Nature Protocols

Article	Citations
Design and application of the transformer base editor in mammalian cells and mice	1024
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	481
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	435
Cytosine and adenosine base editing in human pluripotent stem cells using transient reporters for editing enrichment	353
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	331
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	313
Open thoracic surgical implantation of cardiac pacemakers in rats	269
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	254
Isoform-specific RNA structure determination using Nano-DMS-MaP	227
Routine culture and study of adult human brain cells from neurosurgical specimens	226
Generating human bone marrow organoids for disease modeling and drug discovery	196
Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline	193
Generation of heart-forming organoids from human pluripotent stem cells	190
Purification and functional characterization of novel human skeletal stem cell lineages	185
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	179
Reproducible strategy for excisional skin-wound-healing studies in mice	175
Protocols for clinical use at Nature Protocols	171
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	163
Implantation of Neuropixels probes for chronic recording of neuronal activity in freely behaving mice and rats	162
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells	160
Quantitative molecular imaging using deep magnetic resonance fingerprinting	159
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	159
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	152
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	145
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	144

Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	134
Fabrication of electron tunneling probes for measuring single-protein conductance	131
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	130
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	129
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	121
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	119
How to isolate channel-forming membrane proteins using the E. coli expression system	117
Small RNA structural biochemistry in a post-sequencing era	113
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	113
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	112
Tutorial: using nanoneedles for intracellular delivery	110
Stable isotope tracing to assess tumor metabolism in vivo	108
Precise tracking of nanoparticles in plant roots	108
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance	108
Chromatin accessibility profiling by ATAC-seq	100
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	100
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	96
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	96
mRNA lipid nanoparticle formulation, characterization and evaluation	90
Honey bee functional genomics using symbiont-mediated RNAi	87
Large-scale growth of C. elegans and isolation of membrane protein complexes	87
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	86
Collections from Nature Protocols	86
Gene expression and chromatin state mapped in space	86
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	85
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	85
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	84
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	83
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	81
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	81
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	78
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	78
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	77
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	76
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	75
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	74
Author Correction: Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells	74
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	72
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	69
Inverse electron demand Diels–Alder click chemistry for pretargeted PET imaging and radioimmunotherapy	69
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	68
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting	66
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	65
Scalable tissue labeling and clearing of intact human organs	65
All-optical interrogation of neural circuits in behaving mice	65
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	64
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	62
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	62
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	62
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	62

An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality	62
Web-based multi-omics integration using the Analyst software suite	62
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	62
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	61
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	61
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	60
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	59
Enhancing consistency in brain imaging research for population neuroimaging	58
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	56
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	54
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	54
Easy and accurate protein structure prediction using ColabFold	52
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	52
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
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	50
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	50
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	50
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	49
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	49
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	49
Construction of complex bacteriogenic protocells from living material assembly	49
Outcome devaluation as a method for identifying goal-directed behaviors in rats	48
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	48
Analyzing somatic mutations by single-cell whole-genome sequencing	47
In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability	47
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	47
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	47
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	46
Annotating genetic variants to target genes using H-MAGMA	46
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	46
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents	44
Stabilization and structure determination of integral membrane proteins by termini restraining	44
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	44
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	44
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience	44
Use of deep learning to develop continuous-risk models for adverse event prediction from electronic health records	44
Capture of the newly transcribed RNA interactome using click chemistry	43
Thrombin generation test based on a 96-channel pipettor for evaluation of FXIa procoagulant activity in pharmaceuticals	43
High-speed laser-scanning biological microscopy using FACED	42
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	42
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	42
Whole-brain functional ultrasound imaging in awake head-fixed mice	41
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	41
RNA sample optimization for cryo-EM analysis	41
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	41
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	41
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	40
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	40
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	40
YCharOS protocol for antibody validation	39
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	39
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	39
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	39
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	39
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	38
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	38
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	38
Simultaneous ribosome profiling of hundreds of microbes from the human microbiome	37
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	36
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	36
A multi-glycomic platform for the analysis of food carbohydrates	36
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	35
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	35
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	34
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	34
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	34
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	34
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP	33
Protocols and risks: when less is more	33
Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo	33
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	33
A consensus platform for antibody characterization	33
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	32
Tutorial: a guide to diffusion MRI and structural connectomics	32
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	32
Determining chromatin architecture with Micro Capture-C	32
Purification of mammalian telomeric DNA for single-molecule analysis	32
Testing physiologically relevant conditions in minimal inhibitory concentration assays	31
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS	31

A new era begins at Nature Protocols	31
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules	31
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection	31
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach	31
Generic acquisition protocol for quantitative MRI of the spinal cord	31
Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry	30
BAR-Seq clonal tracking of gene-edited cells	30
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells	30
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging	29
The GFP thermal shift assay for screening ligand and lipid interactions to solute carrier transporters	29
A practical guide to large-scale docking	29
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties	29
Precise mutagenesis in zebrafish using cytosine base editors	28
Designing and executing prime editing experiments in mammalian cells	28
Design of metal-mediated protein assemblies via hydroxamic acid functionalities	28
Tutorial: practical considerations for tissue clearing and imaging	28
Translation of 11C-labeled tracer synthesis to a CGMP environment as exemplified by [11C]ER176 for PET imaging of human TSPO	28
High spatial and temporal resolution Ca2+ imaging of myocardial strips from human, pig and rat	28
Generation of quality-controlled SARS-CoV-2 variant stocks	27
Molecular recording using DNA Typewriter	27
Ultra-fast supercritically solvothermal polymerization for large single-crystalline covalent organic frameworks	26
Large-scale preparation of fluorescence multiplex host cell reactivation (FM-HCR) reporters	26
Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2)	26
A guide to reverse metabolomics—a framework for big data discovery strategy	26
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes	26
The OBSERVE guidelines provide refinement criteria for rodent oncology models	26
Scanorama: integrating large and diverse single-cell transcriptomic datasets	25
Precise kilobase-scale genomic insertions in mammalian cells using PASTE	25
Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection	25
The use of methanol as a C1 building block	25
Publisher Correction: Precision genome editing using cytosine and adenine base editors in mammalian cells	25
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	25
Surgical implantation of wireless, battery-free optoelectronic epidural implants for optogenetic manipulation of spinal cord circuits in mice	25
Retina-specific laminin-based generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions	25
In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation	24
Formulation of two lipid-based membrane–core nanoparticles for FOLFOX combination therapy	24
Author Correction: Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging	24
Reprogramming fibroblast into human iBlastoids	24
A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues	24
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy	23
Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters	23
Real-time imaging of axonal membrane protein life cycles	23
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units	23
A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification	23
Correlative light and electron microscopy for human brain and other biological models	23
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	22
Optimizing the Cell Painting assay for image-based profiling	22
Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures	22
Author Correction: Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells	22
Scale-up approach for the preparation of magnetic ferrite nanocubes and other shapes with benchmark performance for magnetic hyperthermia applications	22
Reply to: Byproducts in the synthesis of [68Ga]Ga-PSMA-11	22
Click chemistry: a transformative technology in nuclear medicine	22
Assembly of a stem cell-derived human postimplantation embryo model	22
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection	22
Integrative structural modeling of macromolecular complexes using Assembline	22
A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure	22
Pooled genetic perturbation screens with image-based phenotypes	22
A multimodal imaging pipeline to decipher cell-specific metabolic functions and tissue microenvironment dynamics	21
Transcriptomic profiling of individual bacteria by MATQ-seq	21
Generation of mouse–human chimeric embryos	21
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples	21
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds	21
Publisher Correction: A practical guide to large-scale docking	21
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors	21
Induction of human trophoblast stem cells	21
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq	20
Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes	20
Subretinal injection in mice to study retinal physiology and disease	20
Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids	20
Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq	20
Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry	20
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin	20
Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test	20
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors	20
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments	20
An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction	20
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control	19
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V	19
Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing	19
Preparation of single-cell suspensions of mouse glomeruli for high-throughput analysis	19
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells	19
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain	19
Streamlining spatial omics data analysis with Pysodb	19
Multiplexed single-cell analysis of organoid signaling networks	19
A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues	19
Metagenome-assembled genome extraction and analysis from microbiomes using KBase	18
Fabricating and printing chemiresistors based on monolayer-capped metal nanoparticles	18
Multigram synthesis of N-alkyl bis-ureas for asymmetric hydrogen bonding phase-transfer catalysis	18
A practical guide to machine-learning scoring for structure-based virtual screening	18
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport	18
Creating hierarchical pores in metal–organic frameworks via postsynthetic reactions	18
High-resolution topographic surveying and change detection with the iPhone LiDAR	18
Expression and characterization of SARS-CoV-2 spike proteins	18
Using clusterProfiler to characterize multiomics data	18
Pair correlation microscopy of intracellular molecular transport	18