a Guided Open Access pilot. Here’s how it works.