Nature Methods

Introducing Antscan, a public database of synchrotron X-ray CT images of 800 ant species.

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Next-generation multicolor indicators for in vivo imaging of norepinephrine - Nature Methods Improved red and green indicators for norepinephrine and their characterization are reported. These indicators allow detection of norepinephrine release in awake behaving mice in dual-color fiber phot...

Improved red and green indicators for norepinephrine detect norepinephrine release in awake behaving mice. @tpatriarchi.bsky.social

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A unified framework for multiomics deconvolution - Nature Methods The new algorithm DECODE transcends the limitations of omics-specific methods, and provides a unified framework for the deconvolution of transcriptomic, proteomic and metabolomic datasets.

Also read the N&V highlighting the work here:

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DECODE: a universal deconvolution framework for transcriptomic, proteomic and metabolomic data.

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Nanobiotechnology for Precision Medicine and Tissue Engineering This Nature Conference on Nanobiotechnology for Precision Medicine and Tissue Engineering is organized by Nature Nanotechnology, Nature Materials, Nature Communications and Nature Reviews Materials in...

Conference alert!!

Please join the Nature Conference on Nanobiotechnology for Precision Medicine and Tissue Engineering in Tel Aviv, May 26-28!

natureconferences.streamgo.live/nanobiotechn...

Our February issue is now live! www.nature.com/nmeth/volume...

On the cover, self-supervised reconstruction structured illumination imaging of VACV-induced actin comet tails. Paper here: www.nature.com/articles/s41...

Deep-coverage, high-throughput single-cell metabolomics - Nature Methods Current single-cell metabolomics methods show low sensitivity and limited coverage of small-molecule metabolites. We developed an ion mobility-resolved mass cytometry technology that incorporates sele...

Also read the Research Briefing highlighting this work:

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Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry - Nature Methods An ion mobility-resolved mass cytometry method for single-cell metabolomics enables multidimensional metabolomic profiling. The approach was used to curate a metabolic single-cell atlas containing 45,...

An ion mobility-resolved mass cytometry method enables multidimensional metabolomic profiling of single cells.

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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A Resource presents a global SARS-CoV-2 phylogenetic tree of 4.4 million high-quality genomes.

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Rate variation and recurrent sequence errors in pandemic-scale phylogenetics - Nature Methods Performing pandemic-scale phylogenetic analysis poses multifaceted challenges. This study develops methods for identifying and accounting for mutation rate variation and recurrent sequence errors, lea...

A new paper reports methods for identifying and accounting for mutation rate variation and recurrent sequence errors, presenting an improved phylogenetic tree of SARS-CoV-2 genomes.

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Here is an associated blog post.

communities.springernature.com/posts/daycar...

Not all scientific conferences offer childcare, but when they do, parents are happy. @vivienm.bsky.social asked conference attendees who are also mothers - and their children - about conference daycare.

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and
rdcu.be/e1y16

...James Zou & Kyle Swanson, Stanford University; John Pak Biohub San Francisco

The story includes Shirley Knauer & Mike Blüggel, University of Duisburg-Essen; Lauren Eyssen & Kelly Parker, Rosalind Franklin Institute; Jan Steyaert, Vlaams Institut voor Biotechnologie/Vrije Universiteit Brussel Center for Structural Biology...

What nanobodies can do for you - Nature Methods Since the chance discovery of nanobodies in the late 1980s, their uses and applications have kept growing. Researchers are now exploring new ways to harness nanobody versatility.

Researchers are exploring new ways to harness the versatility of nanobodies, which are smaller camelid antibodies. @vivienm.bsky.social asked scientists about some of their current and future nanobody work.

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and rdcu.be/e1yTd

HumanBase: an interactive AI platform for human biology - Nature Methods Nature Methods - HumanBase: an interactive AI platform for human biology

HumanBase: an interactive AI platform for human biology

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The missing data for intelligent scientific instruments - Nature Methods Most scientific instruments currently discard rich streams of commands, data and metadata from which AI systems could learn to conduct experiments with expert-level decision-making and troubleshooting...

A Comment discusses how commands, data, and metadata currently discarded by scientific instruments could be used to train AI systems to learn to conduct experiments. @henrypinkard.bsky.social @nilsnorlin.bsky.social

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The jellyfish Clytia hemisphaerica - Nature Methods The jellyfish Clytia hemisphaerica has long been established as a model for studying embryogenesis and gametogenesis because of its transparency, simple tissue architecture and evolutionary position. ...

Our latest Creature Column features the jellyfish Clytia hemisphaerica, a model for studying embryogenesis and gametogenesis.

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For a quick summary, read the Research Briefing here:
www.nature.com/articles/s41...

MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery - Nature Methods MaAsLin 3 is a comprehensive and flexible framework for microbiome association studies with expanded toolsets of statistical models, tests and types of inference.

MaAsLin 3: a comprehensive, flexible framework for microbiome association studies. @hutlab.bsky.social

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Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus - Nature Methods DBiTplus represents an integrated experimental and computational workflow that unifies sequencing-based and imaging-based spatial omics, demonstrated by combining transcriptomic profiling and multiple...

DBiTplus: a workflow unifying sequencing-based and imaging-based spatial omics on the same tissue section.

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In this month's Editorial, we highlight some of the Nature Methods editorial team members' favorite papers we published in 2025!

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SpatialZ generates virtual single-cell transcriptomics slices between experimentally measured sections, enabling accurate and efficient building of 3D cell atlases of different tissues.

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Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social

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Our January issue is now live! 🥳
nature.com/nmeth/volume...

On the cover, a network of illuminated grids forms a cell-like shape representing Squidiff’s ability to predict continuous cell-state transitions under differentiation and perturbations. Paper: doi.org/10.1038/s415...

For a quick summary, read the Research Briefing on this work:
www.nature.com/articles/s41...

For a quick summary, read the Research Briefing on this work: www.nature.com/articles/s41...

cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.

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SmartEM: a smart machine learning-based pipeline for electron microscopy-based data acquisition for connectomics.

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TransBrain translates brain phenotypes between mouse and human via homology mapping.

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