Nature Protocols

Article	Citations
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	1161
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	582
Isoform-specific RNA structure determination using Nano-DMS-MaP	512
Open thoracic surgical implantation of cardiac pacemakers in rats	485
Design and application of the transformer base editor in mammalian cells and mice	411
Generation of heart-forming organoids from human pluripotent stem cells	379
Reproducible strategy for excisional skin-wound-healing studies in mice	372
Generating human bone marrow organoids for disease modeling and drug discovery	355
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	288
Spontaneous and experimental models of lymph node metastasis	265
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	251
Routine culture and study of adult human brain cells from neurosurgical specimens	248
Inducible CRISPR–Cas9 screening platform to interrogate non-proliferative cellular states	240
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	235
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	195
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	189
Purification and functional characterization of novel human skeletal stem cell lineages	188
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	185
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	177
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	167
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	167
How to isolate channel-forming membrane proteins using the E. coli expression system	166
Preparation and biomedical applications of single-metal atom catalysts	164
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	159
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	139

Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	138
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	138
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	136
Small RNA structural biochemistry in a post-sequencing era	129
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	126
Fabrication of electron tunneling probes for measuring single-protein conductance	120
Precise tracking of nanoparticles in plant roots	118
Quantitative molecular imaging using deep magnetic resonance fingerprinting	116
Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing	110
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	108
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	107
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance	103
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	103
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells	102
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	101
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	100
Chromatin accessibility profiling by ATAC-seq	98
Large-scale growth of C. elegans and isolation of membrane protein complexes	93
Collections from Nature Protocols	89
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	88
Gene expression and chromatin state mapped in space	87
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	84
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	82
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	79
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	79
Fibrous polyisocyanide hydrogels for 3D cell culture applications	78
mRNA lipid nanoparticle formulation, characterization and evaluation	77
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	75
Achieving transient and reversible optical transparency in live mice with tartrazine	74
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	74
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	73
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	73
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	73
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	71
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	70
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	70
Honey bee functional genomics using symbiont-mediated RNAi	68
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	66
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	66
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	66
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	64
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	64
Identification of immunogenic commensal antigens using phage display	64
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	62
Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy	61
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	60
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	60
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	60
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	59
Scalable tissue labeling and clearing of intact human organs	59

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting	59
All-optical interrogation of neural circuits in behaving mice	58
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	57
Web-based multi-omics integration using the Analyst software suite	55
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	54
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	53
Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples	53
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	53
Enhancing consistency in brain imaging research for population neuroimaging	53
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	53
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	52
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	52
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	52
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	51
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	51
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	51
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	50
Easy and accurate protein structure prediction using ColabFold	50
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	50
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	49
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	49
Integrating optical neuroscience tools into touchscreen operant systems	49
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	47
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	47
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	46
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	46
In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability	46
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	46
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	46
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	46
Outcome devaluation as a method for identifying goal-directed behaviors in rats	45
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	45
Annotating genetic variants to target genes using H-MAGMA	44
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	44
Construction of complex bacteriogenic protocells from living material assembly	43
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	43
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	42
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	41
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	41
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	41
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	40
Analyzing somatic mutations by single-cell whole-genome sequencing	40
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience	40
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents	39
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	38
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	37
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	37
RNA sample optimization for cryo-EM analysis	36
Microfluidic gradients create a stem cell model of the human central nervous system	35
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	35
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	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
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	35
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	35
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	33
Stabilization and structure determination of integral membrane proteins by termini restraining	33
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	32
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	32
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	32
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	31
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	31
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	31
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	31
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	30
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	30
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	30
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	30
YCharOS protocol for antibody validation	30
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	30
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	30
A multi-glycomic platform for the analysis of food carbohydrates	29
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	29
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	29
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	28
A consensus platform for antibody characterization	28
Purification of mammalian telomeric DNA for single-molecule analysis	28
Tutorial: a guide to diffusion MRI and structural connectomics	28
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	28
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	28
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	28

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	28
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP	28
Protocols and risks: when less is more	27
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	27
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS	27
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	27
A new era begins at Nature Protocols	27
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	27
Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo	27
Determining chromatin architecture with Micro Capture-C	27
Labeling, isolation and characterization of cell-type-specific exosomes derived from mouse skin tissue	27