Nature Methods offers a unique interdisciplinary forum for the publication of novel methods. Nature Methods focuses on the life sciences, combining practical, technique-driven subject matter with rigorous peer-review standards to ensure that readers are consistently presented with only the most valuable and highest quality methodological research. The journal offers its readers primary research papers as well as an array of opinions, reviews and short journalistic pieces to provide busy researchers with a broad, yet easily absorbed perspective of important methodological developments in the life sciences. http://feeds.nature.com/nmeth/rss/current Nature Publishing Group en © 2026 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Nature Methods © 2026 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. permissions@nature.com https://www.nature.com/uploads/product/nmeth/rss.gif http://feeds.nature.com/nmeth/rss/current https://www.nature.com/articles/s41592-026-03100-2 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.]]> Pumin LiAndras HatosMiljan PetrovicGian Marco FranceschiniLuca NanniDaniele TavernariGiovanni Ciriello doi:10.1038/s41592-026-03100-2 Nature Methods, Published online: 2026-05-27; | doi:10.1038/s41592-026-03100-2 2026-05-27 Nature Methods 10.1038/s41592-026-03100-2 https://www.nature.com/articles/s41592-026-03100-2 https://www.nature.com/articles/s41592-026-03115-9 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.]]> Matthew RosenblattMaya L. FosterBrendan D. AdkinsonLink TejavibulyaMilana KhaitovaJean YeHuili SunRaimundo X. RodriguezChris C. CampAsh ChintaMarie C. McCuskerLing HanChristopher T. FieldsSaloni MehtaDustin Scheinost doi:10.1038/s41592-026-03115-9 Nature Methods, Published online: 2026-05-27; | doi:10.1038/s41592-026-03115-9 2026-05-27 Nature Methods 10.1038/s41592-026-03115-9 https://www.nature.com/articles/s41592-026-03115-9 https://www.nature.com/articles/s41592-026-03112-y 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.]]> Julia Peukes doi:10.1038/s41592-026-03112-y Nature Methods, Published online: 2026-05-25; | doi:10.1038/s41592-026-03112-y 2026-05-25 Nature Methods 10.1038/s41592-026-03112-y https://www.nature.com/articles/s41592-026-03112-y https://www.nature.com/articles/s41592-026-03101-1 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.]]> Vivien Marx doi:10.1038/s41592-026-03101-1 Nature Methods, Published online: 2026-05-25; | doi:10.1038/s41592-026-03101-1 2026-05-25 Nature Methods 10.1038/s41592-026-03101-1 https://www.nature.com/articles/s41592-026-03101-1 https://www.nature.com/articles/s41592-026-03113-x 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.]]> Johannes LinderDavid R. Kelley doi:10.1038/s41592-026-03113-x Nature Methods, Published online: 2026-05-25; | doi:10.1038/s41592-026-03113-x 2026-05-25 Nature Methods 10.1038/s41592-026-03113-x https://www.nature.com/articles/s41592-026-03113-x https://www.nature.com/articles/s41592-026-03109-7 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.]]> Hannah OchnerBuse IsbilirSonja BlascheDavid ScheidweilerYuexuan ZhangZhexin WangTom SmithCatarina FrancoRob BradleyKiran R. PatilTanmay A. M. Bharat doi:10.1038/s41592-026-03109-7 Nature Methods, Published online: 2026-05-25; | doi:10.1038/s41592-026-03109-7 2026-05-25 Nature Methods 10.1038/s41592-026-03109-7 https://www.nature.com/articles/s41592-026-03109-7 https://www.nature.com/articles/s41592-026-03095-w 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.]]> Stefan OberlinNeil Q. TayAlbert XueRuzbeh MosadeghiHarold PimentelMichael T. McManus doi:10.1038/s41592-026-03095-w Nature Methods, Published online: 2026-05-25; | doi:10.1038/s41592-026-03095-w 2026-05-25 Nature Methods 10.1038/s41592-026-03095-w https://www.nature.com/articles/s41592-026-03095-w https://www.nature.com/articles/s41592-026-03102-0 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.]]> Avantika LalAlexander KarollusLaura GunsalusDavid GarfieldSurag NairAlex M. TsengM. Grace GordonJohn BlischakBryce Van De GeijnTushar BhangaleJenna L. CollierNathaniel DiamantTommaso BiancalaniHector Corrada BravoGabriele ScaliaGokcen Eraslan doi:10.1038/s41592-026-03102-0 Nature Methods, Published online: 2026-05-25; | doi:10.1038/s41592-026-03102-0 2026-05-25 Nature Methods 10.1038/s41592-026-03102-0 https://www.nature.com/articles/s41592-026-03102-0