Nature Methods

Article	Citations
Chromoscope: interactive multiscale visualization for structural variation in human genomes	6528
Interpreting and comparing neural activity across systems by geometric deep learning	1146
Tamir Gonen	823
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	778
Modeling locomotion from environment to neurons	736
More dimensions of the 3D genome	716
Exoskeleton empowers large-scale neural recordings in freely roaming mice	715
Analyzing submicron spatial transcriptomics data at their original resolution	703
GWAS and eQTL disparity	626
Annotating unknown metabolites	621
Line-scanning speeds up Brillouin microscopy	549
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	516
Antibody stabilization for thermally accelerated deep immunostaining	469
Unlocking the power of spatial omics with AI	466
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	431
Fast and efficient template-mediated synthesis of genetic variants	346
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	343
Prediction of protein subcellular localization in single cells	318
Best practices and tools for reporting reproducible fluorescence microscopy methods	317
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	316
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	292
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	291
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	268
Maximum-likelihood model fitting for quantitative analysis of SMLM data	264
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	256

SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	250
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	243
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	241
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	233
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	228
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	225
Efficient targeted insertion of large DNA fragments without DNA donors	224
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	218
How noncoding RNAs began to leave the junkyard	207
BIONIC: biological network integration using convolutions	205
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	203
Detecting and correcting false transients in calcium imaging	203
Using machine learning to predict the structure of proteins that bind to DNA and RNA	202
When labs welcome under-represented groups	197
ENTERing the world of immune cells	195
BATTLES: high-throughput screening of antigen recognition under force	194
Quest: my postdoc home	191
Non-invasive metabolic imaging of brown adipose tissue	190
Sensitive protein analysis with plexDIA	188
Trawling the ocean virome	178
Setting standards for stem cells	178
The tidyomics ecosystem: enhancing omic data analyses	178
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	171
The crustacean Parhyale	171
Comparing classifier performance with baselines	170
Peer review demystified: part 2	168
The placozoan Trichoplax	167
Author Correction: Learning single-cell perturbation responses using neural optimal transport	165
How developmental cell atlases inform stem cell embryo models	164
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	163
One cell, two cell, dead cell, true cell	163
Tardigrades	162
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	162
Publisher Correction: Museum of spatial transcriptomics	161
Tracking gene transfer using RNA tools	159
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	156
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	154
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	153
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	152
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	151
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	151
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	146
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	145
StayGold variants for molecular fusion and membrane-targeting applications	145
Long-read sequencing in the era of epigenomics and epitranscriptomics	144
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	141
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	139
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	138
Indexing and searching petabase-scale nucleotide resources	135
From GWAS to single-cell MPRA	135

LIVECell—A large-scale dataset for label-free live cell segmentation	135
Deciphering subcellular organization with multiplexed imaging and deep learning	131
The LGBTQ+ job hunt	131
A graph neural network that combines scRNA-seq and protein–protein interaction data	130
A method for quantitative and base-resolution sequencing of pseudouridine	130
Neural networks built with biomolecules	130
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	127
Enabling global image data sharing in the life sciences	127
The future of bioimage analysis: a dialog between mind and machine	124
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	124
Propensity score weighting	124
Science while parenting	123
Multimodal large language models for bioimage analysis	122
Combining compact human protein domains with CRISPR systems for robust gene activation	122
What makes a Nature Methods paper	122
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	120
Building an automated three-dimensional flight agent for neural network reconstruction	118
Method of the Year: protein structure prediction	117
Mackenzie Weygandt Mathis	115
Genomics beyond complete genomes	113
Vector choices, vector surprises	112
CAD we share? Publishing reproducible microscope hardware	111
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	110
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	110
A guide to the optogenetic regulation of endogenous molecules	109
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	105
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	103
Comparison of transformations for single-cell RNA-seq data	103
Tackling tumor complexity with single-cell proteomics	103
Image processing tools for petabyte-scale light sheet microscopy data	101
SODB facilitates comprehensive exploration of spatial omics data	101
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes	100
The evolution of embryo models	100
Principles and challenges of modeling temporal and spatial omics data	99
Analyzing single-cell bisulfite sequencing data with MethSCAn	98
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	98
Method of the Year 2024: spatial proteomics	97
Learning single-cell perturbation responses using neural optimal transport	96
RNA-Puzzles Round V: blind predictions of 23 RNA structures	96
Inside the chase after those elusive proteoforms	96
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	95
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	94
Metrics reloaded: recommendations for image analysis validation	93
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	93
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	93
What makes an author	92
Lighting up oxytocin dynamics in the brain with MTRIAOT	92
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	92
The bearded dragon Pogona vitticeps	90
Publisher Correction: Fast and flexible analysis of linked microbiome data with mako	89
Modeling morphogenesis	89
Author Correction: Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	89
First-gen scientists leap hurdles and give back	88
An exceptionally photostable mScarlet3 mutant	88
Learning the immunological repertoire	88
Trapping virus in a shell	88
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	86
The impact of AlphaFold2 one year on	86
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	85
Mapping effective connectivity by virtually perturbing a surrogate brain	85
A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	85
Regression modeling of time-to-event data with censoring	85
Smart parallel automated cryo-electron tomography	84
Illuminating life processes by vibrational probes	84
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	83
Jasmine and Iris: population-scale structural variant comparison and analysis	83
Assessment of 3D MINFLUX data for quantitative structural biology in cells	83
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	82
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	82
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	81
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	80
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	80
Estimation of skeletal kinematics in freely moving rodents	79
METLIN-CCS: an ion mobility spectrometry collision cross section database	78
Repurposing large-format microarrays for scalable spatial transcriptomics	77
Deep 3D histology powered by tissue clearing, omics and AI	77
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	77
ShareLoc — an open platform for sharing localization microscopy data	76
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	76
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	75

Segmentation metric misinterpretations in bioimage analysis	75
CAVE: Connectome Annotation Versioning Engine	75
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	74
Sequencing RNA isoforms in brain tissue	73
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	73
Spike sorting with Kilosort4	73
Incorporating the image formation process into deep learning improves network performance	73
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	73
A diamond microscope	72
Towards a full picture of the total transcriptome	72
A new member of the spatial omics family	72
Augmented translation via multitailed mRNA	72
Predicted protein structures expand the CATH database	71
A peek into early human embryogenesis	71
Inferring how animals deform improves cell tracking	70
Author Correction: Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	70
Mapping deformations and increasing quantitative accuracy in expansion microscopy	70
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	70
Neural engineering with photons as synaptic transmitters	68
A structural learning method to uncover how information between single cells flows	68
Summer school in wartime	68
Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model	68
Gapr for large-scale collaborative single-neuron reconstruction	68
Entering the era of deep single-cell proteomics	67
ScanNet uncovers binding motifs in protein structures with deep learning	67
Chemical space exploration with quantum computing	67
Data sharing is the future	66
The big picture in science	66
POLCAM: instant molecular orientation microscopy for the life sciences	66
Structure prediction for orphan proteins	65
Small data methods in omics: the power of one	65
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	65
JIPipe: visual batch processing for ImageJ	65
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	64
Selective-plane-activation structured illumination microscopy	64
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	64
Long-read mapping to repetitive reference sequences using Winnowmap2	62
Barcoded CRISPR screens reveal RNA regulatory networks	62
Microscopes are coming for your job	62
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	62
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	61
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	61
Molecular pixelation: spatial proteomics of single cells by sequencing	61
Seeing data as t-SNE and UMAP do	59
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	59
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	59
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	59
Protein structure predictions to atomic accuracy with AlphaFold	59
Multi-animal pose estimation, identification and tracking with DeepLabCut	59
Open microscopy in the life sciences: quo vadis?	59
Base editing in mitochondrial DNA	58
Development of the human head	58
Spotting T and B cell receptors	58
A closer look at FluoroCubes	57
Completing human genomes	56
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	56
Fluorescent actinometers for fast and simple quantitative measurement of light intensity	56
Peter Sorger	56
Hydrogel fibers that enable optogenetic pain inhibition during locomotion	56
In situ electro-sequencing	56
A genome-scale approach for determining the function of phosphorylation sites	55
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation	55
Immune intestine interfaces in vitro	55
Extended culture of 2D gastruloids to model human mesoderm development	55
Next-generation expansion microscopy	55
Miniature three-photon microscopy maximized for scattered fluorescence collection	54
3D reconstruction of spatial expression	54
CarboTag: a modular approach for live and functional imaging of plant cell walls	53
Year in review 2023	53
TREX reveals proteins that bind to specific RNA regions in living cells	52
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible	52
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging	52
Challenges and perspectives in computational deconvolution of genomics data	52
Not if but when nanopore protein sequencing meets single-cell proteomics	52
FIOLA: an accelerated pipeline for fluorescence imaging online analysis	52
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads	52
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology	51
Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla	51
A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments	51
Parallel cryo electron tomography on in situ lamellae	51
Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq	50
Nanopores distinguish RNA modifications	50
Diving deeper in the 3D genome	50
A method to map single-cell lineages in the mouse brain by CRISPR-based barcoding	50
The Cell Tracking Challenge: 10 years of objective benchmarking	50
Dissecting gene regulation with multimodal sequencing	50
Adventures in AI	50
3D holograms of embryos	49
Optimal transport for single-cell genomics	49
Enhancing functional gene set analysis with large language models	49
SCUBA-D: a freshly trained diffusion model generates high-quality protein structures	49
HYBRiD: a simple method for clearing and visualizing mammalian bodies	49
Fast and flexible analysis of linked microbiome data with mako	48
CRISPR inspirations from nature	48
Unlocking human immune system complexity through AI	48