Nature Methods

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	7546
Interpreting and comparing neural activity across systems by geometric deep learning	1371
Tamir Gonen	1001
More dimensions of the 3D genome	977
Exoskeleton empowers large-scale neural recordings in freely roaming mice	919
Modeling locomotion from environment to neurons	891
Analyzing submicron spatial transcriptomics data at their original resolution	761
Annotating unknown metabolites	751
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	607
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	595
BIONIC: biological network integration using convolutions	518
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	490
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	442
Unlocking the power of spatial omics with AI	429
GWAS and eQTL disparity	373
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	369
Efficient targeted insertion of large DNA fragments without DNA donors	355
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	338
Maximum-likelihood model fitting for quantitative analysis of SMLM data	307
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	304
SNAP-tag2 improves live-cell imaging	285
How noncoding RNAs began to leave the junkyard	274
Line-scanning speeds up Brillouin microscopy	265
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	261
Chromoscope: interactive multiscale visualization for structural variation in human genomes	256

Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	247
Prediction of protein subcellular localization in single cells	247
Antibody stabilization for thermally accelerated deep immunostaining	246
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	246
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	242
Fast and efficient template-mediated synthesis of genetic variants	241
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	239
Detecting and correcting false transients in calcium imaging	236
MRIcroGL: voxel-based visualization for neuroimaging	235
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	231
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	226
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	216
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	216
Quest: my postdoc home	215
BATTLES: high-throughput screening of antigen recognition under force	207
Using machine learning to predict the structure of proteins that bind to DNA and RNA	205
Setting standards for stem cells	202
Non-invasive metabolic imaging of brown adipose tissue	201
Sensitive protein analysis with plexDIA	197
Tracking gene transfer using RNA tools	197
One cell, two cell, dead cell, true cell	187
The placozoan Trichoplax	175
Benchmarking genomic language models	174
Road trip home to start a lab	169
Author Correction: Learning single-cell perturbation responses using neural optimal transport	167
Bat organoids at bat	167
How developmental cell atlases inform stem cell embryo models	167
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	165
Trawling the ocean virome	165
ENTERing the world of immune cells	153
Peer review demystified: part 2	153
When labs welcome under-represented groups	152
Comparing classifier performance with baselines	147
Publisher Correction: Museum of spatial transcriptomics	145
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	145
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	145
The tidyomics ecosystem: enhancing omic data analyses	144
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	143
The crustacean Parhyale	142
Long-read sequencing in the era of epigenomics and epitranscriptomics	141
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	136
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	136
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	132
Tardigrades	131
From GWAS to single-cell MPRA	129
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	128
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	128
The Hodge Laplacian advances inference of single-cell trajectories	128
Nicheformer: a foundation model for single-cell and spatial omics	127
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	123

Detection of m6A from direct RNA sequencing using a multiple instance learning framework	123
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	123
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	121
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	121
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	120
StayGold variants for molecular fusion and membrane-targeting applications	118
Indexing and searching petabase-scale nucleotide resources	118
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	117
A method for quantitative and base-resolution sequencing of pseudouridine	116
A graph neural network that combines scRNA-seq and protein–protein interaction data	116
The LGBTQ+ job hunt	114
Deciphering subcellular organization with multiplexed imaging and deep learning	113
Neural networks built with biomolecules	112
Science while parenting	111
Combining compact human protein domains with CRISPR systems for robust gene activation	111
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	110
What makes a Nature Methods paper	109
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	109
CAD we share? Publishing reproducible microscope hardware	109
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	108
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	108
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	108
Analyzing single-cell bisulfite sequencing data with MethSCAn	107
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	107
Inside the chase after those elusive proteoforms	106
Enabling global image data sharing in the life sciences	106
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	105
Mackenzie Weygandt Mathis	104
Building an automated three-dimensional flight agent for neural network reconstruction	103
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	102
Genomics beyond complete genomes	102
Merging conformational landscapes in a single consensus space with FlexConsensus algorithm	101
Vector choices, vector surprises	101
The future of bioimage analysis: a dialog between mind and machine	100
Tackling tumor complexity with single-cell proteomics	100
Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes	99
Image processing tools for petabyte-scale light sheet microscopy data	99
Principles and challenges of modeling temporal and spatial omics data	99
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	99
Method of the Year: protein structure prediction	98
The evolution of embryo models	97
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	97
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	96
Learning single-cell perturbation responses using neural optimal transport	96
Propensity score weighting	96
SODB facilitates comprehensive exploration of spatial omics data	95
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	93
RNA-Puzzles Round V: blind predictions of 23 RNA structures	93
Method of the Year 2024: spatial proteomics	92
Metrics reloaded: recommendations for image analysis validation	92
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	91
Comparison of transformations for single-cell RNA-seq data	91
Multimodal large language models for bioimage analysis	90
Lighting up oxytocin dynamics in the brain with MTRIAOT	89
Author Correction: Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	89
Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	89
First-gen scientists leap hurdles and give back	89
Publisher Correction: Fast and flexible analysis of linked microbiome data with mako	89
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace	88
Modeling morphogenesis	88
Learning the immunological repertoire	87
Regression modeling of time-to-event data with censoring	87
The bearded dragon Pogona vitticeps	87
Mapping effective connectivity by virtually perturbing a surrogate brain	86
Unravelling cellular interactions using flow cytometry	85
An exceptionally photostable mScarlet3 mutant	85
Author Correction: iPipet: sample handling using a tablet	85
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics	85
Improved structure prediction of protein complexes is within GRASP	84
Repurposing large-format microarrays for scalable spatial transcriptomics	84
Machine learning for accelerating discovery from single-molecule data	83
Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq	82
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes	82
DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research	80
Assessment of 3D MINFLUX data for quantitative structural biology in cells	79
Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function	79
Highly multiplexed 3D profiling of cell states and immune niches in human tumors	78
Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes	78
ShareLoc — an open platform for sharing localization microscopy data	78
Segmentation metric misinterpretations in bioimage analysis	78

A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging	77
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	75
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations	75
Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase	75
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	75
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	74
Illuminating life processes by vibrational probes	74
Deep 3D histology powered by tissue clearing, omics and AI	73
Smart parallel automated cryo-electron tomography	73
Incorporating the image formation process into deep learning improves network performance	73
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior	73
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks	72
Estimation of skeletal kinematics in freely moving rodents	71
METLIN-CCS: an ion mobility spectrometry collision cross section database	70
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference	70
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	70
Jasmine and Iris: population-scale structural variant comparison and analysis	69
The impact of AlphaFold2 one year on	68
Spike sorting with Kilosort4	67
Sequencing RNA isoforms in brain tissue	67
CAVE: Connectome Annotation Versioning Engine	67
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput	67
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics	67
Augmented translation via multitailed mRNA	66
A diamond microscope	66
Towards a full picture of the total transcriptome	66
A new member of the spatial omics family	66
A structural learning method to uncover how information between single cells flows	65
A peek into early human embryogenesis	65
ScanNet uncovers binding motifs in protein structures with deep learning	65
Mapping deformations and increasing quantitative accuracy in expansion microscopy	65
Predicted protein structures expand the CATH database	65
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community	64
Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model	64
Entering the era of deep single-cell proteomics	64
Summer school in wartime	64
Automated classification of cellular expression in multiplexed imaging data with Nimbus	63
Structure prediction for orphan proteins	63
Selective-plane-activation structured illumination microscopy	63
Author Correction: Segment Anything for Microscopy	63
Small data methods in omics: the power of one	63
Author Correction: Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	63
Peptide sequencing based on host–guest interaction-assisted nanopore sensing	62
Barcoded CRISPR screens reveal RNA regulatory networks	62
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids	62
Inferring how animals deform improves cell tracking	62
Chemical space exploration with quantum computing	62
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	62
Guinea pigs as embryo models	62
Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing	61
Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s	60
JIPipe: visual batch processing for ImageJ	60
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms	59
Neural engineering with photons as synaptic transmitters	59
Gapr for large-scale collaborative single-neuron reconstruction	59
GeneAgent: self-verification language agent for gene-set analysis using domain databases	59
Molecular pixelation: spatial proteomics of single cells by sequencing	59
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines	59
The big picture in science	58
Machine learning-trained protein domain insertion for the design of switchable proteins	58
Self-supervised learning of molecular representations	58
Combating hallucination in digital pathology	58
Open microscopy in the life sciences: quo vadis?	58
Microscopes are coming for your job	57
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples	57
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data	57
Seeing data as t-SNE and UMAP do	56
POLCAM: instant molecular orientation microscopy for the life sciences	56
Protein structure predictions to atomic accuracy with AlphaFold	56
Long-read mapping to repetitive reference sequences using Winnowmap2	56
Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging	56
Data sharing is the future	56
Base editing in mitochondrial DNA	55
Multi-animal pose estimation, identification and tracking with DeepLabCut	55
Spotting T and B cell receptors	54
A closer look at FluoroCubes	54
Completing human genomes	53
In situ electro-sequencing	53
Next-generation expansion microscopy	53
Peter Sorger	53
A genome-scale approach for determining the function of phosphorylation sites	53
A flexible system for tissue-specific gene expression in mice using adeno-associated virus	53
Development of the human head	53
Fluorescent actinometers for fast and simple quantitative measurement of light intensity	52
Extended culture of 2D gastruloids to model human mesoderm development	52
3D reconstruction of spatial expression	52
Immune intestine interfaces in vitro	52
A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments	52
Year in review 2023	52
Cichlid fishes	52
CarboTag: a modular approach for live and functional imaging of plant cell walls	52
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible	51
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology	51
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation	51
Parallel cryo electron tomography on in situ lamellae	51