Nature Methods

Article	Citations
Chromoscope: interactive multiscale visualization for structural variation in human genomes	6287
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	1091
Interpreting and comparing neural activity across systems by geometric deep learning	786
Tamir Gonen	727
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	716
Modeling locomotion from environment to neurons	696
More dimensions of the 3D genome	678
How noncoding RNAs began to leave the junkyard	675
Exoskeleton empowers large-scale neural recordings in freely roaming mice	607
Analyzing submicron spatial transcriptomics data at their original resolution	603
GWAS and eQTL disparity	535
Maximum-likelihood model fitting for quantitative analysis of SMLM data	503
Annotating unknown metabolites	439
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	423
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	417
Line-scanning speeds up Brillouin microscopy	328
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	322
Detecting and correcting false transients in calcium imaging	306
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	300
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	287
Antibody stabilization for thermally accelerated deep immunostaining	282
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	264
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	259
Fast and efficient template-mediated synthesis of genetic variants	259
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	248

DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	246
Unlocking the power of spatial omics with AI	244
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	241
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	236
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	231
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	222
Understanding the invisible hands of sample preparation for cryo-EM	220
Efficient targeted insertion of large DNA fragments without DNA donors	220
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	217
BIONIC: biological network integration using convolutions	216
Best practices and tools for reporting reproducible fluorescence microscopy methods	209
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	204
When labs welcome under-represented groups	198
Using machine learning to predict the structure of proteins that bind to DNA and RNA	198
ENTERing the world of immune cells	196
BATTLES: high-throughput screening of antigen recognition under force	196
Quest: my postdoc home	187
Non-invasive metabolic imaging of brown adipose tissue	186
Setting standards for stem cells	186
Sensitive protein analysis with plexDIA	186
From GWAS to single-cell MPRA	184
Publisher Correction: Museum of spatial transcriptomics	183
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	175
wwPDB biocuration: on the front line of structural biology	172
Tardigrades	169
Trawling the ocean virome	165
Long-read sequencing in the era of epigenomics and epitranscriptomics	162
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	161
Comparing classifier performance with baselines	159
The placozoan Trichoplax	158
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	158
Peer review demystified: part 2	158
Author Correction: Learning single-cell perturbation responses using neural optimal transport	157
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	156
How developmental cell atlases inform stem cell embryo models	156
One cell, two cell, dead cell, true cell	155
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	155
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	154
Indexing and searching petabase-scale nucleotide resources	152
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	152
The crustacean Parhyale	150
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	148
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	148
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	146
LIVECell—A large-scale dataset for label-free live cell segmentation	144
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	143
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	143
The tidyomics ecosystem: enhancing omic data analyses	142
StayGold variants for molecular fusion and membrane-targeting applications	141
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	139

The LGBTQ+ job hunt	136
Deciphering subcellular organization with multiplexed imaging and deep learning	135
Neural networks built with biomolecules	132
A method for quantitative and base-resolution sequencing of pseudouridine	130
A graph neural network that combines scRNA-seq and protein–protein interaction data	129
Image processing tools for petabyte-scale light sheet microscopy data	126
Enabling global image data sharing in the life sciences	126
Inside the chase after those elusive proteoforms	123
Analyzing single-cell bisulfite sequencing data with MethSCAn	122
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	122
Tackling tumor complexity with single-cell proteomics	122
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	122
The future of bioimage analysis: a dialog between mind and machine	120
Method of the Year 2024: spatial proteomics	119
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	119
Propensity score weighting	118
SODB facilitates comprehensive exploration of spatial omics data	117
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	117
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	115
Comparison of transformations for single-cell RNA-seq data	114
What makes a Nature Methods paper	113
Science while parenting	113
Combining compact human protein domains with CRISPR systems for robust gene activation	113
Multimodal large language models for bioimage analysis	110
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	109
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	109
CAD we share? Publishing reproducible microscope hardware	108
Building an automated three-dimensional flight agent for neural network reconstruction	107
Method of the Year: protein structure prediction	105
Mackenzie Weygandt Mathis	105
Genomics beyond complete genomes	104
Vector choices, vector surprises	103
A guide to the optogenetic regulation of endogenous molecules	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	100
Learning single-cell perturbation responses using neural optimal transport	98
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	98
The evolution of embryo models	97
Metrics reloaded: recommendations for image analysis validation	96
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	96
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	96
Principles and challenges of modeling temporal and spatial omics data	95
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	95
Lighting up oxytocin dynamics in the brain with MTRIAOT	95
What makes an author	94
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	94
Assessment of 3D MINFLUX data for quantitative structural biology in cells	93
Repurposing large-format microarrays for scalable spatial transcriptomics	93
The bearded dragon Pogona vitticeps	92
Publisher Correction: Fast and flexible analysis of linked microbiome data with mako	92
Author Correction: Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	91
Modeling morphogenesis	90
Trapping virus in a shell	90
First-gen scientists leap hurdles and give back	90
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	89
The impact of AlphaFold2 one year on	89
Learning the immunological repertoire	89
Segmentation metric misinterpretations in bioimage analysis	88
Deep 3D histology powered by tissue clearing, omics and AI	87
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	87
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	86
An exceptionally photostable mScarlet3 mutant	85
Mapping effective connectivity by virtually perturbing a surrogate brain	84
A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells	84
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	84
Regression modeling of time-to-event data with censoring	83
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	83
A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	83
Estimation of skeletal kinematics in freely moving rodents	82
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	82
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	82
METLIN-CCS: an ion mobility spectrometry collision cross section database	82
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	81
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	80
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	79
Jasmine and Iris: population-scale structural variant comparison and analysis	79
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	79
ShareLoc — an open platform for sharing localization microscopy data	79
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	78
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	78

Incorporating the image formation process into deep learning improves network performance	78
Spike sorting with Kilosort4	78
CAVE: Connectome Annotation Versioning Engine	78
Smart parallel automated cryo-electron tomography	77
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	77
Sequencing RNA isoforms in brain tissue	76
Towards a full picture of the total transcriptome	75
A new member of the spatial omics family	75
A diamond microscope	74
Augmented translation via multitailed mRNA	73
Predicted protein structures expand the CATH database	73
A peek into early human embryogenesis	73
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	72
Mapping deformations and increasing quantitative accuracy in expansion microscopy	72
Inferring how animals deform improves cell tracking	72
Author Correction: Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	71
Open microscopy in the life sciences: quo vadis?	71
Neural engineering with photons as synaptic transmitters	70
Single-cell multiomics to probe relationships between histone modifications and transcription	70
Expanding capabilities and infrastructure for cryo-EM	70
Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model	70
Gapr for large-scale collaborative single-neuron reconstruction	69
Summer school in wartime	69
Microscopes are coming for your job	69
A structural learning method to uncover how information between single cells flows	68
ScanNet uncovers binding motifs in protein structures with deep learning	68
Entering the era of deep single-cell proteomics	67
Chemical space exploration with quantum computing	67
JIPipe: visual batch processing for ImageJ	66
The big picture in science	66
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	66
Molecular pixelation: spatial proteomics of single cells by sequencing	66
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	65
Data sharing is the future	65
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	63
Seeing data as t-SNE and UMAP do	63
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	63
POLCAM: instant molecular orientation microscopy for the life sciences	63
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	63
Structure prediction for orphan proteins	63
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	62
Long-read mapping to repetitive reference sequences using Winnowmap2	62
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	62
Protein structure predictions to atomic accuracy with AlphaFold	61
Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution	61
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	61
Small data methods in omics: the power of one	60
Selective-plane-activation structured illumination microscopy	59
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	59
Multi-animal pose estimation, identification and tracking with DeepLabCut	59
Year in review 2023	58
Spotting T and B cell receptors	58
Development of the human head	58
Base editing in mitochondrial DNA	58
In situ electro-sequencing	57
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	57
A closer look at FluoroCubes	57
Peter Sorger	57
A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments	56
Hydrogel fibers that enable optogenetic pain inhibition during locomotion	56
Fluorescent actinometers for fast and simple quantitative measurement of light intensity	56
Completing human genomes	56
Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq	56
Next-generation expansion microscopy	55
A genome-scale approach for determining the function of phosphorylation sites	55
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads	54
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation	54
3D reconstruction of spatial expression	54
Immune intestine interfaces in vitro	54
Not if but when nanopore protein sequencing meets single-cell proteomics	53
A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM	53
Challenges and perspectives in computational deconvolution of genomics data	53
Miniature three-photon microscopy maximized for scattered fluorescence collection	53
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging	53
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible	52
FIOLA: an accelerated pipeline for fluorescence imaging online analysis	52
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
Diving deeper in the 3D genome	51
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology	51
Parallel cryo electron tomography on in situ lamellae	51
Dissecting gene regulation with multimodal sequencing	51
The Cell Tracking Challenge: 10 years of objective benchmarking	51
Jie Xiao	50
A method to map single-cell lineages in the mouse brain by CRISPR-based barcoding	50
Adventures in AI	50
Nanopores distinguish RNA modifications	50
Optimal transport for single-cell genomics	49
HYBRiD: a simple method for clearing and visualizing mammalian bodies	49
A celebration of structural biology	49
Combined sequencing of genomes and epigenomes	49
SCUBA-D: a freshly trained diffusion model generates high-quality protein structures	49
Enhancing functional gene set analysis with large language models	49
3D holograms of embryos	48
Identification of phosphosites that alter protein thermal stability	48