Nature Methods

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	7933
Interpreting and comparing neural activity across systems by geometric deep learning	1076
Tamir Gonen	984
More dimensions of the 3D genome	952
Exoskeleton empowers large-scale neural recordings in freely roaming mice	882
Modeling locomotion from environment to neurons	823
Analyzing submicron spatial transcriptomics data at their original resolution	666
Annotating unknown metabolites	636
SNAP-tag2 improves live-cell imaging	628
How noncoding RNAs began to leave the junkyard	560
Line-scanning speeds up Brillouin microscopy	502
Fast and efficient template-mediated synthesis of genetic variants	454
Detecting and correcting false transients in calcium imaging	391
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	390
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	386
Chromoscope: interactive multiscale visualization for structural variation in human genomes	359
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	344
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	335
Optimism for abundant whole-brain connectomes and connectomic screening	334
Method of the Year 2025: electron microscopy-based connectomics	291
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	285
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	284
Antibody stabilization for thermally accelerated deep immunostaining	281
BIONIC: biological network integration using convolutions	274
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	273

GWAS and eQTL disparity	265
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	264
Prediction of protein subcellular localization in single cells	261
Maximum-likelihood model fitting for quantitative analysis of SMLM data	258
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	257
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	246
Unlocking the power of spatial omics with AI	246
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	236
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	228
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	228
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	222
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	211
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	201
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	197
Efficient targeted insertion of large DNA fragments without DNA donors	194
MRIcroGL: voxel-based visualization for neuroimaging	185
BATTLES: high-throughput screening of antigen recognition under force	183
Quest: my postdoc home	183
Using machine learning to predict the structure of proteins that bind to DNA and RNA	173
Setting standards for stem cells	170
Sensitive protein analysis with plexDIA	164
Non-invasive metabolic imaging of brown adipose tissue	164
Tracking gene transfer using RNA tools	159
One cell, two cell, dead cell, true cell	158
Benchmarking genomic language models	154
The placozoan Trichoplax	154
Road trip home to start a lab	152
Author Correction: Learning single-cell perturbation responses using neural optimal transport	151
Bat organoids at bat	149
Peer review demystified: part 2	147
ENTERing the world of immune cells	147
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	145
From GWAS to single-cell MPRA	145
The crustacean Parhyale	143
The Hodge Laplacian advances inference of single-cell trajectories	140
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	138
Trawling the ocean virome	137
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	136
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	135
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	135
Computational strategies for cross-species knowledge transfer	134
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	132
Publisher Correction: Museum of spatial transcriptomics	131
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	131
Systematic scRNA-seq screens profile neural organoid response to morphogens	130
When labs welcome under-represented groups	130
Indexing and searching petabase-scale nucleotide resources	130
Long-read sequencing in the era of epigenomics and epitranscriptomics	129
How developmental cell atlases inform stem cell embryo models	127
Nicheformer: a foundation model for single-cell and spatial omics	126

The tidyomics ecosystem: enhancing omic data analyses	125
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	123
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	122
Comparing classifier performance with baselines	122
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	122
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	121
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	120
Tardigrades	120
StayGold variants for molecular fusion and membrane-targeting applications	118
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	117
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	116
A graph neural network that combines scRNA-seq and protein–protein interaction data	115
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	115
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	115
A method for quantitative and base-resolution sequencing of pseudouridine	115
Neural networks built with biomolecules	114
Deciphering subcellular organization with multiplexed imaging and deep learning	114
The LGBTQ+ job hunt	114
Science while parenting	113
Combining compact human protein domains with CRISPR systems for robust gene activation	112
What makes a Nature Methods paper	110
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	109
Building an automated three-dimensional flight agent for neural network reconstruction	108
Mackenzie Weygandt Mathis	108
Genomics beyond complete genomes	108
Merging conformational landscapes in a single consensus space with FlexConsensus algorithm	107
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	106
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	106
The future of bioimage analysis: a dialog between mind and machine	106
Vector choices, vector surprises	106
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	105
Analyzing single-cell bisulfite sequencing data with MethSCAn	105
Inside the chase after those elusive proteoforms	104
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	103
Multimodal large language models for bioimage analysis	102
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes	101
RNA-Puzzles Round V: blind predictions of 23 RNA structures	101
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	100
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	100
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	99
Tackling tumor complexity with single-cell proteomics	99
Propensity score weighting	98
CAD we share? Publishing reproducible microscope hardware	98
Method of the Year: protein structure prediction	98
MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony	97
Enabling global image data sharing in the life sciences	96
Method of the Year: EM connectomics	95
Differentiable simulation expands frontiers for biophysical neural models	94
Image processing tools for petabyte-scale light sheet microscopy data	93
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	93
The evolution of embryo models	93
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	92
Comparison of transformations for single-cell RNA-seq data	91
Metrics reloaded: recommendations for image analysis validation	91
SODB facilitates comprehensive exploration of spatial omics data	91
Principles and challenges of modeling temporal and spatial omics data	91
Learning single-cell perturbation responses using neural optimal transport	89
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	89
Method of the Year 2024: spatial proteomics	89
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	88
Lighting up oxytocin dynamics in the brain with MTRIAOT	88
Modeling morphogenesis	87
Publisher Correction: Fast and flexible analysis of linked microbiome data with mako	87
First-gen scientists leap hurdles and give back	87
The bearded dragon Pogona vitticeps	86
Learning the immunological repertoire	85
Regression modeling of time-to-event data with censoring	85
Author Correction: iPipet: sample handling using a tablet	85
An exceptionally photostable mScarlet3 mutant	84
Estimation of skeletal kinematics in freely moving rodents	84
Unravelling cellular interactions using flow cytometry	84
Assessment of 3D MINFLUX data for quantitative structural biology in cells	84
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	83
Imaging the genome in motion	83
Machine learning for accelerating discovery from single-molecule data	83
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	82
Improved structure prediction of protein complexes is within GRASP	82
A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	81
ShareLoc — an open platform for sharing localization microscopy data	81
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	79

Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes	78
TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing	78
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	77
Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase	77
Segmentation metric misinterpretations in bioimage analysis	76
Deep 3D histology powered by tissue clearing, omics and AI	76
Jasmine and Iris: population-scale structural variant comparison and analysis	76
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference	74
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	74
Illuminating life processes by vibrational probes	73
Smart parallel automated cryo-electron tomography	73
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	72
METLIN-CCS: an ion mobility spectrometry collision cross section database	72
CAVE: Connectome Annotation Versioning Engine	72
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	71
Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq	71
The impact of AlphaFold2 one year on	71
Repurposing large-format microarrays for scalable spatial transcriptomics	70
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	69
Mapping effective connectivity by virtually perturbing a surrogate brain	69
DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research	69
Incorporating the image formation process into deep learning improves network performance	69
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	68
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	68
Spike sorting with Kilosort4	68
Sequencing RNA isoforms in brain tissue	67
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	67
Augmented translation via multitailed mRNA	67
Highly multiplexed 3D profiling of cell states and immune niches in human tumors	67
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	67
Towards a full picture of the total transcriptome	67
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	67
A diamond microscope	66
A new member of the spatial omics family	66
Mapping deformations and increasing quantitative accuracy in expansion microscopy	66
ScanNet uncovers binding motifs in protein structures with deep learning	65
Predicted protein structures expand the CATH database	65
A peek into early human embryogenesis	65
Summer school in wartime	64
A structural learning method to uncover how information between single cells flows	64
Author Correction: Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	63
Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model	63
Author Correction: Segment Anything for Microscopy	63
Predicting cellular responses with conditional diffusion models	63
Data sharing is the future	62
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	62
Selective-plane-activation structured illumination microscopy	62
Chemical space exploration with quantum computing	62
ESPRESSO: spatiotemporal omics based on organelle phenotyping	62
CaBLAM: a high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferase	62
Structure prediction for orphan proteins	62
Barcoded CRISPR screens reveal RNA regulatory networks	61
Guinea pigs as embryo models	60
Combating hallucination in digital pathology	60
Inferring how animals deform improves cell tracking	60
The big picture in science	59
Cell typing by electrophysiology	59
Entering the era of deep single-cell proteomics	59
Self-supervised learning of molecular representations	58
Machine learning-trained protein domain insertion for the design of switchable proteins	58
Intrinsic protein disorder at scale	58
Open microscopy in the life sciences: quo vadis?	58
Automated classification of cellular expression in multiplexed imaging data with Nimbus	57
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	56
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	56
Gapr for large-scale collaborative single-neuron reconstruction	56
Microscopes are coming for your job	56
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	56
POLCAM: instant molecular orientation microscopy for the life sciences	56
GeneAgent: self-verification language agent for gene-set analysis using domain databases	56
Long-read mapping to repetitive reference sequences using Winnowmap2	55
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	55
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	55
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines	55
JIPipe: visual batch processing for ImageJ	55
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	55
Seeing data as t-SNE and UMAP do	55
Multi-animal pose estimation, identification and tracking with DeepLabCut	54
Protein structure predictions to atomic accuracy with AlphaFold	54
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	54
Small data methods in omics: the power of one	54
Neural engineering with photons as synaptic transmitters	53
Development of the human head	53
A closer look at FluoroCubes	53
Molecular pixelation: spatial proteomics of single cells by sequencing	53
Spotting T and B cell receptors	53
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	53
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	53
Peter Sorger	53
In situ electro-sequencing	52
Fluorescent actinometers for fast and simple quantitative measurement of light intensity	52
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	52
A genome-scale approach for determining the function of phosphorylation sites	52
Next-generation expansion microscopy	52
Immune intestine interfaces in vitro	51