Nature Methods

(The TQCC of Nature Methods is 24. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)
ColabFold: making protein folding accessible to all3511
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation2603
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm1767
Cellpose: a generalist algorithm for cellular segmentation1455
Sensitive protein alignments at tree-of-life scale using DIAMOND1311
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction843
Feature-based molecular networking in the GNPS analysis environment667
Single-cell chromatin state analysis with Signac634
Martini 3: a general purpose force field for coarse-grained molecular dynamics585
Macromolecular modeling and design in Rosetta: recent methods and frameworks512
Method of the Year: spatially resolved transcriptomics445
metaFlye: scalable long-read metagenome assembly using repeat graphs438
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices425
Benchmarking atlas-level data integration in single-cell genomics420
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition406
Effective gene expression prediction from sequence by integrating long-range interactions394
Museum of spatial transcriptomics380
Advances and challenges for fluorescence nanothermometry351
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks315
Squidpy: a scalable framework for spatial omics analysis313
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network308
CellRank for directed single-cell fate mapping301
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram295
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines293
Next-generation GRAB sensors for monitoring dopaminergic activity in vivo289
Spatial omics and multiplexed imaging to explore cancer biology288
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells280
Philosopher: a versatile toolkit for shotgun proteomics data analysis271
Cellpose 2.0: how to train your own model268
Deciphering molecular interactions by proximity labeling266
Joint probabilistic modeling of single-cell multi-omic data with totalVI249
Improvement of cryo-EM maps by density modification244
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes239
An optimized acetylcholine sensor for monitoring in vivo cholinergic activity222
Evaluation and development of deep neural networks for image super-resolution in optical microscopy220
Low-N protein engineering with data-efficient deep learning216
SLEAP: A deep learning system for multi-animal pose tracking210
The emerging landscape of single-molecule protein sequencing technologies198
Critical assessment of protein intrinsic disorder prediction195
DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning193
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing192
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes192
Screening for functional circular RNAs using the CRISPR–Cas13 system185
Multi-animal pose estimation, identification and tracking with DeepLabCut179
SpaceM reveals metabolic states of single cells175
Spatially resolved transcriptomics adds a new dimension to genomics173
Joint profiling of histone modifications and transcriptome in single cells from mouse brain171
The power of imaging to understand extracellular vesicle biology in vivo168
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 polishing163
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging163
A general method to optimize and functionalize red-shifted rhodamine dyes161
Exosome detection via the ultrafast-isolation system: EXODUS156
Protein structure predictions to atomic accuracy with AlphaFold156
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research152
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution151
AlphaFill: enriching AlphaFold models with ligands and cofactors151
Predicting 3D genome folding from DNA sequence with Akita149
SNT: a unifying toolbox for quantification of neuronal anatomy149
Critical Assessment of Metagenome Interpretation: the second round of challenges143
An expanded palette of dopamine sensors for multiplex imaging in vivo141
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads141
The triumphs and limitations of computational methods for scRNA-seq141
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco140
Defining the carrier proteome limit for single-cell proteomics140
Targeted Perturb-seq enables genome-scale genetic screens in single cells137
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data137
High-throughput and single-cell T cell receptor sequencing technologies136
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq135
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing135
Spatially resolved single-cell genomics and transcriptomics by imaging133
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing129
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels127
Deep learning enables fast and dense single-molecule localization with high accuracy126
Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals126
Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning125
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data125
Up to 100-fold speed-up and multiplexing in optimized DNA-PAINT122
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures121
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ121
LIVECell—A large-scale dataset for label-free live cell segmentation120
An efficient KRAB domain for CRISPRi applications in human cells120
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging117
The SEIRS model for infectious disease dynamics117
Metabolite discovery through global annotation of untargeted metabolomics data116
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma115
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography115
Systematic evaluation of chromosome conformation capture assays115
Single-molecule FRET imaging of GPCR dimers in living cells114
Geometric deep learning enables 3D kinematic profiling across species and environments114
Intelligent image-based deformation-assisted cell sorting with molecular specificity114
Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins111
SMAP: a modular super-resolution microscopy analysis platform for SMLM data111
DeepC: predicting 3D genome folding using megabase-scale transfer learning111
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI110
A systematic evaluation of the design and context dependencies of massively parallel reporter assays110 genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations109
The impact of AlphaFold2 one year on108
DOME: recommendations for supervised machine learning validation in biology108
FlyWire: online community for whole-brain connectomics107
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM106
A practical guide to cancer subclonal reconstruction from DNA sequencing106
METLIN MS2 molecular standards database: a broad chemical and biological resource105
A compact Cascade–Cas3 system for targeted genome engineering104
Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq104
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets103
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes102
A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects102
Lineage recording in human cerebral organoids100
3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing99
Reproducibility standards for machine learning in the life sciences99
Deep learning-based point-scanning super-resolution imaging99
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging98
O-Pair Search with MetaMorpheus for O-glycopeptide characterization97
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration97
Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes97
neuromaps: structural and functional interpretation of brain maps96
DeepLC can predict retention times for peptides that carry as-yet unseen modifications95
Understudied proteins: opportunities and challenges for functional proteomics94
GPCRmd uncovers the dynamics of the 3D-GPCRome93
Time-resolved cryo-EM using Spotiton93
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy92
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms92
Click-ExM enables expansion microscopy for all biomolecules92
ZipSeq: barcoding for real-time mapping of single cell transcriptomes91
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning91
DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes89
Three-photon head-mounted microscope for imaging deep cortical layers in freely moving rats89
Plasmonic scattering imaging of single proteins and binding kinetics89
Putative cell type discovery from single-cell gene expression data89
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing87
Long-read mapping to repetitive reference sequences using Winnowmap287
MARS: discovering novel cell types across heterogeneous single-cell experiments87
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set86
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco386
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels85
Live-cell super-resolved PAINT imaging of piconewton cellular traction forces85
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers84
CRISPR-assisted detection of RNA–protein interactions in living cells84
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks83
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM81
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies81
Method of the year: long-read sequencing81
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender80
ReDU: a framework to find and reanalyze public mass spectrometry data80
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment79
Optimizing imaging speed and excitation intensity for single-molecule localization microscopy79
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes78
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy78
T cell antigen discovery77
High-definition imaging using line-illumination modulation microscopy77
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation77
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data76
Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles76
Human organoid models to study SARS-CoV-2 infection75
Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification75
Alignment and integration of spatial transcriptomics data75
Spatially resolved isotope tracing reveals tissue metabolic activity75
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge75
Deep learning-enhanced light-field imaging with continuous validation75
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy74
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis74
A ‘Build and Retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins74
A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells74
Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes73
Genome-scale deconvolution of RNA structure ensembles73
Method of the Year 2020: spatially resolved transcriptomics72
The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences72
Optogenetic control of gene expression in plants in the presence of ambient white light72
Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines71
Deep learning and protein structure modeling71
Understanding the invisible hands of sample preparation for cryo-EM71
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising71
Efficient targeted insertion of large DNA fragments without DNA donors71
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation70
Engineered HaloTag variants for fluorescence lifetime multiplexing70
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction70
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry69
MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets69
Joint single-cell measurements of nuclear proteins and RNA in vivo69
Mid-infrared metabolic imaging with vibrational probes69
High-sensitivity and high-specificity biomechanical imaging by stimulated Brillouin scattering microscopy68
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology67
Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval67
Highly specific multiplexed RNA imaging in tissues with split-FISH65
Screening cell–cell communication in spatial transcriptomics via collective optimal transport65
Metagenome assembly of high-fidelity long reads with hifiasm-meta64
Best practices and tools for reporting reproducible fluorescence microscopy methods64
Avoiding a replication crisis in deep-learning-based bioimage analysis64
Quantum computing at the frontiers of biological sciences64
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy64
Challenges in benchmarking metagenomic profilers64
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues63
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO63
Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution63
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome62
Spatially resolved transcriptomics in neuroscience62
Best practice standards for circular RNA research62
Directed evolution of adeno-associated virus for efficient gene delivery to microglia62
Detection of m6A from direct RNA sequencing using a multiple instance learning framework61
Mechanistic modeling of chromatin folding to understand function61
Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors60
Improved AlphaFold modeling with implicit experimental information60
Impact of phosphorylation on thermal stability of proteins60
Parallel cryo electron tomography on in situ lamellae59
NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells59
Removing independent noise in systems neuroscience data using DeepInterpolation59
Transgenic mice for in vivo epigenome editing with CRISPR-based systems58
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-257
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions57
Homogeneous multifocal excitation for high-throughput super-resolution imaging56
Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers56
Automated segmentation and tracking of mitochondria in live-cell time-lapse images56
3DFlex: determining structure and motion of flexible proteins from cryo-EM55
Challenges and opportunities for the next generation of cardiovascular tissue engineering55
Pycro-Manager: open-source software for customized and reproducible microscope control55
CODA: quantitative 3D reconstruction of large tissues at cellular resolution55
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging55
A genetically encoded sensor for in vivo imaging of orexin neuropeptides54
Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization54
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics54
RefMet: a reference nomenclature for metabolomics54
Animal models in SARS-CoV-2 research54
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice53
MSNovelist: de novo structure generation from mass spectra53
Single-cell metabolomics hits its stride53
Advances in nanopore direct RNA sequencing52
Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane52
EthoLoop: automated closed-loop neuroethology in naturalistic environments52
Real-time 3D movement correction for two-photon imaging in behaving animals51
Quantitative shotgun proteome analysis by direct infusion50
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions50
Elasticizing tissues for reversible shape transformation and accelerated molecular labeling50
Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging50
Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales50
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments49
Investigating higher-order interactions in single-cell data with scHOT49
Functional ultrasound localization microscopy reveals brain-wide neurovascular activity on a microscopic scale48
Metabolomic profiling of single enlarged lysosomes48
Universal Spectrum Identifier for mass spectra47
DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide47
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution47
Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library47
An adaptive optics module for deep tissue multiphoton imaging in vivo47
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms47
Illumination guidelines for ultrafast pump–probe experiments by serial femtosecond crystallography47
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data46
jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths46
Chronically implantable LED arrays for behavioral optogenetics in primates45
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis45
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals44