Nature Methods

Article	Citations
ColabFold: making protein folding accessible to all	4721
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation	3444
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm	2331
Cellpose: a generalist algorithm for cellular segmentation	1873
Sensitive protein alignments at tree-of-life scale using DIAMOND	1821
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction	1000
Single-cell chromatin state analysis with Signac	805
Martini 3: a general purpose force field for coarse-grained molecular dynamics	702
Benchmarking atlas-level data integration in single-cell genomics	559
Method of the Year: spatially resolved transcriptomics	540
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices	531
Museum of spatial transcriptomics	527
Effective gene expression prediction from sequence by integrating long-range interactions	504
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition	493
Cellpose 2.0: how to train your own model	435
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines	433
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network	430
Squidpy: a scalable framework for spatial omics analysis	424
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	391
CellRank for directed single-cell fate mapping	387
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks	366
Spatial omics and multiplexed imaging to explore cancer biology	345
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells	331
Deciphering molecular interactions by proximity labeling	314
Joint probabilistic modeling of single-cell multi-omic data with totalVI	294

SLEAP: A deep learning system for multi-animal pose tracking	282
Low-N protein engineering with data-efficient deep learning	251
Evaluation and development of deep neural networks for image super-resolution in optical microscopy	251
Multi-animal pose estimation, identification and tracking with DeepLabCut	229
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing	226
The emerging landscape of single-molecule protein sequencing technologies	225
Critical assessment of protein intrinsic disorder prediction	219
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	217
Screening for functional circular RNAs using the CRISPR–Cas13 system	214
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	213
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution	206
SNT: a unifying toolbox for quantification of neuronal anatomy	206
Spatially resolved transcriptomics adds a new dimension to genomics	204
AlphaFill: enriching AlphaFold models with ligands and cofactors	204
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning	198
The power of imaging to understand extracellular vesicle biology in vivo	198
Joint profiling of histone modifications and transcriptome in single cells from mouse brain	195
SpaceM reveals metabolic states of single cells	194
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research	191
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	184
Exosome detection via the ultrafast-isolation system: EXODUS	182
Protein structure predictions to atomic accuracy with AlphaFold	182
The triumphs and limitations of computational methods for scRNA-seq	172
Critical Assessment of Metagenome Interpretation: the second round of challenges	172
High-throughput and single-cell T cell receptor sequencing technologies	166
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	166
Defining the carrier proteome limit for single-cell proteomics	164
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads	162
Spatially resolved single-cell genomics and transcriptomics by imaging	154
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	152
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data	152
Deep learning enables fast and dense single-molecule localization with high accuracy	151
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations	150
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender	150
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	149
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing	149
neuromaps: structural and functional interpretation of brain maps	148
LIVECell—A large-scale dataset for label-free live cell segmentation	147
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes	146
FlyWire: online community for whole-brain connectomics	144
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	143
Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning	141
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ	141
Systematic evaluation of chromosome conformation capture assays	140
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography	137
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
DOME: recommendations for supervised machine learning validation in biology	130
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging	130
Metabolite discovery through global annotation of untargeted metabolomics data	129

Geometric deep learning enables 3D kinematic profiling across species and environments	127
The impact of AlphaFold2 one year on	125
Method of the year: long-read sequencing	120
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI	119
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM	118
Reproducibility standards for machine learning in the life sciences	118
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets	118
A practical guide to cancer subclonal reconstruction from DNA sequencing	118
Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes	117
DeepLC can predict retention times for peptides that carry as-yet unseen modifications	116
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy	116
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging	115
Lineage recording in human cerebral organoids	113
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	113
Alignment and integration of spatial transcriptomics data	112
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry	112
Screening cell–cell communication in spatial transcriptomics via collective optimal transport	112
Deep learning-based point-scanning super-resolution imaging	112
Understudied proteins: opportunities and challenges for functional proteomics	111
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers	109
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	108
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation	107
Long-read mapping to repetitive reference sequences using Winnowmap2	107
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing	107
Click-ExM enables expansion microscopy for all biomolecules	105
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3	105
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels	105
DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes	102
Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification	102
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction	101
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set	100
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data	100
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	98
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy	97
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies	96
High-definition imaging using line-illumination modulation microscopy	94
Spatially resolved isotope tracing reveals tissue metabolic activity	93
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM	92
Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines	92
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising	91
Engineered HaloTag variants for fluorescence lifetime multiplexing	90
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy	90
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes	89
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
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis	87
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	87
Genome-scale deconvolution of RNA structure ensembles	87
Understanding the invisible hands of sample preparation for cryo-EM	86
A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells	85
Metagenome assembly of high-fidelity long reads with hifiasm-meta	85
Removing independent noise in systems neuroscience data using DeepInterpolation	85
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome	83
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
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO	82
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues	82
Deep learning-enhanced light-field imaging with continuous validation	82
Human organoid models to study SARS-CoV-2 infection	81
Best practice standards for circular RNA research	81
Efficient targeted insertion of large DNA fragments without DNA donors	81
Avoiding a replication crisis in deep-learning-based bioimage analysis	80
Deep learning and protein structure modeling	80
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy	79
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA	78
A ‘Build and Retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins	78
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2	78
Method of the Year 2020: spatially resolved transcriptomics	77
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments	77
Challenges and opportunities for the next generation of cardiovascular tissue engineering	77
scGPT: toward building a foundation model for single-cell multi-omics using generative AI	76
Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution	75
CODA: quantitative 3D reconstruction of large tissues at cellular resolution	74
Joint single-cell measurements of nuclear proteins and RNA in vivo	74
Challenges in benchmarking metagenomic profilers	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

Spatially resolved transcriptomics in neuroscience	71
Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers	71
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology	70
A genetically encoded sensor for in vivo imaging of orexin neuropeptides	69
Best practices and tools for reporting reproducible fluorescence microscopy methods	69
Improved AlphaFold modeling with implicit experimental information	68
Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale	68
Extending support for mouse data in the Molecular Signatures Database (MSigDB)	68
Animal models in SARS-CoV-2 research	68
Transgenic mice for in vivo epigenome editing with CRISPR-based systems	66
Impact of phosphorylation on thermal stability of proteins	66
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics	65
Automated segmentation and tracking of mitochondria in live-cell time-lapse images	65
Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization	65
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging	65
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice	64
Protein structure prediction has reached the single-structure frontier	64
MSNovelist: de novo structure generation from mass spectra	64
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions	64
Cell type-specific inference of differential expression in spatial transcriptomics	64
Single-cell metabolomics hits its stride	63
Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales	63
RefMet: a reference nomenclature for metabolomics	62
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions	62
DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide	62
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
scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks	61
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution	61
An adaptive optics module for deep tissue multiphoton imaging in vivo	60
Pycro-Manager: open-source software for customized and reproducible microscope control	60
Quantitative shotgun proteome analysis by direct infusion	59
Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA	59
Advances and opportunities in RNA structure experimental determination and computational modeling	58
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
Self-supervised deep learning encodes high-resolution features of protein subcellular localization	56
Chronically implantable LED arrays for behavioral optogenetics in primates	56
MultiVI: deep generative model for the integration of multimodal data	56
Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane	56
Direct identification of A-to-I editing sites with nanopore native RNA sequencing	55
DNA-PAINT MINFLUX nanoscopy	55
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins	54
Annotation of spatially resolved single-cell data with STELLAR	53
Metabolomic profiling of single enlarged lysosomes	53
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis	53
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	53
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations	53
Structured illumination microscopy with noise-controlled image reconstructions	53
SODB facilitates comprehensive exploration of spatial omics data	52
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies	52
Comparison of transformations for single-cell RNA-seq data	52
Event-triggered STED imaging	51
Photoblueing of organic dyes can cause artifacts in super-resolution microscopy	51
The Cell Tracking Challenge: 10 years of objective benchmarking	51
Universal Spectrum Identifier for mass spectra	50
Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM)	50
Ultrasensitive ultrasound imaging of gene expression with signal unmixing	50
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
Direct prediction of intrinsically disordered protein conformational properties from sequence	48
Directed evolution in mammalian cells	47
The class imbalance problem	47
Event-driven acquisition for content-enriched microscopy	47
Cross-modal coherent registration of whole mouse brains	47
Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain	47
Targeted deubiquitination rescues distinct trafficking-deficient ion channelopathies	47
A three-dimensional virtual mouse generates synthetic training data for behavioral analysis	47
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics	47
Mass-sensitive particle tracking to elucidate the membrane-associated MinDE reaction cycle	46
Assembloids	46
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data	46
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies	46
Method of the Year: protein structure prediction	46
QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy	46
NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster	46
Molecular-scale axial localization by repetitive optical selective exposure	45
Sampling the proteome by emerging single-molecule and mass spectrometry methods	45
Photoswitching fingerprint analysis bypasses the 10-nm resolution barrier	45
DecoID improves identification rates in metabolomics through database-assisted MS/MS deconvolution	44
Antigen identification and high-throughput interaction mapping by reprogramming viral entry	44
Diversity in immunogenomics: the value and the challenge	44
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data	44
RNA secondary structure packages evaluated and improved by high-throughput experiments	44
High-speed low-light in vivo two-photon voltage imaging of large neuronal populations	44
MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity	43
Jasmine and Iris: population-scale structural variant comparison and analysis	43
Field-dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging	43
Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition	43
Context-aware transcript quantification from long-read RNA-seq data with Bambu	42