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	1108
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	546
Open thoracic surgical implantation of cardiac pacemakers in rats	428
Isoform-specific RNA structure determination using Nano-DMS-MaP	392
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	381
Routine culture and study of adult human brain cells from neurosurgical specimens	379
Design and application of the transformer base editor in mammalian cells and mice	332
Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline	324
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	272
Reproducible strategy for excisional skin-wound-healing studies in mice	269
Spontaneous and experimental models of lymph node metastasis	251
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	231
Purification and functional characterization of novel human skeletal stem cell lineages	231
Generating human bone marrow organoids for disease modeling and drug discovery	216
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	213
Generation of heart-forming organoids from human pluripotent stem cells	190
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	183
Quantitative molecular imaging using deep magnetic resonance fingerprinting	180
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	170
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	169
Fabrication of electron tunneling probes for measuring single-protein conductance	169
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	166
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	160
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells	154
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	153

Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	151
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	145
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	144
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	132
How to isolate channel-forming membrane proteins using the E. coli expression system	131
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	131
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	131
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance	130
Small RNA structural biochemistry in a post-sequencing era	127
Stable isotope tracing to assess tumor metabolism in vivo	117
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	113
Preparation and biomedical applications of single-metal atom catalysts	105
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	103
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	101
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	99
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	99
Chromatin accessibility profiling by ATAC-seq	99
Precise tracking of nanoparticles in plant roots	99
Large-scale growth of C. elegans and isolation of membrane protein complexes	97
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	97
Collections from Nature Protocols	96
Gene expression and chromatin state mapped in space	95
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	94
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	92
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	85
Fibrous polyisocyanide hydrogels for 3D cell culture applications	84
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	82
Achieving transient and reversible optical transparency in live mice with tartrazine	80
mRNA lipid nanoparticle formulation, characterization and evaluation	78
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	77
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	76
Honey bee functional genomics using symbiont-mediated RNAi	75
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	74
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	74
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	73
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	70
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	70
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	68
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	67
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	65
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	64
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	63
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	62
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	61
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	59
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting	59
Identification of immunogenic commensal antigens using phage display	58
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	58
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	57
All-optical interrogation of neural circuits in behaving mice	57

Scalable tissue labeling and clearing of intact human organs	57
Web-based multi-omics integration using the Analyst software suite	56
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	56
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	55
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	55
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	55
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	54
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	54
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	53
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	53
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	52
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	51
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	51
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	50
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	50
Enhancing consistency in brain imaging research for population neuroimaging	50
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	50
Easy and accurate protein structure prediction using ColabFold	49
Integrating optical neuroscience tools into touchscreen operant systems	49
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	49
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	49
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	49
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	48
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	48
Construction of complex bacteriogenic protocells from living material assembly	48
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	48
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	47
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	47
Analyzing somatic mutations by single-cell whole-genome sequencing	46
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	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 graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	45
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	45
Outcome devaluation as a method for identifying goal-directed behaviors in rats	45
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	44
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	44
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience	43
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	43
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	42
Annotating genetic variants to target genes using H-MAGMA	42
RNA sample optimization for cryo-EM analysis	41
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	41
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	41
Stabilization and structure determination of integral membrane proteins by termini restraining	40
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	39
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents	39
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	39
Capture of the newly transcribed RNA interactome using click chemistry	39
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	38
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	38
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	38
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	38
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	38
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	37
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	36
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	36
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	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	34
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	34
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	34
YCharOS protocol for antibody validation	34
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	34
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	34
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	34
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	32
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	31
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	31
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	31
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	30
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP	30
A multi-glycomic platform for the analysis of food carbohydrates	30
Purification of mammalian telomeric DNA for single-molecule analysis	30
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	29
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	29
A consensus platform for antibody characterization	29
Protocols and risks: when less is more	29
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	29
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	28
Tutorial: a guide to diffusion MRI and structural connectomics	28
Determining chromatin architecture with Micro Capture-C	28

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	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	27
A new era begins at Nature Protocols	27
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	27
Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo	27
scGPT: end-to-end protocol for fine-tuned retinal cell type annotation	26
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells	26
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach	26
The GFP thermal shift assay for screening ligand and lipid interactions to solute carrier transporters	26
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS	26
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection	26
The OBSERVE guidelines provide refinement criteria for rodent oncology models	25
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties	25
Synthesis of ordered mesoporous metal oxides by solvent evaporation-induced cooperative assembly	25
Generation of quality-controlled SARS-CoV-2 variant stocks	25
A practical guide to large-scale docking	25
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules	25
Facile synthesis of mesoporous TiO2 architectures with tunable configurations and nanometer precision	25
A guide to reverse metabolomics—a framework for big data discovery strategy	25
Designing and executing prime editing experiments in mammalian cells	25
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging	25
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes	24
Generation and characterization of vestibular inner ear organoids from human pluripotent stem cells	24
Precise mutagenesis in zebrafish using cytosine base editors	24
The use of methanol as a C1 building block	24
Integration of diverse bioactivity data into the Chemical Checker compound universe	24
Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection	24
Molecular recording using DNA Typewriter	24
A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues	23
Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2)	23
Publisher Correction: Precision genome editing using cytosine and adenine base editors in mammalian cells	23
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	23
Author Correction: Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging	23
Scanorama: integrating large and diverse single-cell transcriptomic datasets	23
Ultra-fast supercritically solvothermal polymerization for large single-crystalline covalent organic frameworks	23
Detection of intramolecular protein dynamics on nanosecond-to-microsecond timescales by nanoparticle-assisted NMR spin relaxation (NASR)	22
Retina-specific laminin-based generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions	22
In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation	22
Reply to: Byproducts in the synthesis of [68Ga]Ga-PSMA-11	22
Correlative light and electron microscopy for human brain and other biological models	22
Real-time imaging of axonal membrane protein life cycles	22
Precise kilobase-scale genomic insertions in mammalian cells using PASTE	22
A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification	22
Reprogramming fibroblast into human iBlastoids	22
Pooled genetic perturbation screens with image-based phenotypes	22
Integrative structural modeling of macromolecular complexes using Assembline	21
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection	21
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units	21
Scale-up approach for the preparation of magnetic ferrite nanocubes and other shapes with benchmark performance for magnetic hyperthermia applications	21
Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters	21
Click chemistry: a transformative technology in nuclear medicine	21
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy	21
A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure	20
Formulation of two lipid-based membrane–core nanoparticles for FOLFOX combination therapy	20
Author Correction: Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells	20
Optimizing the Cell Painting assay for image-based profiling	20
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	20
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq	19
Publisher Correction: A practical guide to large-scale docking	19
A multimodal imaging pipeline to decipher cell-specific metabolic functions and tissue microenvironment dynamics	19
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds	19
Transcriptomic profiling of individual bacteria by MATQ-seq	19
Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR	19
Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures	19
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples	19
Modeling heart rhythm using human engineered heart tissues	19
Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq	18
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors	18
Induction of human trophoblast stem cells	18
Assembly of a stem cell-derived human postimplantation embryo model	18
Consensus guidelines for the use of concurrent TMS-fMRI in cognitive and clinical neuroscience	18
Subretinal injection in mice to study retinal physiology and disease	18
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors	18
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments	18
Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes	17
Controlled synthesis of noble metal aerogels mediated by salts	17
Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing	17
Multiplexed single-cell analysis of organoid signaling networks	17
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain	17
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin	17
A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues	17
Streamlining spatial omics data analysis with Pysodb	17
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells	17
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control	17
Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids	17
High-resolution topographic surveying and change detection with the iPhone LiDAR	17
Expression and characterization of SARS-CoV-2 spike proteins	17
An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction	17
Metagenome-assembled genome extraction and analysis from microbiomes using KBase	16
A practical guide to machine-learning scoring for structure-based virtual screening	16
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V	16
Using clusterProfiler to characterize multiomics data	16
Creating hierarchical pores in metal–organic frameworks via postsynthetic reactions	16
A multiwell plate approach to increase the sample throughput during tissue clearing	15