Nature Methods

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	6972
Tamir Gonen	1240
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	884
Modeling locomotion from environment to neurons	864
More dimensions of the 3D genome	801
Exoskeleton empowers large-scale neural recordings in freely roaming mice	797
Analyzing submicron spatial transcriptomics data at their original resolution	775
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	684
GWAS and eQTL disparity	670
Annotating unknown metabolites	590
Chromoscope: interactive multiscale visualization for structural variation in human genomes	575
How noncoding RNAs began to leave the junkyard	548
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	518
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	464
Unlocking the power of spatial omics with AI	407
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	385
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	381
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	360
Line-scanning speeds up Brillouin microscopy	337
Detecting and correcting false transients in calcium imaging	337
Fast and efficient template-mediated synthesis of genetic variants	309
Maximum-likelihood model fitting for quantitative analysis of SMLM data	293
Prediction of protein subcellular localization in single cells	277
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	261
Antibody stabilization for thermally accelerated deep immunostaining	257

MRIcroGL: voxel-based visualization for neuroimaging	257
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	255
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	237
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	231
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	225
BIONIC: biological network integration using convolutions	222
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	221
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	219
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	216
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	214
Efficient targeted insertion of large DNA fragments without DNA donors	210
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	205
Using machine learning to predict the structure of proteins that bind to DNA and RNA	205
ENTERing the world of immune cells	204
BATTLES: high-throughput screening of antigen recognition under force	203
Quest: my postdoc home	200
Non-invasive metabolic imaging of brown adipose tissue	192
Sensitive protein analysis with plexDIA	191
Setting standards for stem cells	186
Trawling the ocean virome	183
The crustacean Parhyale	182
From GWAS to single-cell MPRA	180
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	175
Comparing classifier performance with baselines	175
Bat organoids at bat	172
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	172
Long-read sequencing in the era of epigenomics and epitranscriptomics	171
Indexing and searching petabase-scale nucleotide resources	171
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	169
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	166
The tidyomics ecosystem: enhancing omic data analyses	164
One cell, two cell, dead cell, true cell	162
How developmental cell atlases inform stem cell embryo models	162
Author Correction: Learning single-cell perturbation responses using neural optimal transport	162
Peer review demystified: part 2	158
Tardigrades	157
Tracking gene transfer using RNA tools	155
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	154
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	153
Publisher Correction: Museum of spatial transcriptomics	149
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	147
When labs welcome under-represented groups	147
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	146
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	145
The placozoan Trichoplax	144
StayGold variants for molecular fusion and membrane-targeting applications	143
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	141
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	140
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	132
LIVECell—A large-scale dataset for label-free live cell segmentation	131

Deciphering subcellular organization with multiplexed imaging and deep learning	130
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	130
The LGBTQ+ job hunt	130
Neural networks built with biomolecules	130
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	130
A method for quantitative and base-resolution sequencing of pseudouridine	127
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	122
A graph neural network that combines scRNA-seq and protein–protein interaction data	122
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	121
The future of bioimage analysis: a dialog between mind and machine	120
Science while parenting	120
What makes a Nature Methods paper	119
Combining compact human protein domains with CRISPR systems for robust gene activation	114
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	114
Building an automated three-dimensional flight agent for neural network reconstruction	111
Genomics beyond complete genomes	111
Mackenzie Weygandt Mathis	111
Vector choices, vector surprises	110
Multimodal large language models for bioimage analysis	110
Propensity score weighting	109
Method of the Year: protein structure prediction	109
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	108
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	107
CAD we share? Publishing reproducible microscope hardware	106
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	105
Tackling tumor complexity with single-cell proteomics	104
Enabling global image data sharing in the life sciences	103
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	102
Image processing tools for petabyte-scale light sheet microscopy data	102
Comparison of transformations for single-cell RNA-seq data	101
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes	101
The evolution of embryo models	100
SODB facilitates comprehensive exploration of spatial omics data	99
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	99
A guide to the optogenetic regulation of endogenous molecules	99
Analyzing single-cell bisulfite sequencing data with MethSCAn	98
Inside the chase after those elusive proteoforms	97
Principles and challenges of modeling temporal and spatial omics data	96
Method of the Year 2024: spatial proteomics	95
RNA-Puzzles Round V: blind predictions of 23 RNA structures	95
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	94
Metrics reloaded: recommendations for image analysis validation	94
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	93
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	93
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	93
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	93
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	92
Learning single-cell perturbation responses using neural optimal transport	92
Lighting up oxytocin dynamics in the brain with MTRIAOT	92
Publisher Correction: Fast and flexible analysis of linked microbiome data with mako	91
Modeling morphogenesis	91
Author Correction: Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	91
Incorporating the image formation process into deep learning improves network performance	90
First-gen scientists leap hurdles and give back	90
Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq	90
Trapping virus in a shell	90
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	89
Segmentation metric misinterpretations in bioimage analysis	88
Learning the immunological repertoire	88
What makes an author	88
Regression modeling of time-to-event data with censoring	87
A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	86
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	85
The bearded dragon Pogona vitticeps	83
Repurposing large-format microarrays for scalable spatial transcriptomics	83
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	82
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	82
Assessment of 3D MINFLUX data for quantitative structural biology in cells	82
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	81
Smart parallel automated cryo-electron tomography	81
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference	80
Mapping effective connectivity by virtually perturbing a surrogate brain	80
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	80
CAVE: Connectome Annotation Versioning Engine	80
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	79
Jasmine and Iris: population-scale structural variant comparison and analysis	78
DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research	78
Illuminating life processes by vibrational probes	78
Deep 3D histology powered by tissue clearing, omics and AI	78
Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes	78

A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	77
ShareLoc — an open platform for sharing localization microscopy data	77
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	76
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	76
An exceptionally photostable mScarlet3 mutant	75
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	75
Estimation of skeletal kinematics in freely moving rodents	75
The impact of AlphaFold2 one year on	74
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	74
Spike sorting with Kilosort4	74
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	74
METLIN-CCS: an ion mobility spectrometry collision cross section database	73
Towards a full picture of the total transcriptome	72
Sequencing RNA isoforms in brain tissue	72
A new member of the spatial omics family	72
Augmented translation via multitailed mRNA	71
A peek into early human embryogenesis	71
A diamond microscope	71
Mapping deformations and increasing quantitative accuracy in expansion microscopy	70
Predicted protein structures expand the CATH database	70
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	70
Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model	69
Author Correction: Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	69
Summer school in wartime	68
Neural engineering with photons as synaptic transmitters	68
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	67
GeneAgent: self-verification language agent for gene-set analysis using domain databases	67
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	67
Selective-plane-activation structured illumination microscopy	67
A structural learning method to uncover how information between single cells flows	66
POLCAM: instant molecular orientation microscopy for the life sciences	66
ScanNet uncovers binding motifs in protein structures with deep learning	66
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	66
Small data methods in omics: the power of one	66
Gapr for large-scale collaborative single-neuron reconstruction	66
Self-supervised learning of molecular representations	65
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	65
Author Correction: Segment Anything for Microscopy	64
Structure prediction for orphan proteins	63
The big picture in science	63
Molecular pixelation: spatial proteomics of single cells by sequencing	62
Open microscopy in the life sciences: quo vadis?	61
Microscopes are coming for your job	61
JIPipe: visual batch processing for ImageJ	61
Chemical space exploration with quantum computing	60
Barcoded CRISPR screens reveal RNA regulatory networks	60
Data sharing is the future	60
Entering the era of deep single-cell proteomics	60
Guinea pigs as embryo models	60
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	59
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	59
Long-read mapping to repetitive reference sequences using Winnowmap2	59
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	59
Seeing data as t-SNE and UMAP do	59
Protein structure predictions to atomic accuracy with AlphaFold	58
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	58
Inferring how animals deform improves cell tracking	58
Multi-animal pose estimation, identification and tracking with DeepLabCut	58
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	58
Spotting T and B cell receptors	57
Development of the human head	56
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	56
Base editing in mitochondrial DNA	56
Peter Sorger	56
A closer look at FluoroCubes	56
In situ electro-sequencing	56
Immune intestine interfaces in vitro	55
Completing human genomes	55
Extended culture of 2D gastruloids to model human mesoderm development	55
Next-generation expansion microscopy	55
Fluorescent actinometers for fast and simple quantitative measurement of light intensity	55
FIOLA: an accelerated pipeline for fluorescence imaging online analysis	55
A genome-scale approach for determining the function of phosphorylation sites	55
Hydrogel fibers that enable optogenetic pain inhibition during locomotion	55
Year in review 2023	54
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation	54
A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments	54
Not if but when nanopore protein sequencing meets single-cell proteomics	53
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible	53
3D reconstruction of spatial expression	53
The Cell Tracking Challenge: 10 years of objective benchmarking	53
Miniature three-photon microscopy maximized for scattered fluorescence collection	53
CarboTag: a modular approach for live and functional imaging of plant cell walls	53
Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq	53
TREX reveals proteins that bind to specific RNA regions in living cells	52
Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla	52
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology	52
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging	52
Parallel cryo electron tomography on in situ lamellae	52
From 2D to 3D and beyond: the evolution and impact of in vitro tumor models in cancer research	52
Challenges and perspectives in computational deconvolution of genomics data	52
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads	52
Adventures in AI	51
Dissecting gene regulation with multimodal sequencing	51
Diving deeper in the 3D genome	51