Nature Methods

nature.comSolid-state nanopore sensing: the next workhorse of biophysical characterization - Nature MethodsThis Perspective discusses opportunities and challenges of using solid-state nanopores for broader biophysical characterization.

A Perspective discusses opportunities and challenges of using solid-state nanopores in molecular biophysics. www.nature.com/articles/s41...

nature.comGo figure: transparency in neuroscience images preserves context and clarifies interpretation - Nature MethodsThis Perspective highlights the need for transparent thresholding rather than only showing results beyond fixed P values, to avoid the loss of valuable information and to improve the reporting of neur...

A Perspective discusses how to improve the reporting of neuroscience results. www.nature.com/articles/s41...

nature.comNear-infrared photochromic miniprotein enables photoacoustic molecular imaging of acute inflammation and intracellular antigens - Nature MethodsA small, photoswitchable and genetically encodable protein operating in the near-infrared window is reported for photoacoustic tomography applications.

A small, photoswitchable, genetically encodable protein operating in the near-IR window enables applications in photoacoustic tomography. www.nature.com/articles/s41...

nature.comTangermeme: a toolkit for understanding cis-regulatory logic using deep learning models - Nature MethodsThe tangermeme software package is a comprehensive, flexible and efficient Swiss Army knife for deep learning-based cis-regulatory pattern identification and analysis.

Tangermeme: software for comprehensive, flexible and efficient cis-regulatory pattern identification and analysis. www.nature.com/articles/s41...

nature.comTowards high-quality large-scale T cell receptor antigen specificity data: challenges and promises - Nature MethodsAntigen recognition by T cells through their highly diverse T cell receptors (TCRs) is central to adaptive immunity, and recent high‑throughput methods and databases have greatly expanded the availabi...

Bottlenecks in the study of TCR-antigen specificity: www.nature.com/articles/s41...

nature.comHuman stewardship in the age of organoids - Nature MethodsOrganoids are transforming biomedical science, but their promise hinges on shifting from episodic ethics review to sustained, integrated stewardship. We argue that such stewardship must evolve alongsi...

Stewardship of organoids: www.nature.com/articles/s41...

nature.comConfounders of lncRNA screens: sources, consequences and possible solutions - Nature MethodsRe-analysis of published long non-coding RNA (lncRNA) screens has revealed unexpectedly high false-positive rates in some reports, indicating that high-throughput genetic perturbations are more prone ...

Detecting, monitoring and mitigating false positives in lncRNA screens. www.nature.com/articles/s41...

nature.comA FAIR road to a bioAFM databank - Nature MethodsIn this Comment, we direct attention to initial efforts to establish a high-quality databank of atomic force microscopy (AFM) data: bioAFM-DB. We outline the state of this endeavor, its challenges, an...

Introducing bioAFM-DB, a databank for atomic force microscopy data. www.nature.com/articles/s41...

nature.comEngaging figures - Nature MethodsSome visualizations resonate while others are forgotten. Why that is can be understood with the principles of creating ‘proximity’.

In a new Points of View, our columnists describe the application of 'principles of proximity' to generate engaging scientific figures. www.nature.com/articles/s41...

nature.comHow to write a rebuttal letter - Nature MethodsThe rebuttal letter is a vitally important document when revising a manuscript for a journal. Here we discuss how to communicate about your manuscript revisions in the best possible light.

In this month's Editorial, we provide some tips for writing well-structured and professional rebuttal letters for editors and peer reviewers to evaluate. www.nature.com/articles/s41...

Our October issue is live! 🎉 www.nature.com/nmeth/volume... On the cover, polygenic risk score prediction in diverse populations is made possible with a new computational tool, SPLENDID. Paper: www.nature.com/articles/s41...

nature.comAccurate and well-powered case–control analysis of spatial molecular data - Nature MethodsVIMA uses deep-learning architecture to identify differentially enriched features within spatial datasets.

VIMA: a deep learning-based method to identify differentially enriched features in spatial datasets. www.nature.com/articles/s41...

nature.comFlexible discovery of disease-associated tissue structures - Nature MethodsIdentification of disease-associated patterns in spatial molecular data is challenging. We introduce variational inference-based microniche analysis (VIMA), a deep learning-based statistical method th...

Read the associated Research Briefing, here: www.nature.com/articles/s41...

nature.comResolving cell–cell interaction networks and their molecular logic in complex tissues - Nature MethodsCCI-seq leverages combinatorial cell clump indexing and single-cell sequencing to capture large-scale cell–cell interaction networks.

CCI-seq leverages combinatorial cell clump indexing and single-cell sequencing to capture large-scale cell-cell interaction networks. www.nature.com/articles/s41...

nature.comTimes are changing but order matters: transferable prediction of small-molecule liquid chromatography retention times - Nature MethodsA method for transferable retention time prediction across chromatographic conditions and compound classes is presented. The approach makes use of a two-step strategy that first predicts a condition-a...

Transferable retention time prediction across liquid chromatographic conditions and compound classes. www.nature.com/articles/s41...

nature.comCytoVI: deep generative modeling of antibody-based single cell data - Nature MethodsCytoVI is a deep generative model for statistically rigorous analysis of antibody-based single-cell data.

CytoVI: a deep generative model for statistically rigorous analysis of antibody-based single cell data. www.nature.com/articles/s41...

nature.comNobel Prize in Physiology or Medicine 2026The 2026 Nobel Prize in Physiology or Medicine has been awarded jointly to Karl Deisseroth, Peter Hegemann and Georg Nagel “for discoveries leading to ...

Check out the @natureportfolio.nature.com Collection of articles related to this year's Nobel Prize in Physiology or Medicine, here: www.nature.com/collections/...

nature.comNature Methods - Volume 8 Issue 1, January 2011Optogenetics, our pick for Method of the Year 2010, is rapidly becoming a vital tool for neurobiologists, who are applying it to study both basic biology and...

Back in 2010 when we selected optogenetics as our Method of the Year, we had already observed the transformative impact that it was making on basic research in neuroscience. www.nature.com/nmeth/volume... www.nature.com/articles/nme... It's exciting to see how far the technology has come!

Nobel Prize@nobelprize.org

BREAKING NEWS The 2026 Nobel Prize in Physiology or Medicine has been awarded to Karl Deisseroth, Peter Hegemann and Georg Nagel “for their discoveries concerning light-gated ion channels and optogenetics.”

nature.comSpatially resolved chromatin architectures in mammalian brain tissues - Nature MethodsSpatial Hi-C allows the study of chromatin organization in a spatially resolved manner. This approach shows regional and cell-type-specific differences in the adult and developing mouse brain.

Spatial Hi-C allows the study of chromatin in a spatially resolved manner, as applied to adult and developing mouse brains. www.nature.com/articles/s41...

nature.comControl of ice thickness in cryo-EM via confinement - Nature MethodsThis study explores the use of graphene reservoirs formed over perforated supporting films as a method to precisely control ice thickness during cryo-EM sample preparation.

Graphene reservoirs formed over perforated support films precisely control ice thickness during cryo-EM sample preparation. www.nature.com/articles/s41...

nature.comResolVI: addressing noise and bias in spatial transcriptomics - Nature MethodsSegmentation and quantification of spatial transcriptomics data is plagued by specific noise and bias. ResolVI tackles this challenge by generating error- and batch-corrected probabilistic representat...

ResolVI: error and batch correction for spatial transcriptomics data. www.nature.com/articles/s41...

nature.comSVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples - Nature MethodsSVPG performs accurate pangenome-facilitated structural variant detection and accelerates pangenome graph augmentation using long-read sequencing data.

SVPG: accurate pangenome-facilitated structural variant detection from long-read sequencing data. www.nature.com/articles/s41...

NanoTS: deep learning-based tool for nanopore long-read transcriptome sequencing-based SNP detection and genotype calling. www.nature.com/articles/s41...

nature.comCFM: confinement force microscopy—a dynamic, precise and stable microconfiner for traction force microscopy in spatial confinement - Nature MethodsCFM enables tunable cell confinement for measuring traction forces exerted by single cells and cell aggregates in tissue-mimicking microenvironments.

Confinement force microscopy enables tunable cell confinement for measuring traction forces exerted by single cells and cell aggregates. www.nature.com/articles/s41...

nature.comSPLENDID incorporates continuous genetic ancestry in biobank-scale data to improve polygenic risk prediction across diverse populations - Nature MethodsRather than relying on pre-specified ancestry labels, which often fail to capture the full genetic heterogeneity of diverse populations, SPLENDID treats ancestry as a continuum and improves polygenic ...

SPLENDID treats ancestry as a continuum to improve polygenic risk score prediction for biobank-scale datasets. www.nature.com/articles/s41...

nature.comAn ultralow-background far-red light-responsive optogenetic tool based on an engineered biliverdin-binding domain - Nature MethodsA compact protein pair that heterodimerizes upon red light activation, FenixS and Ash1, is developed for optogenetic applications.

A compact protein pair, FenixS and Ash1, heterodimerizes upon red light activation for optogenetics. @chemuoft.bsky.social @giangle-1.bsky.social www.nature.com/articles/s41...

nature.comA wireless modular platform for neuro-behavioral recording and closed-loop manipulation in small animals - Nature MethodsWILD is a wireless device that can record neuronal activity, perform optogenetic stimulations, record animal movements, record the environment or eye movements via an integrated camera, analyze the da...

WILD: a wireless device for studies of brain activity in freely moving animals under naturalistic conditions. www.nature.com/articles/s41...

nature.comWireless neural recordings from groups of mice inside and outside the laboratory - Nature MethodsStudying the brain mechanisms of natural behaviors is experimentally challenging. We developed a miniaturized, wireless platform to record and manipulate neural and physiological activity in small ani...

Read the associated Research Briefing here: www.nature.com/articles/s41...

nature.comMemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography - Nature MethodsMemBrain v2 enables streamlined analysis of membranes in cryo-electron tomography by providing user-friendly tools for membrane segmentation, membrane protein localization and spatial analysis, suppor...

MemBrain v2: streamlined analysis of membranes in cryo-ET with tools for membrane segmentation, protein localization and spatial analysis. www.nature.com/articles/s41...

nature.comReconstructing signaling histories of single cells via perturbation screens and transfer learning - Nature MethodsIRIS learns conserved signaling representations from in vitro perturbation data to reconstruct signaling states and histories across diverse in vivo cellular contexts.

IRIS learns conserved signaling representations from in vivo perturbation data to reconstruct cell signaling states and histories. www.nature.com/articles/s41...

nature.comRapid robust high-fidelity 3D neuronal extraction from multiview calcium imaging datasets - Nature MethodsDeepWonder3D is a pipeline for neuronal extraction from volumetric calcium imaging data acquired with a variety of one-photon or two-photon microscopy modalities.

DeepWonder3D: a pipeline for neuronal extraction from volumetric calcium imaging data. www.nature.com/articles/s41...

nature.comSpatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types - Nature MethodsSpl-ISO-Seq2, Spl-IsoQuant-2 and Spl-IsoFind enable isoform sequencing, barcode calling of >450 million barcodes, and spatially variable isoform detection with high spatial resolution as demonstrat...

Spatial isoform sequencing at single cell resolution, as demonstrated in mouse brain slices. www.nature.com/articles/s41...

nature.comLarge-scale single-molecule analysis of tau proteoforms - Nature MethodsIterative Mapping of proteoforms enables large-scale measurement of intact proteoforms with single-molecule resolution. The approach is demonstrated here by quantifying tau proteoform groups across co...

Iterative Mapping of proteoforms technology allows measuring intact proteoforms at the single molecule level. www.nature.com/articles/s41...

nature.comRevealing distinctive traits of individual proteins - Nature MethodsTau: distinguishing the good, the bad and the ugly.

Read the News & Views highlighting this interesting work, here: www.nature.com/articles/s41...

nature.comNature Methods - Focus on AI in biological researchThis month, several review and opinion pieces discuss how AI is having an impact across nearly all areas of biological research.See Editorial

Our September issue is live! 🎉 www.nature.com/nmeth/volume... This special issue includes a Focus on AI in biological research. AI is everywhere these days, and is impacting nearly all fields of biology. To learn more, read our Editorial and check out the focus content!

nature.comOpen and sustainable AI: challenges, opportunities and the road ahead in the life sciences - Nature MethodsThis Perspective provides recommendations for open and sustainable AI and associated resources facilitating exploration and implementation.

Perspective: www.nature.com/articles/s41...

nature.comAI-empowered super-resolution microscopy: a revolution in nanoscale cellular imaging - Nature MethodsThis Review provides a comprehensive discussion of how methods in machine learning and computer vision have been used to improve super-resolution microscopy to gain insights into subcellular biology.

Review: www.nature.com/articles/s41...

nature.comFrom pixels to patterns: the AI revolution in stem cell-derived models - Nature MethodsThis Perspective examines the role of AI-based image analysis when applied to stem cell-derived models.

Perspective: www.nature.com/articles/s41...

nature.comBenchmarking biomedical foundation models - Nature MethodsFoundation models are becoming increasingly popular across various biological domains, yet rigorous methods to comprehensively evaluate their full potential remain underdeveloped. This Perspective dis...

Perspective: www.nature.com/articles/s41...

nature.comDisruption of the research software landscape through AI software generation - Nature MethodsSpecialized research software has historically been costly and time-consuming to create, but large language models (LLMs) have become capable enough at code generation to fundamentally change this. We...

Comment: www.nature.com/articles/s41...

nature.comAI proteomics: from protein identification to virtual cells - Nature MethodsThis Perspective highlights key research areas within mass spectrometry-based proteomics where AI is poised to drive significant advances.

Perspective: www.nature.com/articles/s41...

nature.comTowards predictive virtual embryos with genomics and AI - Nature MethodsPredictive virtual embryo systems that integrate single-cell and spatial data with artificial intelligence (AI) techniques offer a promising avenue for modeling mammalian embryogenesis across scales a...

Comment: www.nature.com/articles/s41...

Comment: www.nature.com/articles/s41...

nature.comnature.com

nature.comEmbedding AI in biology — part 2 - Nature MethodsArtificial intelligence is rapidly changing the landscape of how biological data are acquired and analyzed. Almost no corner of biological research has been left untouched.

Editorial: www.nature.com/articles/s41...

nature.comThe physics of sculpting a living creature - Nature MethodsCell biologists have long known that mechanical forces, such as tension and compression, influence tissue differentiation. Now, advanced methods are letting them observe and manipulate these forces in...

3 Sept

In our latest Technology Feature, Caroline Seydel explores how mechanical forces such as tension and compression influence tissue differentiation, and how cell biologists are observing and manipulating such forces in living systems. www.nature.com/articles/s41...

nature.comSpatial chromatin architecture and accessibility co-profiling of mammalian tissues - Nature MethodsSpatial-ATAC-Hi-C enables the profiling of both chromatin accessibility and organization in a spatially resolved manner, as demonstrated on mouse brain and human glioblastoma and astrocytoma samples.

3 Sept

Spatial-ATAC-Hi-C enables profiling chromatin accessibility and spatial organization, as shown in mouse and human brain samples. www.nature.com/articles/s41...

Nature Methods reposted

go.nature.com4th Frontiers in Electron and Scanning Probe Microscopy for the Physical and Life SciencesAdvances in electron microscopy instrumentation and methods continue to drive progress in the physical and life sciences. The 4th edition of this conference will bring together researchers from physic...

13 Aug

Join Nature Methods and other Nature journal editors at Princeton University this October to hear the latest electron microscopy instrumentation and methods driving progress in the physical and life sciences. go.nature.com/4h0zAME

1 Sept

A Perspective from Deininger, Caldarelli, Zernicka-Goetz, and Mikut examines the role of AI-based image analysis as applied to stem cell-derived models. nature.com/articles/s41...

1 Sept

In their Perspective, Matthias Mann, Bing Zhang, Tiannan Guo and colleagues discuss key areas in proteomics where AI is poised to drive advances. www.nature.com/articles/s41...