Nature Methods

Article	Citations
Combined sequencing of genomes and epigenomes	5315
Super-resolution 3D live cell imaging	2661
A celebration of structural biology	2068
Human tonsils in a dish	896
Jie Xiao	781
Genome-wide analysis of structural variation	628
Expanding views of the transcriptome	577
iSCAT gets a signal boost	569
Mapping human hematopoiesis	542
Methods lead the way	519
New happenings at Nature Methods	511
Author Correction: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision	486
Author Correction: Arkitekt: streaming analysis and real-time workflows for microscopy	481
Capture of membrane proteins in their native membrane milieu	431
Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity	412
A multimodal whole-body atlas	366
Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering	366
Seeking more nucleases	346
When peace arrives	336
Inferring biological age from the transcriptome with RAPToR	319
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	278
How’s your health, forests?	265
Deep learning method for the prediction of glycan structures from mass spectrometry data	264
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data	253
BIONIC: biological network integration using convolutions	240

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments	237
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics	237
Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain	232
Nonnegative spatial factorization applied to spatial genomics	229
Local shape descriptors for neuron segmentation	227
Cell type-specific inference of differential expression in spatial transcriptomics	210
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set	208
FlyWire: online community for whole-brain connectomics	206
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	201
SCITO-seq: single-cell combinatorial indexed cytometry sequencing	196
MSNovelist: de novo structure generation from mass spectra	195
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia	188
Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library	185
Best practices for reporting throughput in biomedical research	182
Chroma is a generative model for protein design	182
Artificial intelligence gives neuron reconstruction a performance boost	178
The long and winding road of development: a coordinated song of transcription factors	177
Line-scanning speeds up Brillouin microscopy	174
Fluorophores’ talk turns them dark	171
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice	164
Doubling the resolution of light-sheet fluorescence microscopy	164
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	163
ReX: an integrative tool for quantifying and optimizing measurement reliability for the study of individual differences	162
Neural networks learn the motions of molecular machines	161
A general method for chemogenetic control of peptide function	152
GWAS and eQTL disparity	148
Long-term monosynaptic tracing	147
Phasor plots and the future of spectral and lifetime imaging	147
DART.2: bidirectional synaptic pharmacology with thousandfold cellular specificity	146
Assembling organs in vitro	144
Dissecting subcellular architecture of whole cells	143
Light-Seq: from microscopy to transcriptomics and back	142
Deep-learning language models help to improve protein sequence alignment	140
Ultra-long-working-distance multiphoton objective unlocks new possibilities for imaging	137
Computation and biology: a partnership	136
Breaking barriers for intravital imaging	136
Vascular subtypes on a dish	135
Diving deeper in the 3D genome	133
Deep brain imaging on the move	131
LocMoFit quantifies cellular structures in super-resolution data	131
Targeted illumination confocal microscopy enables in vivo voltage imaging in thick tissue	130
LiMCA: Hi-C gets an RNA twist	129
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	128
Integrating one’s LGBTQ+ identity into one’s science	128
Reconstruction of dynamic mammary mini gland in vitro for normal physiology and oncogenesis	127
Spatially resolved multiomics	123
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	122
Better detection for localization microscopy	120
Synthetic tissue environments	119
Chromoscope: interactive multiscale visualization for structural variation in human genomes	119

Accessible computing platforms democratize neuroimaging data analysis	119
SynNotch tuned for tension	118
Navigating two-body challenges	118
Soil researchers dig deeper into dirt’s complexity	117
Modeling condensate formation in silico	116
Deep learning identifies A-to-I RNA edits using nanopore sequencing data	116
Tamir Gonen	115
Editing naive CD4+ T cells	113
A method to map single-cell lineages in the mouse brain by CRISPR-based barcoding	113
Nanopores distinguish RNA modifications	112
Ex utero synthetic embryos	112
How regulatory sequences learn cell representations	108
The chemistry of microbiome–host togetherness	106
Reporting T cell proliferation	106
Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling	105
Fast and robust metagenomic sequence comparison through sparse chaining with skani	105
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	104
Synthetic condensates probe chromatin viscoelasticity	104
Adventures in AI	100
Ringside seats to a pandemic	100
Analyzing submicron spatial transcriptomics data at their original resolution	99
Disentangling parallel processes with BEYOND	98
A decade of neuroscience	98
Neural optimal transport predicts perturbation responses at the single-cell level	95
Art appreciation	95
Dissecting gene regulation with multimodal sequencing	94
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging	94
Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding	93
Identification of phosphosites that alter protein thermal stability	93
Spatiotemporal, optogenetic control of gene expression in organoids	92
CherryML: scalable maximum likelihood estimation of phylogenetic models	92
Scientists set out to connect the dots on long COVID	91
Spatial landmark detection and tissue registration with deep learning	90
Accurate determination of molecular formulae using tandem mass spectrometry	88
In vivo traction force microscopy	88
Sharpen SV detection	87
Spatially resolved epigenomics	87
Conservation genomics in practice	87
Unlocking human immune system complexity through AI	85
Modeling locomotion from environment to neurons	85
Light-gated potassium channels from nature	83
Early-career navigation tips	82
Anterograde transneuronal tracing and genetic control with engineered yellow fever vaccine YFV-17D	82
Homotrimer barcodes enable accurate counting of RNA molecules during high-throughput RNA sequencing	82
Profiling single molecules in solution	82
Modeling fragment counts improves single-cell ATAC-seq analysis	81
Long road to long-read assembly	81
CellBender removes technical artifacts from single-cell RNA sequencing data	81
RepoRT: a comprehensive repository for small molecule retention times	81
Single-cell profiling of microbes	80
Antibody stabilization for thermally accelerated deep immunostaining	80
CRISPR inspirations from nature	80
Applying interpretable machine learning in computational biology—pitfalls, recommendations and opportunities for new developments	79
Toward learning a foundational representation of cells and genes	79
Unlocking the power of spatial omics with AI	77
Extending the sensitivity, consistency and depth of single-cell proteomics	77
Unlocking gene regulation with sequence-to-function models	77
Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution	75
Moculus: an immersive virtual reality system for mice incorporating stereo vision	75
Understanding the invisible hands of sample preparation for cryo-EM	74
Single-molecule FRET on its way to structural biology in live cells	74
iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells	74
Decoding the protein composition of whole nucleosomes with Nuc-MS	73
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells	72
Let’s talk about diversity in human neuroscience	71
Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels	71
Weighing single protein complexes on the go	70
Visual interpretability of bioimaging deep learning models	69
Advancing sequencing-based spatial transcriptomics with a comprehensive benchmarking study	69
Machine learning in rare disease	69
Fatigue-resistant hydrogel optical fibers enable peripheral nerve optogenetics during locomotion	68
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice	68
CellRank 2: unified fate mapping in multiview single-cell data	68
Imaging without the labels	67
Model organisms on roads less traveled	65
Annotating unknown metabolites	65
Large models for genomics	64
Mapping morphogenesis and mechanics in embryo models	64
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis	64
Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+	64

Advances in measuring cancer cell metabolism with subcellular resolution	64
Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes	63
Maximum-likelihood model fitting for quantitative analysis of SMLM data	63
Pushing the limits of MRI brain imaging	62
Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing	62
Exoskeleton empowers large-scale neural recordings in freely roaming mice	61
SCUBA-D: a freshly trained diffusion model generates high-quality protein structures	61
RNA structure profiling at single-cell resolution reveals new determinants of cell identity	60
Spatially resolved isotope tracing reveals tissue metabolic activity	60
Constructing and personalizing population pangenome graphs	60
Personalized pangenome references	60
Temporal analysis of relative distances (TARDIS) is a robust, parameter-free alternative to single-particle tracking	59
ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology	59
SVision: a deep learning approach to resolve complex structural variants	58
OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data	58
High-resolution line-scan Brillouin microscopy for live imaging of mechanical properties during embryo development	57
Deep learning-enhanced light-field imaging with continuous validation	57
LLMs predict protein phases	56
Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM	56
Screening cell–cell communication in spatial transcriptomics via collective optimal transport	56
Serial lift-out for in situ structural biology of multicellular specimens	56
A machine learning tool for spatial multi-omics	56
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	56
Time-resolved assessment of single-cell protein secretion by sequencing	55
Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework	54
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	54
Context-aware transcript quantification from long-read RNA-seq data with Bambu	54
Orthology inference at scale with FastOMA	54
Development of miniature base editors using engineered IscB nickase	54
High-throughput volumetric mapping of synaptic transmission	53
Best practices and tools for reporting reproducible fluorescence microscopy methods	53
A systematic search for RNA structural switches across the human transcriptome	53
Survival analysis—time-to-event data and censoring	53
Efficient targeted insertion of large DNA fragments without DNA donors	53
Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging	52
Convolutional networks for supervised mining of molecular patterns within cellular context	52
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	52
Detecting and correcting false transients in calcium imaging	52
Robust single-cell matching and multimodal analysis using shared and distinct features	51
Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape	51
High-speed low-light in vivo two-photon voltage imaging of large neuronal populations	51
PyImageJ: A library for integrating ImageJ and Python	50
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	49
How noncoding RNAs began to leave the junkyard	49
Expansion microscopy opens the door to exploring more challenges	49
TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining	49
Reprogrammed anti-tumor NK cells	48
Effective gene expression prediction from sequence by integrating long-range interactions	48
Challenges in benchmarking metagenomic profilers	48
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation	47
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	47
Spatial omics and multiplexed imaging to explore cancer biology	47
Unlocking capacities of genomics for the COVID-19 response and future pandemics	47
Towards foundation models of biological image segmentation	47
DNA-PAINT MINFLUX nanoscopy	47
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions	47
Cryo-electron tomography: observing the cell at the atomic level	46
Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors	46
Flash entropy search to query all mass spectral libraries in real time	46
CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning	46
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	46
Joint probabilistic modeling of single-cell multi-omic data with totalVI	46
Bright and stable monomeric green fluorescent protein derived from StayGold	46
The triumphs and limitations of computational methods for scRNA-seq	46
Author Correction: ‘Ceci n’est pas un embryon?’ The ethics of human embryo model research	45
Publisher Correction: Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density	45
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	45
Author Correction: Points of view: Color blindness	45
Publisher Correction: Towards resolving proteomes in single cells	45
Author Correction: Unsupervised discovery of tissue architecture in multiplexed imaging	45
Author Correction: A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis	44
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	44
Author Correction: Single-cell chromatin state analysis with Signac	44
Integrative mapping of human CD8+ T cells in inflammation and cancer	44
Real-time multi-angle projection imaging of biological dynamics	44
A fluorescent sensor for real-time measurement of extracellular oxytocin dynamics in the brain	43
Fast and flexible analysis of linked microbiome data with mako	43
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	43
Automated segmentation and tracking of mitochondria in live-cell time-lapse images	43
GelMap: intrinsic calibration and deformation mapping for expansion microscopy	43
Fast optical recording of neuronal activity by three-dimensional custom-access serial holography	42
Uncovering cell cycle speed modulations with statistical inference	42
brainlife.io: a decentralized and open-source cloud platform to support neuroscience research	42
Neural space–time model for dynamic multi-shot imaging	42
An analytical framework for interpretable and generalizable single-cell data analysis	42
Systematic molecular evolution enables robust biomolecule discovery	41
Analysis of behavioral flow resolves latent phenotypes	41
More dimensions of the 3D genome	41
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	41
Large language modeling and deep learning shed light on RNA structure prediction	41
Unsupervised discovery of tissue architecture in multiplexed imaging	40
Museum of spatial transcriptomics	40
The end game: respecting major sources of population diversity	40
Method of the year: long-read sequencing	40
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	39