Nature Methods, Published online: 27 May 2026; doi:10.1038/s41592-026-03115-9

This Perspective promotes the use of external validation using independent datasets for human neuroimaging studies.

Nature Methods, Published online: 27 May 2026; doi:10.1038/s41592-026-03100-2

This study benchmarks 43 computational methods for identifying topologically associating domains (TADs), presents a tool based on a consensus strategy that leads to improved performance, and releases a web service to benchmark and use TAD calling methods.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03112-y

A correlative workflow combining cryo-electron microscopy and cryo-electron tomography with secondary ion mass spectrometry generates spatially registered chemical maps from the same vitrified sample, directly linking ultrastructural information with molecular composition. This advance opens new avenues for identifying where drugs, pollutants and signaling molecules reside within cells at nanoscale resolution.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03105-x

ENCORI is a comprehensive analysis platform and resource for exploring RNA–protein and RNA–RNA interactomes.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03093-y

AreTomoLive is an accelerated preprocessing pipeline for cryo-electron tomography that streamlines tomographic alignment, reconstruction and contrast enhancement. This pipeline prioritizes automation and throughput to deliver comprehensively corrected and denoised tomograms, including during data collection at scale.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03102-0

Decima learns to predict cell-type-specific gene expression based on DNA sequences, contributing to the analysis of gene regulation and design of context-specific regulatory elements.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03101-1

Support for colleagues can take many forms. However and whenever it arrives, it is welcome.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03095-w

This paper shows that high MOI sgRNA multiplexing maintains CRISPRi screen performance while enabling reduced cell numbers, challenging conventional reliance on low-MOI infections.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03109-7

A correlative workflow combining cryo-EM and focused ion beam secondary ion mass spectrometry (FIB-SIMS) facilitates subcellular chemical analysis with high spatial resolution.

Nature Methods, Published online: 25 May 2026; doi:10.1038/s41592-026-03113-x

Two new methods show that bulk-trained sequence models can be efficiently adapted to predict gene regulation and variant effects at single-cell resolution.

Nature Methods, Published online: 19 May 2026; doi:10.1038/s41592-026-03080-3

StringTie3 shows enhanced performance in total RNA-seq assembly and quantification by modeling both nascent and mature transcripts, across short-, long- and hybrid-read sequencing data.

Nature Methods, Published online: 18 May 2026; doi:10.1038/s41592-026-03084-z

This Perspective discusses current challenges in macromolecular ensemble prediction and the infrastructure and methodological advances needed to overcome these barriers.

Nature Methods, Published online: 14 May 2026; doi:10.1038/s41592-026-03083-0

This Perspective provides minimum community standards and best-practice guidelines for hydroxyl radical protein footprinting–mass spectrometry, including experimental design, sample preparation and oxidation, processing of oxidized samples, and analysis and interpretation of the resulting data.

Nature Methods, Published online: 14 May 2026; doi:10.1038/s41592-026-03071-4

This resource leverages spatial and single-cell transcriptomics to investigate lncRNAs in cancer and reports 94,795 previously unannotated lncRNAs and new approaches to infer their functions.

Nature Methods, Published online: 11 May 2026; doi:10.1038/s41592-026-03092-z

A device for simultaneous photometry and electrophysiology allows recordings in freely moving mice without restriction or inhibition of movement or entanglement of the fiber and cables.

Nature Methods, Published online: 07 May 2026; doi:10.1038/s41592-026-03090-1

FILM is a mid-infrared photothermal microscopy variant that involves optical boxcar demodulation-based illumination, denoising and spectral deconvolution. Its relatively gentle nature allows imaging of metabolic processes in organelles in cell culture as well as in Caenorhabditis elegans.

Nature Methods, Published online: 07 May 2026; doi:10.1038/s41592-026-03091-0

Optical boxcar-enhanced fluorescence-detected mid-infrared photothermal microscopy (FILM), together with artificial intelligence-assisted data processing, maps the chemical composition of individual cell organelles in their native context. This technique uncovered metabolic heterogeneity of lysosomes and lysosomal changes during physiological aging and pathological conditions.

Nature Methods, Published online: 05 May 2026; doi:10.1038/s41592-026-03082-1

$${\rm{Micro}}{\mathbb{S}}{\rm{plit}}$$ M i c r o S p l i t is a computational unmixing method for multiplexed fluorescence imaging of up to four structures per imaging channel.

Nature Methods, Published online: 04 May 2026; doi:10.1038/s41592-026-03099-6

It is not certain that everything is uncertain. —Blaise Pascal

Nature Methods, Published online: 04 May 2026; doi:10.1038/s41592-026-03051-8

UDMT is a multi-animal tracker for behavioral research that is based on a transformer architecture, which negates the need for manually annotated training data. UDMT is showcased on datasets encompassing mice, rats, Drosophila, C. elegans and betta fish.