Nature Protocols

Article	Citations
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	1343
Open thoracic surgical implantation of cardiac pacemakers in rats	1124
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	754
Fabrication of focused electron beam induced deposition tips for high-speed atomic force microscopy using benchtop scanning electron microscopy	571
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	513
Purification and functional characterization of novel human skeletal stem cell lineages	494
GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery–center axis	349
Automated cGMP optical labeling of FDA-approved antibodies for human use	324
Inducible CRISPR–Cas9 screening platform to interrogate non-proliferative cellular states	303
Patient-derived ependymoma and medulloblastoma tumoroids: generation, biobanking and drug screening	274
Isoform-specific RNA structure determination using Nano-DMS-MaP	270
Spontaneous and experimental models of lymph node metastasis	265
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	260
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	231
Reproducible strategy for excisional skin-wound-healing studies in mice	225
Tutorial: biomembranes in hybrid living bioelectronics	221
Design and application of the transformer base editor in mammalian cells and mice	183
Generating human bone marrow organoids for disease modeling and drug discovery	162
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	161
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	156
Precise tracking of nanoparticles in plant roots	155
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	150
Preparation of C4′-modified nucleoside analogs	138
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	135
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	133

Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	130
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	126
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	125
Photocatalytic low-temperature defluorination of PTFE	124
Quantitative molecular imaging using deep magnetic resonance fingerprinting	124
Simplified ischemia-free liver transplantation with continuous normothermic machine perfusion	122
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	113
Fabrication of electron tunneling probes for measuring single-protein conductance	110
Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing	105
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	101
Small RNA structural biochemistry in a post-sequencing era	100
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	98
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	98
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	97
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	94
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	92
Preparation and biomedical applications of single-metal atom catalysts	90
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	89
How to isolate channel-forming membrane proteins using the E. coli expression system	89
Large-scale growth of C. elegans and isolation of membrane protein complexes	88
Collections from Nature Protocols	88
CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images	87
Gene expression and chromatin state mapped in space	87
Achieving transient and reversible optical transparency in live mice with tartrazine	85
Honey bee functional genomics using symbiont-mediated RNAi	85
A new era for coral functional genomics	78
A modular method for high-throughput measurement of ion channel currents in cardiac myocytes	77
mRNA lipid nanoparticle formulation, characterization and evaluation	77
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	75
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	74
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	73
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	73
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	73
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	73
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	73
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	72
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	71
Fibrous polyisocyanide hydrogels for 3D cell culture applications	68
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	67
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	66
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	65
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	63
Drosophila melanogaster as a model host for studying Pseudomonas aeruginosa feeding infection	63
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	63
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	61
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	61
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	60
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	60
Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants	59
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	59

Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	59
Identification of immunogenic commensal antigens using phage display	57
Screening high-quality lignins extracted from biomass to prepare biobased wood adhesives	57
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	56
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	56
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	55
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	55
Web-based multi-omics integration using the Analyst software suite	53
Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy	53
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	52
Enhancing consistency in brain imaging research for population neuroimaging	51
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	50
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	50
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	49
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	49
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	49
Establishing a long-term versatile culture system for functional mouse mammary organoids from single cells	48
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	48
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	47
Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples	47
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	46
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	45
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	45
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	45
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	44
Integrating optical neuroscience tools into touchscreen operant systems	44
Large-scale genome structure interrogation via recombinase-mediated rearrangements of multiplexed prime edits in repetitive elements	42
Outcome devaluation as a method for identifying goal-directed behaviors in rats	42
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	42
Easy and accurate protein structure prediction using ColabFold	42
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	42
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	42
Construction of complex bacteriogenic protocells from living material assembly	42
Analyzing somatic mutations by single-cell whole-genome sequencing	41
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	41
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	41
Directional conjugation of monoclonal antibodies to nanoparticles using metal-free click chemistry	41
Annotating genetic variants to target genes using H-MAGMA	40
Structural variant calling using Sniffles2	40
Magnetoencephalography in human neuroscience research: planning, piloting, implementation and quality assurance	40
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	40
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	40
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	39
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	39
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	39
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	38
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	38
CRISPR screens in human neural organoids and assembloids	38
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	38
RNA sample optimization for cryo-EM analysis	37
Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform	36
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	36
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	36
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	36
Microfluidic gradients create a stem cell model of the human central nervous system	36
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	36
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	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
YCharOS protocol for antibody validation	35
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	35
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	35
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	35
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	35
Quantitative imaging of apoplastic pH in plant roots via confocal microscopy	34
Multilevel characterization of genome editor nuclease activity with BreakTag	34
Preparation of placenta-tropic mRNA lipid nanoparticles for pregnancy disorders	34
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	34
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	33
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	33
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	33
Bioengineering mini-colons for ex vivo colorectal cancer research	33
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	33
Tutorial: strategies for targeting organelles using nanoparticles	33
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	33
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	33
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	32
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	32
Using tunable hydrogel microparticles to measure cellular forces	31
Synthesis of single-crystal monolayer graphene on Cu/Ni(111) alloy foil	31
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	31

Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	31
Preparation of targeted lipid nanoparticles for precision nucleic acid delivery	30
A multi-glycomic platform for the analysis of food carbohydrates	30
Harnessing intermediate-scale bioreactors for next-generation macrophage production and application	30
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	30
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	29
Fabrication of optically transparent ultrasound transducers to integrate light and sound in multimodal biomedical systems	29
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	29
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	29
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	28
A consensus platform for antibody characterization	28
Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq	28
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	28
Determining chromatin architecture with Micro Capture-C	28
Tutorial: a guide to diffusion MRI and structural connectomics	27
Electrocatalytic reactions involving aqueous nitrate and nitrite	27
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	27
Oscillatory brain state-dependent stimulation with transcranial magnetic stimulation combined with electroencephalography	27
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	27