Nature Methods
@natmethods.nature.com
A scientific journal publishing cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Posts by the editors.
DeepWonder3D: a pipeline for neuronal extraction from volumetric calcium imaging data. www.nature.com/articles/s41...
Rapid robust high-fidelity 3D neuronal extraction from multiview calcium imaging datasets - Nature Methods
DeepWonder3D is a pipeline for neuronal extraction from volumetric calcium imaging data acquired with a variety of one-photon or two-photon microscopy modalities.
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Spatial isoform sequencing at single cell resolution, as demonstrated in mouse brain slices. www.nature.com/articles/s41...
Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types - Nature Methods
Spl-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...
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Iterative Mapping of proteoforms technology allows measuring intact proteoforms at the single molecule level. www.nature.com/articles/s41...
Large-scale single-molecule analysis of tau proteoforms - Nature Methods
Iterative 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...
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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 Methods - Focus on AI in biological research
This month, several review and opinion pieces discuss how AI is having an impact across nearly all areas of biological research.See Editorial
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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...
The physics of sculpting a living creature - Nature Methods
Cell 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...
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Spatial-ATAC-Hi-C enables profiling chromatin accessibility and spatial organization, as shown in mouse and human brain samples. www.nature.com/articles/s41...
Spatial chromatin architecture and accessibility co-profiling of mammalian tissues - Nature Methods
Spatial-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.
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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
4th Frontiers in Electron and Scanning Probe Microscopy for the Physical and Life Sciences
Advances 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...
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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...
From pixels to patterns: the AI revolution in stem cell-derived models - Nature Methods
This Perspective examines the role of AI-based image analysis when applied to stem cell-derived models.
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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...
AI proteomics: from protein identification to virtual cells - Nature Methods
This Perspective highlights key research areas within mass spectrometry-based proteomics where AI is poised to drive significant advances.
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In our August 'Points of View', @helenajambor.bsky.social and Alexander Lex discuss how to reuse, remix and vibe code scientific figures. www.nature.com/articles/s41...
LLMs are allowing researchers to build software tools without support from software engineers. www.nature.com/articles/s41...
Disruption of the research software landscape through AI software generation - Nature Methods
Specialized 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 describe how LLM-assisted programming disrupts the landscape by allowing researchers to build tools without support from software engineers, illustrate this with an example built rapidly by a single LLM-assisted developer, and discuss opportunities and risks.
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SPIFFI enables real-time super-resolution imaging of live cells using a polarimetric approach. www.nature.com/articles/s41...
SPIFFI enables single-shot super-resolution and multidimensional imaging - Nature Methods
Using a polarimetric approach, SPIFFI enables real-time super-resolution imaging of live-cell samples.
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Raman Enhanced Delineation of Cell Atlases in Tissues (REDCAT) integrates stimulated Raman scattering microscopy and high-plex immunofluorescence to profile proteins, lipids, nuclear metabolites and redox metabolism in tissue. www.nature.com/articles/s41...
All-optical multimodal mapping of single-cell-type-specific metabolic activities via REDCAT - Nature Methods
Raman Enhanced Delineation of Cell Atlases in Tissues (REDCAT) integrates stimulated Raman scattering microscopy and high-plex immunofluorescence to profile single-cell proteins, lipids, nuclear metab...
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Science and music have plenty in common. In this story, @vivienm.bsky.social asks two scientists about how they blend their love of music and with their science. www.nature.com/articles/s41...
Composing a science life with music - Nature Methods
Two scientists blend their love of music and science in different ways.
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SACCELERATOR: an open-source and extensible framework for expert-guided spatial clustering analysis. www.nature.com/articles/s41...
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering - Nature Methods
Benchmarking spatially aware clustering is challenging. SACCELERATOR is an open-source, extensible framework that formalizes expert-guided spatial clustering analysis.
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Protein nanocrates help address the air-water interface problem in cryo-EM-based protein structure determination. www.nature.com/articles/s41...
Overcoming air–water interface-induced artifacts in cryo-EM with protein nanocrates - Nature Methods
MS2 bacteriophage-derived protein shells called ‘nanocrates’ help address the air–water interface-induced artifacts in cryo-EM structure determination by encapsulating target proteins and enabling the...
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PASTA: a platform-agnostic signal amplification approach for multiplexed imaging across modalities. www.nature.com/articles/s41...
PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology - Nature Methods
PASTA is a platform-agnostic signal amplification approach for multiplexed imaging across modalities.
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Voltage imaging across the zebrafish brain at 200.8Hz, achieved by optimizing a remote-scanning light-sheet microscope. @eboyden3.bsky.social www.nature.com/articles/s41...
Voltage imaging of neurons distributed across entire brains of larval zebrafish - Nature Methods
Voltage imaging across much of the zebrafish brain is achieved at 200.8 Hz, by optimizing a remote-scanning light-sheet microscope.
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A Kaggle challenge for particle picking in cryo-ET data spurred the development of new algorithms that outperform state of the art software. www.nature.com/articles/s41...
Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography - Nature Methods
A Kaggle challenge for particle picking in experimental cryo-electron tomography data delivered new machine learning algorithms that outperformed state-of-the-art software and provides a critical refe...
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ProteinDPO: a protein language model for stability prediction and generation of thermostable protein sequences. @brianhie.bsky.social www.nature.com/articles/s41...
Aligning protein-generative models to experimental fitness with ProteinDPO - Nature Methods
This Article demonstrates that direct preference optimization (DPO) can be used to effectively align an unsupervised structure-conditioned language model with biophysical information. The aligned mode...
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kpiCells: biomimetic artificial cells for investigating mechanoregulation in cell-cell interactions. www.nature.com/articles/s41...
Decoding mechanoregulation in immunological synapses using biomimetic artificial cells - Nature Methods
kpiCells are a biomimetic artificial cell system to investigate mechanoregulation in cell–cell interactions.
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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
4th Frontiers in Electron and Scanning Probe Microscopy for the Physical and Life Sciences
Advances 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...
go.nature.com
DABEST 2.0: Estimation graphics for multi-group comparisons. www.nature.com/articles/s41...
Getting over ANOVA: estimation graphics for multi-group comparisons - Nature Methods
Nature Methods - Getting over ANOVA: estimation graphics for multi-group comparisons
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MetaboApps: modular web applications for simplifying and enhancing downstream analysis in GNPS2. www.nature.com/articles/s41...
Bridging complexity and accessibility in metabolomics with MetaboApps - Nature Methods
Nature Methods - Bridging complexity and accessibility in metabolomics with MetaboApps
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In this month's Editorial, we discuss the success of our 1-year old program to formally recognize early-career researcher contributions to peer review. www.nature.com/articles/s41...
Early-career researcher co-review, one year in - Nature Methods
A little more than one year ago, Nature Methods rolled out a program to formally recognize early-career researcher contributions to our peer review process. Here we provide an update on the program’s ...
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GHT-SELEX shows that transcription factors are particular about which genomic loci they bind, and C2H2 zinc finger proteins engage different fingers at different sites. www.nature.com/articles/s41...
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors - Nature Methods
GHT-SELEX—high-throughput SELEX with fragmented genomic DNA—shows that transcription factors can be rather particular about which genomic loci they bind, and that C2H2 zinc finger proteins often engag...
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SpaMTP: comprehensive joint analysis of spatial metabolomics and transcriptomics data. www.nature.com/articles/s41...
SpaMTP: integrative statistical analysis and visualization of spatial metabolomics and transcriptomics data - Nature Methods
SpaMTP enables comprehensive joint analysis of spatial metabolomics and transcriptomics data.
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CellTune: high-precision analysis of spatial proteomics data via human-in-the-loop active learning. www.nature.com/articles/s41...
CellTune: an integrative software for accurate cell classification in spatial proteomics - Nature Methods
CellTune enables high precision analysis of spatial proteomics datasets through a human-in-the-loop active learning workflow.
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Our August issue is now live! 🥳 www.nature.com/nmeth/volume... On the cover, a network of neurons communicated via action potentials. Image from Aliphasha Vaziri, Life Science Editors, and Duygu Koldere Vilain. Paper: www.nature.com/articles/s41...
LATeNT: a light-activatable tetanus neurotoxin for spatiotemporally precise inhibition of exocytosis in neurons and other cells. @heegwangroh.bsky.social @aliceyting.bsky.social www.nature.com/articles/s41...
Light-activated tetanus neurotoxin for conditional proteolysis and inducible synaptic inhibition in vivo - Nature Methods
LATeNT is a light-activatable form of tetanus neurotoxin that can be used for spatiotemporally precise inhibition of exocytosis in neurons and other cells. It can inhibit synaptic transmission in vivo...
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