Nature Methods

Article	Citations
ColabFold: making protein folding accessible to all	3511
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation	2603
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm	1767
Cellpose: a generalist algorithm for cellular segmentation	1455
Sensitive protein alignments at tree-of-life scale using DIAMOND	1311
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction	843
Feature-based molecular networking in the GNPS analysis environment	667
Single-cell chromatin state analysis with Signac	634
Martini 3: a general purpose force field for coarse-grained molecular dynamics	585
Macromolecular modeling and design in Rosetta: recent methods and frameworks	512
Method of the Year: spatially resolved transcriptomics	445
metaFlye: scalable long-read metagenome assembly using repeat graphs	438
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices	425
Benchmarking atlas-level data integration in single-cell genomics	420
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition	406
Effective gene expression prediction from sequence by integrating long-range interactions	394
Museum of spatial transcriptomics	380
Advances and challenges for fluorescence nanothermometry	351
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks	315
Squidpy: a scalable framework for spatial omics analysis	313
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network	308
CellRank for directed single-cell fate mapping	301
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	295
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines	293
Next-generation GRAB sensors for monitoring dopaminergic activity in vivo	289

Spatial omics and multiplexed imaging to explore cancer biology	288
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells	280
Philosopher: a versatile toolkit for shotgun proteomics data analysis	271
Cellpose 2.0: how to train your own model	268
Deciphering molecular interactions by proximity labeling	266
Joint probabilistic modeling of single-cell multi-omic data with totalVI	249
Improvement of cryo-EM maps by density modification	244
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes	239
An optimized acetylcholine sensor for monitoring in vivo cholinergic activity	222
Evaluation and development of deep neural networks for image super-resolution in optical microscopy	220
Low-N protein engineering with data-efficient deep learning	216
SLEAP: A deep learning system for multi-animal pose tracking	210
The emerging landscape of single-molecule protein sequencing technologies	198
Critical assessment of protein intrinsic disorder prediction	195
DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning	193
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	192
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing	192
Screening for functional circular RNAs using the CRISPR–Cas13 system	185
Multi-animal pose estimation, identification and tracking with DeepLabCut	179
SpaceM reveals metabolic states of single cells	175
Spatially resolved transcriptomics adds a new dimension to genomics	173
Joint profiling of histone modifications and transcriptome in single cells from mouse brain	171
The power of imaging to understand extracellular vesicle biology in vivo	168
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	163
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing	163
A general method to optimize and functionalize red-shifted rhodamine dyes	161
Exosome detection via the ultrafast-isolation system: EXODUS	156
Protein structure predictions to atomic accuracy with AlphaFold	156
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research	152
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution	151
AlphaFill: enriching AlphaFold models with ligands and cofactors	151
SNT: a unifying toolbox for quantification of neuronal anatomy	149
Predicting 3D genome folding from DNA sequence with Akita	149
Critical Assessment of Metagenome Interpretation: the second round of challenges	143
The triumphs and limitations of computational methods for scRNA-seq	141
An expanded palette of dopamine sensors for multiplex imaging in vivo	141
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads	141
Defining the carrier proteome limit for single-cell proteomics	140
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco	140
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	137
Targeted Perturb-seq enables genome-scale genetic screens in single cells	137
High-throughput and single-cell T cell receptor sequencing technologies	136
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq	135
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing	135
Spatially resolved single-cell genomics and transcriptomics by imaging	133
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	129
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	127
Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals	126
Deep learning enables fast and dense single-molecule localization with high accuracy	126
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data	125

Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning	125
Up to 100-fold speed-up and multiplexing in optimized DNA-PAINT	122
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ	121
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures	121
LIVECell—A large-scale dataset for label-free live cell segmentation	120
An efficient KRAB domain for CRISPRi applications in human cells	120
The SEIRS model for infectious disease dynamics	117
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging	117
Metabolite discovery through global annotation of untargeted metabolomics data	116
Systematic evaluation of chromosome conformation capture assays	115
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma	115
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography	115
Intelligent image-based deformation-assisted cell sorting with molecular specificity	114
Geometric deep learning enables 3D kinematic profiling across species and environments	114
Single-molecule FRET imaging of GPCR dimers in living cells	114
DeepC: predicting 3D genome folding using megabase-scale transfer learning	111
Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins	111
SMAP: a modular super-resolution microscopy analysis platform for SMLM data	111
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI	110
A systematic evaluation of the design and context dependencies of massively parallel reporter assays	110
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations	109
The impact of AlphaFold2 one year on	108
DOME: recommendations for supervised machine learning validation in biology	108
FlyWire: online community for whole-brain connectomics	107
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM	106
A practical guide to cancer subclonal reconstruction from DNA sequencing	106
METLIN MS2 molecular standards database: a broad chemical and biological resource	105
A compact Cascade–Cas3 system for targeted genome engineering	104
Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq	104
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets	103
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes	102
A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects	102
Lineage recording in human cerebral organoids	100
3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing	99
Reproducibility standards for machine learning in the life sciences	99
Deep learning-based point-scanning super-resolution imaging	99
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging	98
O-Pair Search with MetaMorpheus for O-glycopeptide characterization	97
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	97
Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes	97
neuromaps: structural and functional interpretation of brain maps	96
DeepLC can predict retention times for peptides that carry as-yet unseen modifications	95
Understudied proteins: opportunities and challenges for functional proteomics	94
GPCRmd uncovers the dynamics of the 3D-GPCRome	93
Time-resolved cryo-EM using Spotiton	93
Click-ExM enables expansion microscopy for all biomolecules	92
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy	92
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	92
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning	91
ZipSeq: barcoding for real-time mapping of single cell transcriptomes	91
Putative cell type discovery from single-cell gene expression data	89
DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes	89
Three-photon head-mounted microscope for imaging deep cortical layers in freely moving rats	89
Plasmonic scattering imaging of single proteins and binding kinetics	89
MARS: discovering novel cell types across heterogeneous single-cell experiments	87
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing	87
Long-read mapping to repetitive reference sequences using Winnowmap2	87
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3	86
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set	86
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels	85
Live-cell super-resolved PAINT imaging of piconewton cellular traction forces	85
CRISPR-assisted detection of RNA–protein interactions in living cells	84
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers	84
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	83
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM	81
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies	81
Method of the year: long-read sequencing	81
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender	80
ReDU: a framework to find and reanalyze public mass spectrometry data	80
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	79
Optimizing imaging speed and excitation intensity for single-molecule localization microscopy	79
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes	78
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy	78
T cell antigen discovery	77
High-definition imaging using line-illumination modulation microscopy	77
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation	77
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data	76
Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles	76
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge	75
Deep learning-enhanced light-field imaging with continuous validation	75

Human organoid models to study SARS-CoV-2 infection	75
Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification	75
Alignment and integration of spatial transcriptomics data	75
Spatially resolved isotope tracing reveals tissue metabolic activity	75
A ‘Build and Retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins	74
A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells	74
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy	74
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis	74
Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes	73
Genome-scale deconvolution of RNA structure ensembles	73
Optogenetic control of gene expression in plants in the presence of ambient white light	72
Method of the Year 2020: spatially resolved transcriptomics	72
The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences	72
Efficient targeted insertion of large DNA fragments without DNA donors	71
Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines	71
Deep learning and protein structure modeling	71
Understanding the invisible hands of sample preparation for cryo-EM	71
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising	71
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation	70
Engineered HaloTag variants for fluorescence lifetime multiplexing	70
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	70
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry	69
MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets	69
Joint single-cell measurements of nuclear proteins and RNA in vivo	69
Mid-infrared metabolic imaging with vibrational probes	69
High-sensitivity and high-specificity biomechanical imaging by stimulated Brillouin scattering microscopy	68
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology	67
Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval	67
Highly specific multiplexed RNA imaging in tissues with split-FISH	65
Screening cell–cell communication in spatial transcriptomics via collective optimal transport	65
Metagenome assembly of high-fidelity long reads with hifiasm-meta	64
Best practices and tools for reporting reproducible fluorescence microscopy methods	64
Avoiding a replication crisis in deep-learning-based bioimage analysis	64
Quantum computing at the frontiers of biological sciences	64
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy	64
Challenges in benchmarking metagenomic profilers	64
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues	63
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO	63
Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution	63
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome	62
Spatially resolved transcriptomics in neuroscience	62
Best practice standards for circular RNA research	62
Directed evolution of adeno-associated virus for efficient gene delivery to microglia	62
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	61
Mechanistic modeling of chromatin folding to understand function	61
Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors	60
Improved AlphaFold modeling with implicit experimental information	60
Impact of phosphorylation on thermal stability of proteins	60
Removing independent noise in systems neuroscience data using DeepInterpolation	59
Parallel cryo electron tomography on in situ lamellae	59
NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells	59
Transgenic mice for in vivo epigenome editing with CRISPR-based systems	58
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2	57
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions	57
Homogeneous multifocal excitation for high-throughput super-resolution imaging	56
Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers	56
Automated segmentation and tracking of mitochondria in live-cell time-lapse images	56
3DFlex: determining structure and motion of flexible proteins from cryo-EM	55
Challenges and opportunities for the next generation of cardiovascular tissue engineering	55
Pycro-Manager: open-source software for customized and reproducible microscope control	55
CODA: quantitative 3D reconstruction of large tissues at cellular resolution	55
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging	55
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	54
Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization	54
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics	54
RefMet: a reference nomenclature for metabolomics	54
Animal models in SARS-CoV-2 research	54
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice	53
MSNovelist: de novo structure generation from mass spectra	53
Single-cell metabolomics hits its stride	53
Advances in nanopore direct RNA sequencing	52
Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane	52
EthoLoop: automated closed-loop neuroethology in naturalistic environments	52
Real-time 3D movement correction for two-photon imaging in behaving animals	51
Quantitative shotgun proteome analysis by direct infusion	50
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions	50
Elasticizing tissues for reversible shape transformation and accelerated molecular labeling	50
Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging	50
Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales	50
Investigating higher-order interactions in single-cell data with scHOT	49
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments	49
Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale	48
Metabolomic profiling of single enlarged lysosomes	48
Illumination guidelines for ultrafast pump–probe experiments by serial femtosecond crystallography	47
Universal Spectrum Identifier for mass spectra	47
DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide	47
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution	47
Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library	47
An adaptive optics module for deep tissue multiphoton imaging in vivo	47
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms	47
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data	46
jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths	46
Chronically implantable LED arrays for behavioral optogenetics in primates	45
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis	45
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	44