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Nature Methods is a science methodology journal publishing laboratory techniques and methods papers in the life sciences and areas of chemistry relevant to the life sciences.

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Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX

Nature Methods, Published online: 26 May 2022; doi:10.1038/s41592-022-01538-8Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX

Best practice standards for circular RNA research

Nature Methods, Published online: 26 May 2022; doi:10.1038/s41592-022-01487-2This Perspective focuses on experimental techniques developed for circRNA studies, and provides practical guidelines for performing circRNA research.

Polishing high-quality genome assemblies

Nature Methods, Published online: 24 May 2022; doi:10.1038/s41592-022-01515-1A repeat-aware pipeline corrects structural assembly errors and polishes assembly sequences in large repeats without overcorrection.

New near-infrared fluorescent probes and tools

Nature Methods, Published online: 23 May 2022; doi:10.1038/s41592-022-01425-2A novel bright near-infrared fluorescent protein inserted into a nanobody enables visualization of native proteins inside living cells and specific manipulation of cell function, including Boolean protein-based operators.

Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies

Nature Methods, Published online: 23 May 2022; doi:10.1038/s41592-022-01467-6miRFP670nano3 offers improved near-infrared imaging and was used to develop fluorescent nanobodies whose stability and fluorescence strongly depend on antigen binding, with broad implications for detecting and manipulating cellular targets.

Mapping beads on strings

Nature Methods, Published online: 20 May 2022; doi:10.1038/s41592-022-01519-xDiMeLo-seq leverages immunotethered DNA methyltransferases with long-read sequencing to map the locations of chromatin proteins in their natural context.

Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models

Nature Methods, Published online: 16 May 2022; doi:10.1038/s41592-022-01465-8A dynamic model of the 4Pi point spread function enables localization microscopy with exceptional three-dimensional resolution and a simpler optical design. 4Pi-STORM images of neurons and mitochondria reveal new details of nanoscale protein and nucleic acid organization.

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

Nature Methods, Published online: 16 May 2022; doi:10.1038/s41592-022-01480-9This work presents a comprehensive benchmarking analysis of computational methods that integrates spatial and single-cell transcriptomics data for transcript distribution prediction and cell type deconvolution.

Benchmarking spatial and single-cell transcriptomics integration methods

Nature Methods, Published online: 16 May 2022; doi:10.1038/s41592-022-01481-8Tangram, gimVI and SpaGE outperformed other integration methods for predicting the spatial distributions of RNA transcripts, while Cell2location, SpatialDWLS and RCTD were the top-performing methods for the cell type deconvolution of spots in histological sections.

3D reconstruction of spatial expression

Nature Methods, Published online: 16 May 2022; doi:10.1038/s41592-022-01476-5A novel approach to probabilistically align adjacent multiple tissue slices from spatially resolved transcriptomics data provides unprecedented depth for the investigation of tissue architecture and paves the way for new developments in 3D spatial analytics.

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