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.
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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Novae: a graph-based foundation model for spatial transcriptomics modeling and analysis tasks.
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Novae: a graph-based foundation model for spatial transcriptomics data - Nature Methods
Novae, a self-supervised graph attention network, is a foundation model excelling at a diverse spectrum of spatial transcriptomics modeling and analysis tasks.
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December 16, 2025 at 5:46 PM
Novae: a graph-based foundation model for spatial transcriptomics modeling and analysis tasks.
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Carta leverages lineage tracing data to infer the optimal trajectory of cell differentiation.
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Inferring cell differentiation maps from lineage tracing data - Nature Methods
Carta leverages lineage tracing data to infer the optimal trajectory of cell differentiation.
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December 16, 2025 at 5:37 PM
Carta leverages lineage tracing data to infer the optimal trajectory of cell differentiation.
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FACED 2.0: a method for high-speed, large FOV, volumetric 2-photon voltage and calcium imaging in the mouse and zebrafish brain.
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FACED 2.0 enables large-scale voltage and calcium imaging in vivo - Nature Methods
FACED 2.0 builds on and expands the capabilities of the free-space angular-chirp-enhanced delay microscopy approach. Its high speed, large field of view and volumetric coverage enable two-photon volta...
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December 16, 2025 at 5:31 PM
FACED 2.0: a method for high-speed, large FOV, volumetric 2-photon voltage and calcium imaging in the mouse and zebrafish brain.
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CellSAM uses an object detector, CellFinder, to detect cells and prompt the Segment Anything Model to generate segmentations with human-level performance across a range of bioimage data.
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CellSAM: a foundation model for cell segmentation - Nature Methods
CellSAM uses an object detector, CellFinder, to detect cells and prompt the Segment Anything Model (SAM) to generate segmentations. This universal model achieves human-level performance across a range...
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December 16, 2025 at 5:27 PM
CellSAM uses an object detector, CellFinder, to detect cells and prompt the Segment Anything Model to generate segmentations with human-level performance across a range of bioimage data.
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A Method to Watch: Artificial intelligence agents for biology
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Artificial intelligence agents for biology - Nature Methods
Artificial intelligence agents may have a transformative effect on how biological research is performed.
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December 15, 2025 at 5:04 PM
A Method to Watch: Artificial intelligence agents for biology
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A Method to Watch: Protein editing
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Protein editing - Nature Methods
Protein editors complement genome editing tools by enabling direct modifications to protein molecules.
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December 15, 2025 at 5:03 PM
A Method to Watch: Protein editing
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A Method to Watch: Cell typing by electrophysiology
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Cell typing by electrophysiology - Nature Methods
Extracellular recordings provide a wealth of information about neuronal activity but it is difficult to link this information to cell types.
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December 15, 2025 at 5:02 PM
A Method to Watch: Cell typing by electrophysiology
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A Method to Watch: Predicting RNA structures
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Predicting RNA structures - Nature Methods
Predicting the folded structures of RNA molecules poses greater challenges than proteins, but steady progress continues.
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December 15, 2025 at 5:01 PM
A Method to Watch: Predicting RNA structures
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A Method to Watch: Understanding enhancer logic through synthetic design
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Understanding enhancer logic through synthetic design - Nature Methods
Experimental and computational advances have improved enhancer characterization and design.
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December 15, 2025 at 4:59 PM
A Method to Watch: Understanding enhancer logic through synthetic design
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A Method to Watch: Cracking the cancer microbiome
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Cracking the cancer microbiome - Nature Methods
New technologies and computational approaches will illuminate the role of the cancer microbiome.
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December 15, 2025 at 4:58 PM
A Method to Watch: Cracking the cancer microbiome
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A Method to Watch: Intrinsic protein disorder at scale
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Intrinsic protein disorder at scale - Nature Methods
Methods to study the structural and functional properties of proteins that contain intrinsically disordered regions at the proteome scale are on the rise.
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December 15, 2025 at 4:57 PM
A Method to Watch: Intrinsic protein disorder at scale
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A Method to Watch: The virtual cell
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The virtual cell - Nature Methods
Virtual cells based on artificial intelligence models are on the horizon
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December 15, 2025 at 4:55 PM
A Method to Watch: The virtual cell
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