Nature Methods

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	1460
More dimensions of the 3D genome	1377
Exoskeleton empowers large-scale neural recordings in freely roaming mice	1130
Modeling locomotion from environment to neurons	818
Analyzing submicron spatial transcriptomics data at their original resolution	719
SNAP-tag2 improves live-cell imaging	543
Annotating unknown metabolites	520
Optimism for abundant whole-brain connectomes and connectomic screening	477
Appeals: what, why, when, how	474
GWAS and eQTL disparity	470
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	469
Chromoscope: interactive multiscale visualization for structural variation in human genomes	469
Line-scanning speeds up Brillouin microscopy	460
Self-localized ultrafast pencil beam for volumetric multiphoton imaging	424
How noncoding RNAs began to leave the junkyard	382
Fast and efficient template-mediated synthesis of genetic variants	369
BIONIC: biological network integration using convolutions	359
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	355
Method of the Year 2025: electron microscopy-based connectomics	351
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	341
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	302
Antibody stabilization for thermally accelerated deep immunostaining	301
EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control	295
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	294
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	282

Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus	278
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	262
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	237
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	236
Maximum-likelihood model fitting for quantitative analysis of SMLM data	236
Unlocking the power of spatial omics with AI	234
Prediction of protein subcellular localization in single cells	233
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	231
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	225
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	223
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	217
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	217
MRIcroGL: voxel-based visualization for neuroimaging	217
Inference of secreted protein signaling activities in intercellular communication	216
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	214
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	209
Quest: my postdoc home	207
BATTLES: high-throughput screening of antigen recognition under force	204
Using machine learning to predict the structure of proteins that bind to DNA and RNA	195
Non-invasive metabolic imaging of brown adipose tissue	192
Sensitive protein analysis with plexDIA	190
Tracking gene transfer using RNA tools	183
One cell, two cell, dead cell, true cell	182
From GWAS to single-cell MPRA	181
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	181
Benchmarking genomic language models	178
Road trip home to start a lab	177
ENTERing the world of immune cells	176
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	175
Host–microbiome maps	173
Peer review demystified: part 2	172
The Hodge Laplacian advances inference of single-cell trajectories	171
How developmental cell atlases inform stem cell embryo models	171
When labs welcome under-represented groups	170
Mentoring echoes down the generations	168
Author Correction: Learning single-cell perturbation responses using neural optimal transport	167
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	165
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	165
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	164
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	160
The placozoan Trichoplax	160
Setting standards for stem cells	158
The crustacean Parhyale	152
Bridging complexity and accessibility in metabolomics with MetaboApps	151
Systematic scRNA-seq screens profile neural organoid response to morphogens	151
Bat organoids at bat	144
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	143
Tardigrades	139
Computational strategies for cross-species knowledge transfer	134
Circuit manipulation with gap junctions	131

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	130
Quantum image transmission	130
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	128
Long-read sequencing in the era of epigenomics and epitranscriptomics	128
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	128
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	126
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	125
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	125
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	125
StayGold variants for molecular fusion and membrane-targeting applications	124
Indexing and searching petabase-scale nucleotide resources	124
Nicheformer: a foundation model for single-cell and spatial omics	124
Comparing classifier performance with baselines	121
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	121
The tidyomics ecosystem: enhancing omic data analyses	121
The LGBTQ+ job hunt	120
Deciphering subcellular organization with multiplexed imaging and deep learning	119
Vector choices, vector surprises	117
Neural networks built with biomolecules	117
Multimodal large language models for bioimage analysis	117
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	115
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	115
Challenges and recommendations in establishing national human diversity genomic projects	115
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	115
Science while parenting	112
A method for quantitative and base-resolution sequencing of pseudouridine	112
Inside the chase after those elusive proteoforms	112
Method of the Year: EM connectomics	112
Tackling tumor complexity with single-cell proteomics	109
Building an automated three-dimensional flight agent for neural network reconstruction	108
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	107
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	107
Differentiable simulation expands frontiers for biophysical neural models	107
A graph neural network that combines scRNA-seq and protein–protein interaction data	106
MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony	104
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	104
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	103
The evolution of embryo models	102
Combining compact human protein domains with CRISPR systems for robust gene activation	102
Enabling global image data sharing in the life sciences	101
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes	101
Merging conformational landscapes in a single consensus space with FlexConsensus algorithm	101
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability	99
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	99
Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences	99
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	98
Adaptive optical correction for in vivo two-photon fluorescence microscopy with neural fields	98
The future of bioimage analysis: a dialog between mind and machine	98
Analyzing single-cell bisulfite sequencing data with MethSCAn	98
RNA-Puzzles Round V: blind predictions of 23 RNA structures	97
SODB facilitates comprehensive exploration of spatial omics data	96
Propensity score weighting	95
Method of the Year 2024: spatial proteomics	94
CellTune: an integrative software for accurate cell classification in spatial proteomics	94
Comparison of transformations for single-cell RNA-seq data	93
Principles and challenges of modeling temporal and spatial omics data	93
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	92
Learning single-cell perturbation responses using neural optimal transport	92
Metrics reloaded: recommendations for image analysis validation	91
Lighting up oxytocin dynamics in the brain with MTRIAOT	90
First-gen scientists leap hurdles and give back	90
Image processing tools for petabyte-scale light sheet microscopy data	90
The bearded dragon Pogona vitticeps	90
Unravelling cellular interactions using flow cytometry	89
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	88
Learning the immunological repertoire	88
Author Correction: iPipet: sample handling using a tablet	88
An exceptionally photostable mScarlet3 mutant	87
ShareLoc — an open platform for sharing localization microscopy data	87
Imaging the genome in motion	86
Machine learning for accelerating discovery from single-molecule data	86
Improved structure prediction of protein complexes is within GRASP	85
Regression modeling of time-to-event data with censoring	84
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	84
Scientists who decide to pick up and move	84
A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	84
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	83
Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq	83
Modeling morphogenesis	83
Repurposing large-format microarrays for scalable spatial transcriptomics	83

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics	83
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	83
Team updates at Nature Methods	83
Deep 3D histology powered by tissue clearing, omics and AI	82
METLIN-CCS: an ion mobility spectrometry collision cross section database	81
Smart parallel automated cryo-electron tomography	80
Assessment of 3D MINFLUX data for quantitative structural biology in cells	80
Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes	80
Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase	80
Segmentation metric misinterpretations in bioimage analysis	80
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	79
Illuminating life processes by vibrational probes	79
TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing	79
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	78
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	76
Orthrus: toward evolutionary and functional RNA foundation models	76
Design and optimization of a kinase-controlled allosteric switch	76
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	75
Estimation of skeletal kinematics in freely moving rodents	75
AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput	75
A multimodal adaptive optical microscope for in vivo imaging from molecules to organisms	74
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	74
Mapping effective connectivity by virtually perturbing a surrogate brain	73
DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research	73
CAVE: Connectome Annotation Versioning Engine	73
Jasmine and Iris: population-scale structural variant comparison and analysis	72
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	72
Getting over ANOVA: estimation graphics for multi-group comparisons	71
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	71
DECODE: deep learning-based common deconvolution framework for various omics data	71
Highly multiplexed 3D profiling of cell states and immune niches in human tumors	71
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	71
A new member of the spatial omics family	70
Towards a full picture of the total transcriptome	70
Incorporating the image formation process into deep learning improves network performance	70
A peek into early human embryogenesis	70
A diamond microscope	70
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference	70
Mapping deformations and increasing quantitative accuracy in expansion microscopy	70
Augmented translation via multitailed mRNA	70
Spike sorting with Kilosort4	70
A structural learning method to uncover how information between single cells flows	69
Inferring how animals deform improves cell tracking	69
Machine learning-trained protein domain insertion for the design of switchable proteins	69
Self-supervised learning of molecular representations	69
POLCAM: instant molecular orientation microscopy for the life sciences	69
Barcoded CRISPR screens reveal RNA regulatory networks	68
Microscopes are coming for your job	68
Guinea pigs as embryo models	67
Cell typing by electrophysiology	67
Structure prediction for orphan proteins	66
Predicting cellular responses with conditional diffusion models	66
Combating hallucination in digital pathology	66
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	66
The big picture in science	66
Data sharing is the future	66
Author Correction: Segment Anything for Microscopy	65
Gapr for large-scale collaborative single-neuron reconstruction	65
Recommendations and considerations for hydroxyl radical protein footprinting–mass spectrometry	65
Open microscopy in the life sciences: quo vadis?	65
Towards predictive virtual embryos with genomics and AI	64
Predicted protein structures expand the CATH database	64
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	64
Entering the era of deep single-cell proteomics	64
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	64
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	64
Molecular pixelation: spatial proteomics of single cells by sequencing	63
Selective-plane-activation structured illumination microscopy	63
Chemical space exploration with quantum computing	63
Small data methods in omics: the power of one	62
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	61
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	61
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	61
Summer school in wartime	61
Intrinsic protein disorder at scale	61
Neural engineering with photons as synaptic transmitters	60
Seeing data as t-SNE and UMAP do	60
An image-based framework for the integrated analysis of the epithelial-to-mesenchymal transition	60
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	60
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines	60
ESPRESSO: spatiotemporal omics based on organelle phenotyping	60
JIPipe: visual batch processing for ImageJ	60
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	59
GeneAgent: self-verification language agent for gene-set analysis using domain databases	59
CaBLAM: a high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferase	59
Automated classification of cellular expression in multiplexed imaging data with Nimbus	59
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	59
A closer look at FluoroCubes	58
Development of the human head	58
Spotting T and B cell receptors	58
Next-generation expansion microscopy	57
In situ electro-sequencing	57
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	57
Fluorescent actinometers for fast and simple quantitative measurement of light intensity	56
Immune intestine interfaces in vitro	56