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.
In this month's Editorial, we highlight some of the Nature Methods editorial team members' favorite papers we published in 2025!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Client Challenge
www.nature.com
January 14, 2026 at 5:38 PM
In this month's Editorial, we highlight some of the Nature Methods editorial team members' favorite papers we published in 2025!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
SpatialZ generates virtual single-cell transcriptomics slices between experimentally measured sections, enabling accurate and efficient building of 3D cell atlases of different tissues.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 14, 2026 at 4:26 PM
SpatialZ generates virtual single-cell transcriptomics slices between experimentally measured sections, enabling accurate and efficient building of 3D cell atlases of different tissues.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 14, 2026 at 4:20 PM
Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
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...
January 14, 2026 at 3:02 PM
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...
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...
www.nature.com/articles/s41...
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...
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.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com/articles/s41...
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...
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.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A scalable, open source-framework can be used as a benchmarking suite for comparing macromolecular complex structure, interfaces and ligand interactions against experimental data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CELTIC: a context-dependent deep learning model for in silico organelle localization in label-free microscopy images.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 8, 2026 at 8:33 PM
CELTIC: a context-dependent deep learning model for in silico organelle localization in label-free microscopy images.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A new Review covers how machine learning and computer vision methods have empowered super-resolution microscopy.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
January 6, 2026 at 6:24 PM
A new Review covers how machine learning and computer vision methods have empowered super-resolution microscopy.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A Perspective on 3D traction force microscopy provides practical experimental and computational guidance for users. @barrasa-fano.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
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
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Two recent Reviews describe how to select optimal cell migration assays and how to analyze this data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
January 6, 2026 at 5:15 PM
Two recent Reviews describe how to select optimal cell migration assays and how to analyze this data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
SpaceBar: a cellular barcoding approach for simultaneous analysis of cell clonal and spatial identities.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 19, 2025 at 7:37 PM
SpaceBar: a cellular barcoding approach for simultaneous analysis of cell clonal and spatial identities.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The SpatialEx(+) framework uses histology to generate and integrate complementary spatial multi-omics data across samples.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 19, 2025 at 7:31 PM
The SpatialEx(+) framework uses histology to generate and integrate complementary spatial multi-omics data across samples.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Two distinct RNA-regulated destabilization domains support 3-color, live-cell imaging of single mRNAs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 19, 2025 at 7:27 PM
Two distinct RNA-regulated destabilization domains support 3-color, live-cell imaging of single mRNAs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Metient: a statistical framework for inferring patterns of metastatic spread and reconstructing cancer migration history.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 19, 2025 at 7:21 PM
Metient: a statistical framework for inferring patterns of metastatic spread and reconstructing cancer migration history.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multicell: a deep learning method to capture complex cell dynamics in multicellular development.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
MultiCell: geometric learning in multicellular development - Nature Methods
MultiCell is a deep learning method to capture complex cell dynamics during multicellular development.
www.nature.com
December 19, 2025 at 7:21 PM
Multicell: a deep learning method to capture complex cell dynamics in multicellular development.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A Resource paper provides a detailed atlas of morphogen-induced responses in human neural organoids.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 19, 2025 at 7:21 PM
A Resource paper provides a detailed atlas of morphogen-induced responses in human neural organoids.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Self-supervised reconstruction structured illumination microscopy allows long-term imaging of cellular processes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 18, 2025 at 8:39 PM
Self-supervised reconstruction structured illumination microscopy allows long-term imaging of cellular processes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An Analysis compares the performance of 27 single-cell perturbation response prediction methods under comprehensive test conditions.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
December 18, 2025 at 8:34 PM
An Analysis compares the performance of 27 single-cell perturbation response prediction methods under comprehensive test conditions.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
In this month's Creature Column, we feature the ascidian tunicate Ciona, a model for marine systems life sciences.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com/articles/s41...
www.nature.com/articles/s41...