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.
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SmartEM: a smart machine learning-based pipeline for electron microscopy-based data acquisition for connectomics.
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January 9, 2026 at 5:03 PM
For a quick summary, read the Research Briefing on this work:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
For a quick summary, read the Research Briefing on this work: www.nature.com/articles/s41...
TransBrain translates brain phenotypes between mouse and human via homology mapping.
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January 9, 2026 at 5:01 PM
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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January 9, 2026 at 4:57 PM
cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.
www.nature.com/articles/s41...
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SmartEM: a smart machine learning-based pipeline for electron microscopy-based data acquisition for connectomics.
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January 9, 2026 at 4:53 PM
SmartEM: a smart machine learning-based pipeline for electron microscopy-based data acquisition for connectomics.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
TransBrain translates brain phenotypes between mouse and human via homology mapping.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 9, 2026 at 4:50 PM
TransBrain translates brain phenotypes between mouse and human via homology mapping.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 8, 2026 at 8:44 PM
iGluSnFR4f and iGluSnFR4s are the latest generation of genetically encoded glutamate sensors, for tracking rapid dynamics and for recording from large populations of synapses.
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January 8, 2026 at 8:40 PM
iGluSnFR4f and iGluSnFR4s are the latest generation of genetically encoded glutamate sensors, for tracking rapid dynamics and for recording from large populations of synapses.
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A scalable, open source-framework can be used as a benchmarking suite for comparing macromolecular complex structure, interfaces and ligand interactions against experimental data.
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January 8, 2026 at 8:37 PM
A scalable, open source-framework can be used as a benchmarking suite for comparing macromolecular complex structure, interfaces and ligand interactions against experimental data.
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CELTIC: a context-dependent deep learning model for in silico organelle localization in label-free microscopy images.
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January 8, 2026 at 8:33 PM
CELTIC: a context-dependent deep learning model for in silico organelle localization in label-free microscopy images.
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A new Review covers how machine learning and computer vision methods have empowered super-resolution microscopy.
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AI-empowered super-resolution microscopy: a revolution in nanoscale cellular imaging - Nature Methods
This 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.
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January 6, 2026 at 6:24 PM
A new Review covers how machine learning and computer vision methods have empowered super-resolution microscopy.
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A Perspective on 3D traction force microscopy provides practical experimental and computational guidance for users. @barrasa-fano.bsky.social
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Guidance for 3D traction force microscopy today and in the next decade - Nature Methods
This Perspective envisions the future of 3DTFM and provides practical guidelines for experimental and computation strategies for its application.
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January 6, 2026 at 5:30 PM
A Perspective on 3D traction force microscopy provides practical experimental and computational guidance for users. @barrasa-fano.bsky.social
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Two recent Reviews describe how to select optimal cell migration assays and how to analyze this data.
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Selecting the optimal cell migration assay: fundamentals and practical guidelines - Nature Methods
This Review introduces ten cell migration assays, offers practical guidance toward selecting the best assay for a specific biological question and describes how future advances can reveal important in...
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January 6, 2026 at 5:15 PM
Two recent Reviews describe how to select optimal cell migration assays and how to analyze this data.
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SpaceBar: a cellular barcoding approach for simultaneous analysis of cell clonal and spatial identities.
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SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics - Nature Methods
SpaceBar is a cellular barcoding strategy for simultaneous analysis of cell clonal and spatial identities.
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December 19, 2025 at 7:37 PM
SpaceBar: a cellular barcoding approach for simultaneous analysis of cell clonal and spatial identities.
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The SpatialEx(+) framework uses histology to generate and integrate complementary spatial multi-omics data across samples.
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High-parameter spatial multi-omics through histology-anchored integration - Nature Methods
The SpatialEx(+) framework uses histology to generate and integrate complementary spatial multi-omics data across samples.
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December 19, 2025 at 7:31 PM
The SpatialEx(+) framework uses histology to generate and integrate complementary spatial multi-omics data across samples.
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Two distinct RNA-regulated destabilization domains support 3-color, live-cell imaging of single mRNAs.
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Orthogonal RNA-regulated destabilization domains for three-color RNA imaging with minimal RNA perturbation - Nature Methods
This work presents two distinct RNA-regulated destabilization domains that support three-color live-cell imaging of single mRNA molecules, one of which shows minimal impact on RNA stability.
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December 19, 2025 at 7:27 PM
Two distinct RNA-regulated destabilization domains support 3-color, live-cell imaging of single mRNAs.
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Metient: a statistical framework for inferring patterns of metastatic spread and reconstructing cancer migration history.
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Inferring cancer type-specific patterns of metastatic spread using Metient - Nature Methods
Metient is a statistical framework that infers patterns of metastatic spread and reconstructs cancer migration histories.
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December 19, 2025 at 7:21 PM
Metient: a statistical framework for inferring patterns of metastatic spread and reconstructing cancer migration history.
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Multicell: a deep learning method to capture complex cell dynamics in multicellular development.
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MultiCell: geometric learning in multicellular development - Nature Methods
MultiCell is a deep learning method to capture complex cell dynamics during multicellular development.
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December 19, 2025 at 7:21 PM
Multicell: a deep learning method to capture complex cell dynamics in multicellular development.
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A Resource paper provides a detailed atlas of morphogen-induced responses in human neural organoids.
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Systematic scRNA-seq screens profile neural organoid response to morphogens - Nature Methods
This Resource provides a detailed atlas of morphogen-induced responses in human neural organoids.
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December 19, 2025 at 7:21 PM
A Resource paper provides a detailed atlas of morphogen-induced responses in human neural organoids.
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Self-supervised reconstruction structured illumination microscopy allows long-term imaging of cellular processes.
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December 18, 2025 at 8:39 PM
Self-supervised reconstruction structured illumination microscopy allows long-term imaging of cellular processes.
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An Analysis compares the performance of 27 single-cell perturbation response prediction methods under comprehensive test conditions.
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Benchmarking algorithms for generalizable single-cell perturbation response prediction - Nature Methods
This analysis performs comprehensive comparisons of 27 single-cell perturbation response prediction methods using 29 datasets under different test scenarios and against multiple evaluation metrics.
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December 18, 2025 at 8:34 PM
An Analysis compares the performance of 27 single-cell perturbation response prediction methods under comprehensive test conditions.
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In this month's Creature Column, we feature the ascidian tunicate Ciona, a model for marine systems life sciences.
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December 18, 2025 at 8:25 PM
In this month's Creature Column, we feature the ascidian tunicate Ciona, a model for marine systems life sciences.
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December 18, 2025 at 8:21 PM
A Perspective reviews computational methods for cross-species knowledge transfer.
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Computational strategies for cross-species knowledge transfer - Nature Methods
This Perspective reviews computational methods for cross-species knowledge transfer and introduces ‘agnology’, a data-driven concept of functional equivalence independent of evolutionary origin.
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December 18, 2025 at 8:09 PM
A Perspective reviews computational methods for cross-species knowledge transfer.
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A Perspective reviews recent and emerging developments in building multimodal foundation transformer models in genomics.
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Multimodal foundation transformer models for multiscale genomics - Nature Methods
This Perspective overviews recent and emerging developments in building and using multimodal foundation models based on transformers for analyzing various types of genomics data.
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December 18, 2025 at 8:05 PM
A Perspective reviews recent and emerging developments in building multimodal foundation transformer models in genomics.
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An Analysis from benchmarks computational tools for RNA modification detection using nanopore direct RNA sequencing.
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Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing - Nature Methods
This analysis benchmarked computational tools for RNA modification detection using nanopore direct RNA sequencing and showed that retraining with mixed in vitro transcription and real data improves pe...
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December 16, 2025 at 5:49 PM
An Analysis from benchmarks computational tools for RNA modification detection using nanopore direct RNA sequencing.
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