Nature Protocols

Article	Citations
Automated cGMP optical labeling of FDA-approved antibodies for human use	1300
Patient-derived ependymoma and medulloblastoma tumoroids: generation, biobanking and drug screening	1141
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	950
Isoform-specific RNA structure determination using Nano-DMS-MaP	684
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	493
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	491
Open thoracic surgical implantation of cardiac pacemakers in rats	481
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	327
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	308
Fabrication of focused electron beam induced deposition tips for high-speed atomic force microscopy using benchtop scanning electron microscopy	296
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	252
GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery–center axis	249
Purification and functional characterization of novel human skeletal stem cell lineages	240
Spontaneous and experimental models of lymph node metastasis	239
Reproducible strategy for excisional skin-wound-healing studies in mice	235
Generating human bone marrow organoids for disease modeling and drug discovery	220
Inducible CRISPR–Cas9 screening platform to interrogate non-proliferative cellular states	216
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	204
Design and application of the transformer base editor in mammalian cells and mice	171
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	170
How to isolate channel-forming membrane proteins using the E. coli expression system	150
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	149
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	143
Precise tracking of nanoparticles in plant roots	139
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	129

Simplified ischemia-free liver transplantation with continuous normothermic machine perfusion	129
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	128
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	123
Preparation of C4′-modified nucleoside analogs	118
Preparation and biomedical applications of single-metal atom catalysts	117
Quantitative molecular imaging using deep magnetic resonance fingerprinting	114
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	112
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	111
Small RNA structural biochemistry in a post-sequencing era	111
Fabrication of electron tunneling probes for measuring single-protein conductance	110
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	106
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	93
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	92
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	92
Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing	92
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	91
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	90
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	88
Large-scale growth of C. elegans and isolation of membrane protein complexes	88
Collections from Nature Protocols	86
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	83
Gene expression and chromatin state mapped in space	83
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	80
Achieving transient and reversible optical transparency in live mice with tartrazine	80
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	80
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	79
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	79
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	79
mRNA lipid nanoparticle formulation, characterization and evaluation	76
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	75
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	75
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	74
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	73
A new era for coral functional genomics	72
Drosophila melanogaster as a model host for studying Pseudomonas aeruginosa feeding infection	71
Fibrous polyisocyanide hydrogels for 3D cell culture applications	71
A modular method for high-throughput measurement of ion channel currents in cardiac myocytes	70
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	69
Honey bee functional genomics using symbiont-mediated RNAi	69
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	67
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	66
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	66
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	64
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	64
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	64
Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy	61
Identification of immunogenic commensal antigens using phage display	61
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	60
Screening high-quality lignins extracted from biomass to prepare biobased wood adhesives	60
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	58

Scalable tissue labeling and clearing of intact human organs	58
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	58
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	57
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	56
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	56
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	55
Enhancing consistency in brain imaging research for population neuroimaging	54
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	54
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	54
Web-based multi-omics integration using the Analyst software suite	54
Integrating optical neuroscience tools into touchscreen operant systems	52
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	52
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	51
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	50
Establishing a long-term versatile culture system for functional mouse mammary organoids from single cells	49
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	48
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	48
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	48
Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples	47
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	46
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	46
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	45
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	44
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	43
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	43
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	43
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	42
Easy and accurate protein structure prediction using ColabFold	42
Construction of complex bacteriogenic protocells from living material assembly	41
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	41
Analyzing somatic mutations by single-cell whole-genome sequencing	40
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	40
CRISPR screens in human neural organoids and assembloids	40
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	40
Directional conjugation of monoclonal antibodies to nanoparticles using metal-free click chemistry	40
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	40
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	40
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	39
Magnetoencephalography in human neuroscience research: planning, piloting, implementation and quality assurance	39
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	39
Outcome devaluation as a method for identifying goal-directed behaviors in rats	39
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	39
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	38
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	38
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	38
Annotating genetic variants to target genes using H-MAGMA	38
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	37
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	37
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	36
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	36
Microfluidic gradients create a stem cell model of the human central nervous system	36
RNA sample optimization for cryo-EM analysis	35
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	35
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	35
Circular Vectors as an efficient, fully synthetic, cell-free approach for preparing small circular DNA as a plasmid substitute for guide RNA expression in CRISPR–Cas9 genome editing	35
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	35
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	34
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	34
A multi-glycomic platform for the analysis of food carbohydrates	34
YCharOS protocol for antibody validation	34
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	34
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	34
Using tunable hydrogel microparticles to measure cellular forces	33
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	33
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	33
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	33
Quantitative imaging of apoplastic pH in plant roots via confocal microscopy	32
Multilevel characterization of genome editor nuclease activity with BreakTag	32
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	32
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	31
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	31
Bioengineering mini-colons for ex vivo colorectal cancer research	31
Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING	31
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	31
Preparation of placenta-tropic mRNA lipid nanoparticles for pregnancy disorders	31
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	31
Preparation of targeted lipid nanoparticles for precision nucleic acid delivery	31
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	30
Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq	30
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	30

A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	30
Harnessing intermediate-scale bioreactors for next-generation macrophage production and application	30
Fabrication of optically transparent ultrasound transducers to integrate light and sound in multimodal biomedical systems	30
A consensus platform for antibody characterization	29
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	29
Tutorial: a guide to diffusion MRI and structural connectomics	29
Oscillatory brain state-dependent stimulation with transcranial magnetic stimulation combined with electroencephalography	29
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	29
Electrocatalytic reactions involving aqueous nitrate and nitrite	29
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	28
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	28
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	28
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	28
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	28
A comprehensive framework for statistical testing of brain dynamics	27
Determining chromatin architecture with Micro Capture-C	27
scGPT: end-to-end protocol for fine-tuned retinal cell type annotation	27
A new era begins at Nature Protocols	27