Nature Methods

Article	Citations
ColabFold: making protein folding accessible to all	5074
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation	3710
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm	2564
Cellpose: a generalist algorithm for cellular segmentation	2010
Sensitive protein alignments at tree-of-life scale using DIAMOND	1982
Single-cell chromatin state analysis with Signac	855
Martini 3: a general purpose force field for coarse-grained molecular dynamics	760
Benchmarking atlas-level data integration in single-cell genomics	599
Museum of spatial transcriptomics	571
Method of the Year: spatially resolved transcriptomics	564
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices	557
Effective gene expression prediction from sequence by integrating long-range interactions	542
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines	480
Cellpose 2.0: how to train your own model	476
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network	469
Squidpy: a scalable framework for spatial omics analysis	462
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	418
CellRank for directed single-cell fate mapping	412
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks	366
Spatial omics and multiplexed imaging to explore cancer biology	366
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells	347
Deciphering molecular interactions by proximity labeling	337
SLEAP: A deep learning system for multi-animal pose tracking	321
Joint probabilistic modeling of single-cell multi-omic data with totalVI	319
Evaluation and development of deep neural networks for image super-resolution in optical microscopy	267

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning	265
Low-N protein engineering with data-efficient deep learning	264
Multi-animal pose estimation, identification and tracking with DeepLabCut	263
AlphaFill: enriching AlphaFold models with ligands and cofactors	239
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing	236
SNT: a unifying toolbox for quantification of neuronal anatomy	233
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	232
Critical assessment of protein intrinsic disorder prediction	229
The emerging landscape of single-molecule protein sequencing technologies	225
Screening for functional circular RNAs using the CRISPR–Cas13 system	224
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution	224
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	217
SpaceM reveals metabolic states of single cells	210
Spatially resolved transcriptomics adds a new dimension to genomics	210
The power of imaging to understand extracellular vesicle biology in vivo	208
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research	201
Exosome detection via the ultrafast-isolation system: EXODUS	196
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	196
Joint profiling of histone modifications and transcriptome in single cells from mouse brain	195
Critical Assessment of Metagenome Interpretation: the second round of challenges	185
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender	184
The triumphs and limitations of computational methods for scRNA-seq	182
Protein structure predictions to atomic accuracy with AlphaFold	182
High-throughput and single-cell T cell receptor sequencing technologies	177
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	173
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads	171
Defining the carrier proteome limit for single-cell proteomics	171
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	166
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes	165
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	164
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations	163
neuromaps: structural and functional interpretation of brain maps	162
Deep learning enables fast and dense single-molecule localization with high accuracy	161
Spatially resolved single-cell genomics and transcriptomics by imaging	154
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data	152
LIVECell—A large-scale dataset for label-free live cell segmentation	152
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography	148
Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning	147
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ	146
FlyWire: online community for whole-brain connectomics	144
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	143
Method of the year: long-read sequencing	143
Systematic evaluation of chromosome conformation capture assays	140
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging	137
Screening cell–cell communication in spatial transcriptomics via collective optimal transport	136
DOME: recommendations for supervised machine learning validation in biology	136
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma	136
Single-molecule FRET imaging of GPCR dimers in living cells	135
The impact of AlphaFold2 one year on	133
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets	131

Metabolite discovery through global annotation of untargeted metabolomics data	129
Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes	128
Geometric deep learning enables 3D kinematic profiling across species and environments	127
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy	126
Reproducibility standards for machine learning in the life sciences	123
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation	122
Long-read mapping to repetitive reference sequences using Winnowmap2	122
DeepLC can predict retention times for peptides that carry as-yet unseen modifications	119
Understudied proteins: opportunities and challenges for functional proteomics	119
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers	119
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM	118
A practical guide to cancer subclonal reconstruction from DNA sequencing	118
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	118
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data	118
Deep learning-based point-scanning super-resolution imaging	116
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing	116
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging	115
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	113
Lineage recording in human cerebral organoids	113
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry	112
Alignment and integration of spatial transcriptomics data	112
Click-ExM enables expansion microscopy for all biomolecules	111
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	109
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	109
Engineered HaloTag variants for fluorescence lifetime multiplexing	106
Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification	106
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels	105
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3	105
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies	104
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy	104
DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes	102
Metagenome assembly of high-fidelity long reads with hifiasm-meta	100
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set	100
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	98
Genome-scale deconvolution of RNA structure ensembles	95
High-definition imaging using line-illumination modulation microscopy	94
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome	93
Spatially resolved isotope tracing reveals tissue metabolic activity	93
Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines	92
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes	92
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM	92
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising	91
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy	90
Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes	89
3DFlex: determining structure and motion of flexible proteins from cryo-EM	88
Parallel cryo electron tomography on in situ lamellae	88
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge	87
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	87
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis	87
Understanding the invisible hands of sample preparation for cryo-EM	86
Removing independent noise in systems neuroscience data using DeepInterpolation	85
A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells	85
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination	83
Directed evolution of adeno-associated virus for efficient gene delivery to microglia	83
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues	82
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO	82
Deep learning-enhanced light-field imaging with continuous validation	82
Deep learning and protein structure modeling	82
Human organoid models to study SARS-CoV-2 infection	81
Efficient targeted insertion of large DNA fragments without DNA donors	81
Challenges and opportunities for the next generation of cardiovascular tissue engineering	81
Best practice standards for circular RNA research	81
Avoiding a replication crisis in deep-learning-based bioimage analysis	80
Challenges in benchmarking metagenomic profilers	80
Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers	79
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy	79
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2	78
A ‘Build and Retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins	78
Method of the Year 2020: spatially resolved transcriptomics	77
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments	77
scGPT: toward building a foundation model for single-cell multi-omics using generative AI	76
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology	75
Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution	75
Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale	75
Improved AlphaFold modeling with implicit experimental information	74
CODA: quantitative 3D reconstruction of large tissues at cellular resolution	74
Joint single-cell measurements of nuclear proteins and RNA in vivo	74
NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells	73
Quantum computing at the frontiers of biological sciences	73
Advances in nanopore direct RNA sequencing	72

Transgenic mice for in vivo epigenome editing with CRISPR-based systems	71
Spatially resolved transcriptomics in neuroscience	71
Advances and opportunities in RNA structure experimental determination and computational modeling	71
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	69
Best practices and tools for reporting reproducible fluorescence microscopy methods	69
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions	68
Extending support for mouse data in the Molecular Signatures Database (MSigDB)	68
Animal models in SARS-CoV-2 research	68
DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide	67
Impact of phosphorylation on thermal stability of proteins	66
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics	65
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging	65
Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization	65
Automated segmentation and tracking of mitochondria in live-cell time-lapse images	65
scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks	64
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice	64
Protein structure prediction has reached the single-structure frontier	64
Cell type-specific inference of differential expression in spatial transcriptomics	64
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions	64
MSNovelist: de novo structure generation from mass spectra	64
Single-cell metabolomics hits its stride	63
Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales	63
Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging	62
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	62
The Cell Tracking Challenge: 10 years of objective benchmarking	62
Metabolomic profiling of single enlarged lysosomes	61
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution	61
Pycro-Manager: open-source software for customized and reproducible microscope control	60
DNA-PAINT MINFLUX nanoscopy	60
An adaptive optics module for deep tissue multiphoton imaging in vivo	60
Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA	59
Comparison of transformations for single-cell RNA-seq data	59
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms	58
Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library	58
Convolutional networks for supervised mining of molecular patterns within cellular context	57
Universal Spectrum Identifier for mass spectra	57
Self-supervised deep learning encodes high-resolution features of protein subcellular localization	56
Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM)	56
Chronically implantable LED arrays for behavioral optogenetics in primates	56
Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane	56
MultiVI: deep generative model for the integration of multimodal data	56
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies	56
Direct identification of A-to-I editing sites with nanopore native RNA sequencing	55
Direct prediction of intrinsically disordered protein conformational properties from sequence	54
Structured illumination microscopy with noise-controlled image reconstructions	54
The class imbalance problem	54
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins	54
Antigen identification and high-throughput interaction mapping by reprogramming viral entry	54
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations	53
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis	53
Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore	53
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	53
Annotation of spatially resolved single-cell data with STELLAR	53
SODB facilitates comprehensive exploration of spatial omics data	52
Photoblueing of organic dyes can cause artifacts in super-resolution microscopy	51
Event-triggered STED imaging	51
Ultrasensitive ultrasound imaging of gene expression with signal unmixing	50
Mass-sensitive particle tracking to elucidate the membrane-associated MinDE reaction cycle	49
ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells	49
Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments	49
Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology	49
Incorporating the image formation process into deep learning improves network performance	49
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data	49
Metrics reloaded: recommendations for image analysis validation	49
Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla	48
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice	48
Cross-modal coherent registration of whole mouse brains	47
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics	47
Event-driven acquisition for content-enriched microscopy	47
A three-dimensional virtual mouse generates synthetic training data for behavioral analysis	47
Directed evolution in mammalian cells	47
Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain	47
QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy	46
Method of the Year: protein structure prediction	46
Long-read sequencing in the era of epigenomics and epitranscriptomics	46
A fluorescent sensor for real-time measurement of extracellular oxytocin dynamics in the brain	46
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies	46
NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster	46
Unlocking capacities of genomics for the COVID-19 response and future pandemics	46
Assembloids	46
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data	46
Systematic molecular evolution enables robust biomolecule discovery	46
Molecular-scale axial localization by repetitive optical selective exposure	45
Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing	45
Sampling the proteome by emerging single-molecule and mass spectrometry methods	45
Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome	45
Photoswitching fingerprint analysis bypasses the 10-nm resolution barrier	45
High-speed low-light in vivo two-photon voltage imaging of large neuronal populations	44
Diversity in immunogenomics: the value and the challenge	44
MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity	44
Sprod for de-noising spatially resolved transcriptomics data based on position and image information	44
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data	44
DecoID improves identification rates in metabolomics through database-assisted MS/MS deconvolution	44
RNA secondary structure packages evaluated and improved by high-throughput experiments	44
Field-dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging	43