Nature Methods

Article	Citations
ColabFold: making protein folding accessible to all	4018
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation	2928
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm	1962
Cellpose: a generalist algorithm for cellular segmentation	1612
Sensitive protein alignments at tree-of-life scale using DIAMOND	1514
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction	918
Feature-based molecular networking in the GNPS analysis environment	708
Single-cell chromatin state analysis with Signac	702
Martini 3: a general purpose force field for coarse-grained molecular dynamics	636
Benchmarking atlas-level data integration in single-cell genomics	491
Method of the Year: spatially resolved transcriptomics	485
metaFlye: scalable long-read metagenome assembly using repeat graphs	476
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices	467
Museum of spatial transcriptomics	450
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition	442
Effective gene expression prediction from sequence by integrating long-range interactions	437
Advances and challenges for fluorescence nanothermometry	369
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network	369
Squidpy: a scalable framework for spatial omics analysis	366
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	347
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines	342
Cellpose 2.0: how to train your own model	338
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks	337
CellRank for directed single-cell fate mapping	335
Spatial omics and multiplexed imaging to explore cancer biology	316

Next-generation GRAB sensors for monitoring dopaminergic activity in vivo	306
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells	302
Philosopher: a versatile toolkit for shotgun proteomics data analysis	296
Deciphering molecular interactions by proximity labeling	280
Joint probabilistic modeling of single-cell multi-omic data with totalVI	272
Improvement of cryo-EM maps by density modification	248
An optimized acetylcholine sensor for monitoring in vivo cholinergic activity	244
SLEAP: A deep learning system for multi-animal pose tracking	243
Evaluation and development of deep neural networks for image super-resolution in optical microscopy	234
Low-N protein engineering with data-efficient deep learning	231
The emerging landscape of single-molecule protein sequencing technologies	210
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing	208
Critical assessment of protein intrinsic disorder prediction	206
Multi-animal pose estimation, identification and tracking with DeepLabCut	205
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	202
Screening for functional circular RNAs using the CRISPR–Cas13 system	200
Spatially resolved transcriptomics adds a new dimension to genomics	191
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution	186
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	185
The power of imaging to understand extracellular vesicle biology in vivo	182
SpaceM reveals metabolic states of single cells	181
Joint profiling of histone modifications and transcriptome in single cells from mouse brain	179
AlphaFill: enriching AlphaFold models with ligands and cofactors	175
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	174
Protein structure predictions to atomic accuracy with AlphaFold	173
A general method to optimize and functionalize red-shifted rhodamine dyes	171
Exosome detection via the ultrafast-isolation system: EXODUS	170
SNT: a unifying toolbox for quantification of neuronal anatomy	170
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research	166
Predicting 3D genome folding from DNA sequence with Akita	160
Critical Assessment of Metagenome Interpretation: the second round of challenges	152
The triumphs and limitations of computational methods for scRNA-seq	152
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco	151
An expanded palette of dopamine sensors for multiplex imaging in vivo	149
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads	149
Defining the carrier proteome limit for single-cell proteomics	148
High-throughput and single-cell T cell receptor sequencing technologies	147
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq	145
Spatially resolved single-cell genomics and transcriptomics by imaging	144
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing	141
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	141
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	139
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning	137
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data	135
Deep learning enables fast and dense single-molecule localization with high accuracy	134
Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning	133
An efficient KRAB domain for CRISPRi applications in human cells	132
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	132
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ	132
LIVECell—A large-scale dataset for label-free live cell segmentation	131

Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals	130
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma	129
Systematic evaluation of chromosome conformation capture assays	129
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures	128
FlyWire: online community for whole-brain connectomics	126
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography	126
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations	125
Single-molecule FRET imaging of GPCR dimers in living cells	125
neuromaps: structural and functional interpretation of brain maps	122
DOME: recommendations for supervised machine learning validation in biology	122
Geometric deep learning enables 3D kinematic profiling across species and environments	122
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes	121
A systematic evaluation of the design and context dependencies of massively parallel reporter assays	121
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging	121
The impact of AlphaFold2 one year on	120
DeepC: predicting 3D genome folding using megabase-scale transfer learning	120
Metabolite discovery through global annotation of untargeted metabolomics data	119
SMAP: a modular super-resolution microscopy analysis platform for SMLM data	118
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI	115
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	115
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM	112
Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq	112
A compact Cascade–Cas3 system for targeted genome engineering	112
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets	110
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging	109
METLIN MS2 molecular standards database: a broad chemical and biological resource	109
A practical guide to cancer subclonal reconstruction from DNA sequencing	108
Lineage recording in human cerebral organoids	107
DeepLC can predict retention times for peptides that carry as-yet unseen modifications	106
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	105
Deep learning-based point-scanning super-resolution imaging	104
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy	104
3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing	104
Reproducibility standards for machine learning in the life sciences	104
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender	104
Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes	103
O-Pair Search with MetaMorpheus for O-glycopeptide characterization	101
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	100
Understudied proteins: opportunities and challenges for functional proteomics	99
Time-resolved cryo-EM using Spotiton	98
Click-ExM enables expansion microscopy for all biomolecules	97
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing	96
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers	96
Method of the year: long-read sequencing	96
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3	96
Long-read mapping to repetitive reference sequences using Winnowmap2	95
DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes	95
ZipSeq: barcoding for real-time mapping of single cell transcriptomes	95
GPCRmd uncovers the dynamics of the 3D-GPCRome	95
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels	94
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set	94
Alignment and integration of spatial transcriptomics data	93
Plasmonic scattering imaging of single proteins and binding kinetics	92
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry	91
Live-cell super-resolved PAINT imaging of piconewton cellular traction forces	91
MARS: discovering novel cell types across heterogeneous single-cell experiments	90
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation	87
Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification	87
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM	87
Spatially resolved isotope tracing reveals tissue metabolic activity	86
High-definition imaging using line-illumination modulation microscopy	85
Optimizing imaging speed and excitation intensity for single-molecule localization microscopy	84
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	84
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies	84
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge	83
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy	82
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	82
T cell antigen discovery	82
Screening cell–cell communication in spatial transcriptomics via collective optimal transport	81
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data	81
ReDU: a framework to find and reanalyze public mass spectrometry data	81
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	81
Engineered HaloTag variants for fluorescence lifetime multiplexing	80
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis	80
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes	80
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy	80
Human organoid models to study SARS-CoV-2 infection	79
Genome-scale deconvolution of RNA structure ensembles	79
Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes	79
Deep learning-enhanced light-field imaging with continuous validation	79

A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells	79
Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines	78
Understanding the invisible hands of sample preparation for cryo-EM	78
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising	77
Avoiding a replication crisis in deep-learning-based bioimage analysis	77
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues	77
Method of the Year 2020: spatially resolved transcriptomics	75
Efficient targeted insertion of large DNA fragments without DNA donors	75
A ‘Build and Retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins	75
Deep learning and protein structure modeling	75
MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets	74
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation	74
High-sensitivity and high-specificity biomechanical imaging by stimulated Brillouin scattering microscopy	73
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome	73
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy	72
Metagenome assembly of high-fidelity long reads with hifiasm-meta	72
Best practice standards for circular RNA research	70
Joint single-cell measurements of nuclear proteins and RNA in vivo	70
Parallel cryo electron tomography on in situ lamellae	70
Removing independent noise in systems neuroscience data using DeepInterpolation	70
3DFlex: determining structure and motion of flexible proteins from cryo-EM	69
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology	69
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO	68
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2	68
Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution	67
Challenges in benchmarking metagenomic profilers	67
Challenges and opportunities for the next generation of cardiovascular tissue engineering	66
Best practices and tools for reporting reproducible fluorescence microscopy methods	66
Spatially resolved transcriptomics in neuroscience	66
Quantum computing at the frontiers of biological sciences	66
Improved AlphaFold modeling with implicit experimental information	64
NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells	64
Directed evolution of adeno-associated virus for efficient gene delivery to microglia	64
Impact of phosphorylation on thermal stability of proteins	63
Advances in nanopore direct RNA sequencing	63
Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers	61
Automated segmentation and tracking of mitochondria in live-cell time-lapse images	61
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging	61
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice	61
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics	60
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions	60
CODA: quantitative 3D reconstruction of large tissues at cellular resolution	60
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments	60
Animal models in SARS-CoV-2 research	59
Transgenic mice for in vivo epigenome editing with CRISPR-based systems	59
Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale	59
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	59
Single-cell metabolomics hits its stride	57
RefMet: a reference nomenclature for metabolomics	57
Pycro-Manager: open-source software for customized and reproducible microscope control	56
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions	56
Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales	56
Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging	56
Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization	56
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination	55
MSNovelist: de novo structure generation from mass spectra	55
Quantitative shotgun proteome analysis by direct infusion	55
DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide	54
EthoLoop: automated closed-loop neuroethology in naturalistic environments	54
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution	54
An adaptive optics module for deep tissue multiphoton imaging in vivo	53
Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library	52
Protein structure prediction has reached the single-structure frontier	52
Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane	52
scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks	51
Cell type-specific inference of differential expression in spatial transcriptomics	51
Chronically implantable LED arrays for behavioral optogenetics in primates	51
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms	51
Investigating higher-order interactions in single-cell data with scHOT	50
Metabolomic profiling of single enlarged lysosomes	50
Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA	50
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	50
Self-supervised deep learning encodes high-resolution features of protein subcellular localization	50
Universal Spectrum Identifier for mass spectra	50
Convolutional networks for supervised mining of molecular patterns within cellular context	50
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	49
DNA-PAINT MINFLUX nanoscopy	49
Direct identification of A-to-I editing sites with nanopore native RNA sequencing	48
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies	47
A three-dimensional virtual mouse generates synthetic training data for behavioral analysis	47
Structured illumination microscopy with noise-controlled image reconstructions	47
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis	47
ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells	47
Ultrasensitive ultrasound imaging of gene expression with signal unmixing	46
Photoblueing of organic dyes can cause artifacts in super-resolution microscopy	46
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data	46
Advances and opportunities in RNA structure experimental determination and computational modeling	46
Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM)	46
MultiVI: deep generative model for the integration of multimodal data	45
Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments	45
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations	44
Incorporating the image formation process into deep learning improves network performance	44
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	44
Assembloids	44
Cross-modal coherent registration of whole mouse brains	44