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	1140
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	565
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	455
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	451
Design and application of the transformer base editor in mammalian cells and mice	399
Routine culture and study of adult human brain cells from neurosurgical specimens	345
Spontaneous and experimental models of lymph node metastasis	337
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	325
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	281
Generating human bone marrow organoids for disease modeling and drug discovery	259
Isoform-specific RNA structure determination using Nano-DMS-MaP	240
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	240
Reproducible strategy for excisional skin-wound-healing studies in mice	222
Generation of heart-forming organoids from human pluripotent stem cells	221
Purification and functional characterization of novel human skeletal stem cell lineages	215
Open thoracic surgical implantation of cardiac pacemakers in rats	190
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells	188
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	177
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	176
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	172
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	171
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	161
How to isolate channel-forming membrane proteins using the E. coli expression system	160
Preparation and biomedical applications of single-metal atom catalysts	159
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	158

Fabrication of electron tunneling probes for measuring single-protein conductance	157
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	155
Precise tracking of nanoparticles in plant roots	146
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	136
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	134
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	133
Quantitative molecular imaging using deep magnetic resonance fingerprinting	133
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	132
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	121
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	115
Small RNA structural biochemistry in a post-sequencing era	113
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance	110
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	108
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	105
Chromatin accessibility profiling by ATAC-seq	103
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	103
Large-scale growth of C. elegans and isolation of membrane protein complexes	102
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	100
Collections from Nature Protocols	100
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	99
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	99
Gene expression and chromatin state mapped in space	96
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	88
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	87
Achieving transient and reversible optical transparency in live mice with tartrazine	85
Fibrous polyisocyanide hydrogels for 3D cell culture applications	82
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	81
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	80
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	78
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	77
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	76
Honey bee functional genomics using symbiont-mediated RNAi	75
mRNA lipid nanoparticle formulation, characterization and evaluation	73
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	73
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	72
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	72
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	72
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	69
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	66
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	66
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	65
Identification of immunogenic commensal antigens using phage display	64
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	64
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting	64
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	63
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	61
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	61
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	60
Scalable tissue labeling and clearing of intact human organs	59
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	59

Web-based multi-omics integration using the Analyst software suite	58
All-optical interrogation of neural circuits in behaving mice	58
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	58
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	57
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	56
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	55
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	54
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	53
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	53
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	53
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	53
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	53
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	53
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	52
Enhancing consistency in brain imaging research for population neuroimaging	52
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	52
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	51
Integrating optical neuroscience tools into touchscreen operant systems	51
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	51
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	50
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	50
Easy and accurate protein structure prediction using ColabFold	50
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	49
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	48
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	48
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	48
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	48
Outcome devaluation as a method for identifying goal-directed behaviors in rats	47
In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability	47
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	46
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	46
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	46
Construction of complex bacteriogenic protocells from living material assembly	45
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience	44
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	43
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	43
Analyzing somatic mutations by single-cell whole-genome sequencing	43
Annotating genetic variants to target genes using H-MAGMA	42
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	42
Stabilization and structure determination of integral membrane proteins by termini restraining	41
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	41
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents	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	40
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	40
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	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	40
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	39
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
Capture of the newly transcribed RNA interactome using click chemistry	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
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	36
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	35
YCharOS protocol for antibody validation	35
A multi-glycomic platform for the analysis of food carbohydrates	34
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	34
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	34
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	33
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	33
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	32
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	32
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
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	31
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	31
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	30
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	30
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	30
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	30
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	30
Protocols and risks: when less is more	30
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	30
A consensus platform for antibody characterization	30
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	29
Determining chromatin architecture with Micro Capture-C	29
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	28
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	28
Purification of mammalian telomeric DNA for single-molecule analysis	28

Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo	28
Tutorial: a guide to diffusion MRI and structural connectomics	28
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP	28
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	28
The GFP thermal shift assay for screening ligand and lipid interactions to solute carrier transporters	27
Synthesis of ordered mesoporous metal oxides by solvent evaporation-induced cooperative assembly	27
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection	27
Labeling, isolation and characterization of cell-type-specific exosomes derived from mouse skin tissue	27
scGPT: end-to-end protocol for fine-tuned retinal cell type annotation	27
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	27
A new era begins at Nature Protocols	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
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties	27
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach	27
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes	26
Designing and executing prime editing experiments in mammalian cells	26
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging	26
The OBSERVE guidelines provide refinement criteria for rodent oncology models	26
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules	26
Generation of quality-controlled SARS-CoV-2 variant stocks	26
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells	26
In vivo ultrasound-induced luminescence imaging via trianthracene derivatives nanomaterials	25
Facile synthesis of mesoporous TiO2 architectures with tunable configurations and nanometer precision	25
Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection	25
Molecular recording using DNA Typewriter	25
Integration of diverse bioactivity data into the Chemical Checker compound universe	25
Generation and characterization of vestibular inner ear organoids from human pluripotent stem cells	25
Scanorama: integrating large and diverse single-cell transcriptomic datasets	25
Precise mutagenesis in zebrafish using cytosine base editors	25
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	25
A guide to reverse metabolomics—a framework for big data discovery strategy	24
A versatile toolkit for drug metabolism studies with GNPS2: from drug development to clinical monitoring	24
The use of methanol as a C1 building block	24
Retina-specific laminin-based generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions	23
Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2)	23
Author Correction: Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging	23
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units	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
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	22
Integrative structural modeling of macromolecular complexes using Assembline	22
Correlative light and electron microscopy for human brain and other biological models	22
Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters	22
Optimizing the Cell Painting assay for image-based profiling	22
Publisher Correction: Precision genome editing using cytosine and adenine base editors in mammalian cells	22
Click chemistry: a transformative technology in nuclear medicine	22
Formulation of two lipid-based membrane–core nanoparticles for FOLFOX combination therapy	22
Reply to: Byproducts in the synthesis of [68Ga]Ga-PSMA-11	21
Selecting aminoacyl-tRNA synthetase/tRNA pairs for efficient genetic encoding of noncanonical amino acids into proteins	21
Pooled genetic perturbation screens with image-based phenotypes	21
Precise kilobase-scale genomic insertions in mammalian cells using PASTE	21
A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues	21
Reprogramming fibroblast into human iBlastoids	21
A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure	21
Author Correction: Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells	20
In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation	20
A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification	20
Scale-up approach for the preparation of magnetic ferrite nanocubes and other shapes with benchmark performance for magnetic hyperthermia applications	20
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy	20
Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures	20
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection	20
Real-time imaging of axonal membrane protein life cycles	20
A multimodal imaging pipeline to decipher cell-specific metabolic functions and tissue microenvironment dynamics	19
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples	19
Consensus guidelines for the use of concurrent TMS-fMRI in cognitive and clinical neuroscience	19
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq	19
Transcriptomic profiling of individual bacteria by MATQ-seq	19
Modeling heart rhythm using human engineered heart tissues	19
Publisher Correction: A practical guide to large-scale docking	19
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors	19
Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR	19
Subretinal injection in mice to study retinal physiology and disease	18
Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq	18
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments	18
Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing	18
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors	18
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds	18
Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes	18
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin	18
Induction of human trophoblast stem cells	18
Assembly of a stem cell-derived human postimplantation embryo model	18
An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction	18
Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids	17
A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues	17
Controlled synthesis of noble metal aerogels mediated by salts	17
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control	17
Expression and characterization of SARS-CoV-2 spike proteins	17
Multidimensional analysis of host–virus interactions using the virus-encoded CRISPR-based direct readout system (VECOS)	17
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V	17
Streamlining spatial omics data analysis with Pysodb	17
Metagenome-assembled genome extraction and analysis from microbiomes using KBase	17
A practical guide to machine-learning scoring for structure-based virtual screening	17
High-resolution topographic surveying and change detection with the iPhone LiDAR	17
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells	17
Spotting-based differentiation of functional dopaminergic progenitors from human pluripotent stem cells	16