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.
CABLE: a method that uses information about cell or nuclear shape to infer fiber tracts in the brain.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Whole-brain reconstruction of fiber tracts based on cytoarchitectonic organization - Nature Methods
CABLE harnesses cytoarchitectural information such as cell or nuclear shape to infer fiber tracts in the brain of, for example, marmosets, macaques or humans.
www.nature.com
November 7, 2025 at 3:00 PM
CABLE: a method that uses information about cell or nuclear shape to infer fiber tracts in the brain.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Squidiff: a diffusion-based model to predict transcriptome response to perturbations.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Squidiff: predicting cellular development and responses to perturbations using a diffusion model - Nature Methods
Squidiff is a diffusion-based model to predict transcriptomic changes in response to perturbations.
www.nature.com
November 7, 2025 at 2:41 PM
Squidiff: a diffusion-based model to predict transcriptome response to perturbations.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ESPRESSO: a method that extracts functional information about organelles for deep spatiotemporal phenotyping at the single cell level.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ESPRESSO: spatiotemporal omics based on organelle phenotyping - Nature Methods
ESPRESSO leverages functional information obtained from organelles for deep spatiotemporal phenotyping of single cells.
www.nature.com
November 6, 2025 at 5:40 PM
ESPRESSO: a method that extracts functional information about organelles for deep spatiotemporal phenotyping at the single cell level.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cyclone, an acyclovir-controlled poison exon cassette, enables regulation of transgene and endogenous gene expression with minimal background.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A portable poison exon for small-molecule control of mammalian gene expression - Nature Methods
This work introduces Cyclone, an acyclovir-controlled cassette that enables regulation of both transgene and endogenous gene expression with minimal background activity.
www.nature.com
November 6, 2025 at 4:29 PM
Cyclone, an acyclovir-controlled poison exon cassette, enables regulation of transgene and endogenous gene expression with minimal background.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data. @gabrielpeyre.bsky.social @cantinilab.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.
www.nature.com
November 6, 2025 at 4:07 PM
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data. @gabrielpeyre.bsky.social @cantinilab.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
By pretraining on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances building foundation models for spatial single-cell analysis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nicheformer: a foundation model for single-cell and spatial omics - Nature Methods
Pretrained on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances toward building foun...
www.nature.com
November 6, 2025 at 4:02 PM
By pretraining on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances building foundation models for spatial single-cell analysis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 30, 2025 at 3:41 PM
High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
SegmentNT: a general segmentation model for genome annotation that can process DNA sequences up to 50-kb long and shows strong generalization across unseen species.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Annotating the genome at single-nucleotide resolution with DNA foundation models - Nature Methods
By leveraging the power of pretrained DNA foundation models, SegmentNT achieves performant genome annotation through segmenting different genic and regulatory elements.
www.nature.com
October 29, 2025 at 3:41 PM
SegmentNT: a general segmentation model for genome annotation that can process DNA sequences up to 50-kb long and shows strong generalization across unseen species.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Improved reconstruction of single-cell developmental potential with CytoTRACE 2 - Nature Methods
CytoTRACE 2 is an interpretable deep learning framework that leverages single-cell RNA sequencing data to predict absolute developmental potential across datasets.
www.nature.com
October 29, 2025 at 3:14 PM
CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
PHLOWER infers complex cell differentiation trajectories from single-cell multimodal data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories - Nature Methods
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories.
www.nature.com
October 23, 2025 at 3:16 PM
PHLOWER infers complex cell differentiation trajectories from single-cell multimodal data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
scooby achieves DNA sequence-based single-cell level modeling of RNA-seq coverage and ATAC-seq insertion profiles by adapting a deep learning model that predicts bulk RNA-seq coverage. @johahi.bsky.social @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de
www.nature.com/articles/s41...
www.nature.com/articles/s41...
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution - Nature Methods
scooby achieves DNA sequence-based single-cell level modeling of RNA-sequencing coverage and ATAC-sequencing insertion profiles by adapting a deep learning model that predicts bulk RNA-sequencing cove...
www.nature.com
October 22, 2025 at 4:48 PM
scooby achieves DNA sequence-based single-cell level modeling of RNA-seq coverage and ATAC-seq insertion profiles by adapting a deep learning model that predicts bulk RNA-seq coverage. @johahi.bsky.social @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CELLECT learns contrastive embeddings to enable high-fidelity cell tracking.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CELLECT: contrastive embedding learning for large-scale efficient cell tracking - Nature Methods
CELLECT learns contrastive embeddings to enable high-fidelity cell tracking.
www.nature.com
October 22, 2025 at 4:31 PM
CELLECT learns contrastive embeddings to enable high-fidelity cell tracking.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods
gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.
www.nature.com
October 16, 2025 at 3:26 PM
gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Our latest Creature Column features the gray mouse lemur, a model for primate brain evolution, cognition, aging and neurodegenerative diseases.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 14, 2025 at 5:49 PM
Our latest Creature Column features the gray mouse lemur, a model for primate brain evolution, cognition, aging and neurodegenerative diseases.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
MrVI, based on deep generative modeling, is a unified framework for integrative, exploratory, and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets. @justjhong.bsky.social @canergen.bsky.social @elhamazizi.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Deep generative modeling of sample-level heterogeneity in single-cell genomics - Nature Methods
MrVI, based on deep generative modelling, is a unified framework for integrative, exploratory and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets.
www.nature.com
October 14, 2025 at 4:44 PM
MrVI, based on deep generative modeling, is a unified framework for integrative, exploratory, and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets. @justjhong.bsky.social @canergen.bsky.social @elhamazizi.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
In our latest Registered Report, researchers compare computational methods for single-cell multimodal omics data integration and provide recommendations for different tasks and scenarios.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multitask benchmarking of single-cell multimodal omics integration methods - Nature Methods
This Registered Report compares computational methods for single-cell multimodal omics integration and provides recommendations for different tasks and scenarios.
www.nature.com
October 14, 2025 at 4:28 PM
In our latest Registered Report, researchers compare computational methods for single-cell multimodal omics data integration and provide recommendations for different tasks and scenarios.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 10, 2025 at 2:49 PM
In our latest Editorial we discuss some team updates, new editorial projects and initiatives.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
What’s new at Nature Methods - Nature Methods
Team news, editorial projects and initiatives, plus a preview of what’s to come in 2026.
www.nature.com
October 10, 2025 at 2:19 PM
In our latest Editorial we discuss some team updates, new editorial projects and initiatives.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Our October issue is live! 🥳
www.nature.com/nmeth/volume...
On the cover, single-cell DNA-RNA sequencing (SDR-seq) links genetic variants to gene expression. Artwork by Tobias Wuestefeld. Paper here: www.nature.com/articles/s41...
www.nature.com/nmeth/volume...
On the cover, single-cell DNA-RNA sequencing (SDR-seq) links genetic variants to gene expression. Artwork by Tobias Wuestefeld. Paper here: www.nature.com/articles/s41...
October 10, 2025 at 2:07 PM
Our October issue is live! 🥳
www.nature.com/nmeth/volume...
On the cover, single-cell DNA-RNA sequencing (SDR-seq) links genetic variants to gene expression. Artwork by Tobias Wuestefeld. Paper here: www.nature.com/articles/s41...
www.nature.com/nmeth/volume...
On the cover, single-cell DNA-RNA sequencing (SDR-seq) links genetic variants to gene expression. Artwork by Tobias Wuestefeld. Paper here: www.nature.com/articles/s41...
Nimbus predicts the likelihood of marker positivity from multiplexed image data in single cells.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Automated classification of cellular expression in multiplexed imaging data with Nimbus - Nature Methods
Nimbus, a deep learning model, uses a large multiplexed imaging dataset to predict the likelihood of marker positivity in single cells.
www.nature.com
October 8, 2025 at 4:37 PM
Nimbus predicts the likelihood of marker positivity from multiplexed image data in single cells.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
OrganoidTracker 2.0 accurately tracks cells in complex systems such as developing organoids.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cell tracking with accurate error prediction - Nature Methods
OrganoidTracker 2.0 enables fast and accurate cell tracking in complex systems such as developing organoids. A key aspect of the work is determining cell tracks with error probabilities for any tracking feature, from cell cycles to lineage trees.
www.nature.com
October 8, 2025 at 4:24 PM
OrganoidTracker 2.0 accurately tracks cells in complex systems such as developing organoids.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Laser ablation of imaged surface layers under adaptive control enables volumetric imaging of heterogeneous tissue like skull and brain.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 3, 2025 at 1:31 PM
Laser ablation of imaged surface layers under adaptive control enables volumetric imaging of heterogeneous tissue like skull and brain.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods
CaCoFold-R3D is a probabilistic model that simultaneously predicts the RNA 3D motifs jointly with the secondary structure in a structural RNA using evolutionary information.
www.nature.com
October 3, 2025 at 1:25 PM
CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
META-SiM: a foundation model for single-molecule fluorescence microscopy trace classification, segmentation, idealization and stepwise photobleaching analysis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Foundation model for efficient biological discovery in single-molecule time traces - Nature Methods
META-SiM brings foundation model power to single-molecule time traces, excelling across diverse analysis tasks. Paired with the web-based META-SiM Projector and entropy mapping, it rapidly reveals hidden molecular behaviors inaccessible by other means.
www.nature.com
October 3, 2025 at 12:54 PM
META-SiM: a foundation model for single-molecule fluorescence microscopy trace classification, segmentation, idealization and stepwise photobleaching analysis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
HippoMaps: an open-source resource for studying the human hippocampus at different scales and with different modalities.
www.nature.com/articles/s41...
@jordandekraker.bsky.social @borismontreal.bsky.social @jclauneuro.bsky.social @neuroak.bsky.social @sofievalk.bsky.social @donnagift.bsky.social
www.nature.com/articles/s41...
@jordandekraker.bsky.social @borismontreal.bsky.social @jclauneuro.bsky.social @neuroak.bsky.social @sofievalk.bsky.social @donnagift.bsky.social
HippoMaps: multiscale cartography of human hippocampal organization - Nature Methods
HippoMaps provides an open-source resource for studying the human hippocampus at different scales and with different modalities such as histology, fMRI, structural MRI and EEG.
www.nature.com
October 3, 2025 at 12:50 PM
HippoMaps: an open-source resource for studying the human hippocampus at different scales and with different modalities.
www.nature.com/articles/s41...
@jordandekraker.bsky.social @borismontreal.bsky.social @jclauneuro.bsky.social @neuroak.bsky.social @sofievalk.bsky.social @donnagift.bsky.social
www.nature.com/articles/s41...
@jordandekraker.bsky.social @borismontreal.bsky.social @jclauneuro.bsky.social @neuroak.bsky.social @sofievalk.bsky.social @donnagift.bsky.social