Nature Methods

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	7173
Tamir Gonen	1273
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	901
Modeling locomotion from environment to neurons	899
More dimensions of the 3D genome	831
Exoskeleton empowers large-scale neural recordings in freely roaming mice	824
Analyzing submicron spatial transcriptomics data at their original resolution	817
Annotating unknown metabolites	705
Chromoscope: interactive multiscale visualization for structural variation in human genomes	688
How noncoding RNAs began to leave the junkyard	629
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	614
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	562
Detecting and correcting false transients in calcium imaging	544
Line-scanning speeds up Brillouin microscopy	428
Fast and efficient template-mediated synthesis of genetic variants	421
GWAS and eQTL disparity	399
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	386
BIONIC: biological network integration using convolutions	348
Maximum-likelihood model fitting for quantitative analysis of SMLM data	348
MRIcroGL: voxel-based visualization for neuroimaging	319
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	314
Prediction of protein subcellular localization in single cells	285
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	276
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	263
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	259

MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	242
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	237
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	235
Antibody stabilization for thermally accelerated deep immunostaining	233
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	230
Unlocking the power of spatial omics with AI	228
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	228
Efficient targeted insertion of large DNA fragments without DNA donors	223
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	219
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	215
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	213
Using machine learning to predict the structure of proteins that bind to DNA and RNA	210
ENTERing the world of immune cells	210
BATTLES: high-throughput screening of antigen recognition under force	205
Quest: my postdoc home	196
Non-invasive metabolic imaging of brown adipose tissue	192
Setting standards for stem cells	189
Sensitive protein analysis with plexDIA	189
Trawling the ocean virome	189
From GWAS to single-cell MPRA	186
Bat organoids at bat	185
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	182
Indexing and searching petabase-scale nucleotide resources	179
Comparing classifier performance with baselines	179
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	179
When labs welcome under-represented groups	178
The crustacean Parhyale	173
Road trip home to start a lab	171
The tidyomics ecosystem: enhancing omic data analyses	167
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	167
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	163
The placozoan Trichoplax	162
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	161
Publisher Correction: Museum of spatial transcriptomics	160
Author Correction: Learning single-cell perturbation responses using neural optimal transport	159
One cell, two cell, dead cell, true cell	157
How developmental cell atlases inform stem cell embryo models	157
Peer review demystified: part 2	152
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	151
Tracking gene transfer using RNA tools	148
Tardigrades	147
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	146
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	144
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	137
Long-read sequencing in the era of epigenomics and epitranscriptomics	136
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	135
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	134
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	131
StayGold variants for molecular fusion and membrane-targeting applications	129
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	128

Detection of m6A from direct RNA sequencing using a multiple instance learning framework	125
The LGBTQ+ job hunt	123
Deciphering subcellular organization with multiplexed imaging and deep learning	122
A method for quantitative and base-resolution sequencing of pseudouridine	121
Neural networks built with biomolecules	121
The future of bioimage analysis: a dialog between mind and machine	120
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	120
A graph neural network that combines scRNA-seq and protein–protein interaction data	120
Inside the chase after those elusive proteoforms	118
Principles and challenges of modeling temporal and spatial omics data	118
Science while parenting	115
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	115
What makes a Nature Methods paper	114
Combining compact human protein domains with CRISPR systems for robust gene activation	113
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	112
Mackenzie Weygandt Mathis	111
Building an automated three-dimensional flight agent for neural network reconstruction	111
Genomics beyond complete genomes	110
Vector choices, vector surprises	107
Propensity score weighting	105
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	105
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	104
Tackling tumor complexity with single-cell proteomics	103
Image processing tools for petabyte-scale light sheet microscopy data	103
Enabling global image data sharing in the life sciences	103
Analyzing single-cell bisulfite sequencing data with MethSCAn	102
Comparison of transformations for single-cell RNA-seq data	101
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	101
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	100
SODB facilitates comprehensive exploration of spatial omics data	100
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	100
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	99
RNA-Puzzles Round V: blind predictions of 23 RNA structures	99
CAD we share? Publishing reproducible microscope hardware	98
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	98
The evolution of embryo models	97
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	97
Multimodal large language models for bioimage analysis	96
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	96
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes	96
Learning single-cell perturbation responses using neural optimal transport	95
Metrics reloaded: recommendations for image analysis validation	95
Method of the Year 2024: spatial proteomics	95
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	95
Lighting up oxytocin dynamics in the brain with MTRIAOT	93
Method of the Year: protein structure prediction	93
Author Correction: Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	92
Publisher Correction: Fast and flexible analysis of linked microbiome data with mako	92
Modeling morphogenesis	92
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	92
First-gen scientists leap hurdles and give back	91
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	90
Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq	90
Incorporating the image formation process into deep learning improves network performance	90
What makes an author	89
Segmentation metric misinterpretations in bioimage analysis	88
Mapping effective connectivity by virtually perturbing a surrogate brain	87
Learning the immunological repertoire	86
A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	85
Repurposing large-format microarrays for scalable spatial transcriptomics	85
Regression modeling of time-to-event data with censoring	85
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	85
The bearded dragon Pogona vitticeps	83
ShareLoc — an open platform for sharing localization microscopy data	83
Assessment of 3D MINFLUX data for quantitative structural biology in cells	83
Illuminating life processes by vibrational probes	82
An exceptionally photostable mScarlet3 mutant	82
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	82
CAVE: Connectome Annotation Versioning Engine	81
Deep 3D histology powered by tissue clearing, omics and AI	81
DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research	80
Unravelling cellular interactions using flow cytometry	80
Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes	80
Author Correction: iPipet: sample handling using a tablet	79
Smart parallel automated cryo-electron tomography	79
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	79
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference	78
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	78
Estimation of skeletal kinematics in freely moving rodents	78
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	77

A genetically encoded sensor for in vivo imaging of orexin neuropeptides	77
The impact of AlphaFold2 one year on	77
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	77
Spike sorting with Kilosort4	77
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	76
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	75
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	75
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	74
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	74
Sequencing RNA isoforms in brain tissue	74
METLIN-CCS: an ion mobility spectrometry collision cross section database	74
Towards a full picture of the total transcriptome	74
Jasmine and Iris: population-scale structural variant comparison and analysis	74
A new member of the spatial omics family	73
A diamond microscope	72
Augmented translation via multitailed mRNA	72
Predicted protein structures expand the CATH database	71
A peek into early human embryogenesis	71
Mapping deformations and increasing quantitative accuracy in expansion microscopy	71
Author Correction: Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	70
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	70
Neural engineering with photons as synaptic transmitters	69
Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model	69
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	68
Summer school in wartime	68
Small data methods in omics: the power of one	66
Selective-plane-activation structured illumination microscopy	66
Self-supervised learning of molecular representations	65
ScanNet uncovers binding motifs in protein structures with deep learning	65
Molecular pixelation: spatial proteomics of single cells by sequencing	65
A structural learning method to uncover how information between single cells flows	65
POLCAM: instant molecular orientation microscopy for the life sciences	65
Structure prediction for orphan proteins	64
The big picture in science	64
Gapr for large-scale collaborative single-neuron reconstruction	63
JIPipe: visual batch processing for ImageJ	63
Author Correction: Segment Anything for Microscopy	63
Microscopes are coming for your job	62
Data sharing is the future	62
Entering the era of deep single-cell proteomics	62
Guinea pigs as embryo models	62
Chemical space exploration with quantum computing	62
Barcoded CRISPR screens reveal RNA regulatory networks	62
Inferring how animals deform improves cell tracking	61
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	61
Machine learning-trained protein domain insertion for the design of switchable proteins	60
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines	60
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	60
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	60
Combating hallucination in digital pathology	60
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	60
Open microscopy in the life sciences: quo vadis?	59
Protein structure predictions to atomic accuracy with AlphaFold	59
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	59
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	59
Multi-animal pose estimation, identification and tracking with DeepLabCut	59
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	58
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	58
GeneAgent: self-verification language agent for gene-set analysis using domain databases	58
Long-read mapping to repetitive reference sequences using Winnowmap2	58
Base editing in mitochondrial DNA	57
Seeing data as t-SNE and UMAP do	57
Development of the human head	57
Spotting T and B cell receptors	57
A closer look at FluoroCubes	56
In situ electro-sequencing	56
Completing human genomes	55
Peter Sorger	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
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	55
Immune intestine interfaces in vitro	55
Miniature three-photon microscopy maximized for scattered fluorescence collection	54
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads	54
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology	54
Extended culture of 2D gastruloids to model human mesoderm development	54
A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments	54
Year in review 2023	54
Hydrogel fibers that enable optogenetic pain inhibition during locomotion	54
TREX reveals proteins that bind to specific RNA regions in living cells	54
CarboTag: a modular approach for live and functional imaging of plant cell walls	53
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation	53
Not if but when nanopore protein sequencing meets single-cell proteomics	53
Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq	53
3D reconstruction of spatial expression	53
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible	53
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
Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla	52
Parallel cryo electron tomography on in situ lamellae	52
Diving deeper in the 3D genome	51
The Cell Tracking Challenge: 10 years of objective benchmarking	51
Dissecting gene regulation with multimodal sequencing	50