Nature Protocols

Article	Citations
Inducible CRISPR–Cas9 screening platform to interrogate non-proliferative cellular states	1284
Open thoracic surgical implantation of cardiac pacemakers in rats	1051
Design and application of the transformer base editor in mammalian cells and mice	871
Automated cGMP optical labeling of FDA-approved antibodies for human use	662
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	474
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	470
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	458
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	314
Reproducible strategy for excisional skin-wound-healing studies in mice	299
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	296
Generating human bone marrow organoids for disease modeling and drug discovery	248
GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery–center axis	241
Patient-derived ependymoma and medulloblastoma tumoroids: generation, biobanking and drug screening	226
Spontaneous and experimental models of lymph node metastasis	226
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	226
Purification and functional characterization of novel human skeletal stem cell lineages	214
Isoform-specific RNA structure determination using Nano-DMS-MaP	209
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	199
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	168
How to isolate channel-forming membrane proteins using the E. coli expression system	165
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	146
Quantitative molecular imaging using deep magnetic resonance fingerprinting	146
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	143
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	131
Precise tracking of nanoparticles in plant roots	126

Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	125
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	124
Simplified ischemia-free liver transplantation with continuous normothermic machine perfusion	123
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	111
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	110
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	109
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	108
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	107
Small RNA structural biochemistry in a post-sequencing era	107
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	106
Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing	105
Fabrication of electron tunneling probes for measuring single-protein conductance	90
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	90
Preparation of C4′-modified nucleoside analogs	88
Preparation and biomedical applications of single-metal atom catalysts	87
Large-scale growth of C. elegans and isolation of membrane protein complexes	86
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	86
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	86
Collections from Nature Protocols	84
Gene expression and chromatin state mapped in space	82
Drosophila melanogaster as a model host for studying Pseudomonas aeruginosa feeding infection	81
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	80
A new era for coral functional genomics	79
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	78
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	78
Fibrous polyisocyanide hydrogels for 3D cell culture applications	78
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	78
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	74
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	73
Honey bee functional genomics using symbiont-mediated RNAi	72
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	72
Achieving transient and reversible optical transparency in live mice with tartrazine	71
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	71
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	70
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	69
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	68
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	68
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	66
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	65
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	65
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	64
mRNA lipid nanoparticle formulation, characterization and evaluation	63
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	63
Identification of immunogenic commensal antigens using phage display	62
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	62
Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy	61
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	60
Screening high-quality lignins extracted from biomass to prepare biobased wood adhesives	60
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	58
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	57

Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	57
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	55
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	54
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	54
Scalable tissue labeling and clearing of intact human organs	54
Enhancing consistency in brain imaging research for population neuroimaging	53
Web-based multi-omics integration using the Analyst software suite	53
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	51
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	51
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	50
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	50
Integrating optical neuroscience tools into touchscreen operant systems	49
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	48
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	48
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	48
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	47
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	47
Establishing a long-term versatile culture system for functional mouse mammary organoids from single cells	46
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	46
Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples	45
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	45
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	44
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	44
Easy and accurate protein structure prediction using ColabFold	43
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	43
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	41
Directional conjugation of monoclonal antibodies to nanoparticles using metal-free click chemistry	40
Construction of complex bacteriogenic protocells from living material assembly	40
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	40
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	39
Analyzing somatic mutations by single-cell whole-genome sequencing	39
Magnetoencephalography in human neuroscience research: planning, piloting, implementation and quality assurance	39
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	38
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	38
Outcome devaluation as a method for identifying goal-directed behaviors in rats	38
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	38
CRISPR screens in human neural organoids and assembloids	38
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	38
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	37
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	37
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	37
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	37
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	37
Microfluidic gradients create a stem cell model of the human central nervous system	37
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	37
Annotating genetic variants to target genes using H-MAGMA	37
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	36
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	36
RNA sample optimization for cryo-EM analysis	36
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	35
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	35
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	35
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	34
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	34
Bioengineering mini-colons for ex vivo colorectal cancer research	34
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	34
Multilevel characterization of genome editor nuclease activity with BreakTag	34
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	33
A multi-glycomic platform for the analysis of food carbohydrates	32
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	32
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	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	32
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	32
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	32
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	32
Using tunable hydrogel microparticles to measure cellular forces	31
Quantitative imaging of apoplastic pH in plant roots via confocal microscopy	31
YCharOS protocol for antibody validation	31
Preparation of placenta-tropic mRNA lipid nanoparticles for pregnancy disorders	31
Preparation of targeted lipid nanoparticles for precision nucleic acid delivery	30
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	30
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	30
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	30
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	30
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	30
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	30
Oscillatory brain state-dependent stimulation with transcranial magnetic stimulation combined with electroencephalography	29
Tutorial: a guide to diffusion MRI and structural connectomics	29
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	29
Harnessing intermediate-scale bioreactors for next-generation macrophage production and application	29

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	29
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	29
Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq	29
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	29
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	28
A consensus platform for antibody characterization	28
Electrocatalytic reactions involving aqueous nitrate and nitrite	28
Determining chromatin architecture with Micro Capture-C	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
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	28
A comprehensive framework for statistical testing of brain dynamics	27
A new era begins at Nature Protocols	27
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	27
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules	26
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells	26
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties	26
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection	25
scGPT: end-to-end protocol for fine-tuned retinal cell type annotation	25
NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns	25
Labeling, isolation and characterization of cell-type-specific exosomes derived from mouse skin tissue	25
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach	25
Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET	25
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS	25
Synthesis of ordered mesoporous metal oxides by solvent evaporation-induced cooperative assembly	25
Designing and executing prime editing experiments in mammalian cells	24
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes	23
Integration of diverse bioactivity data into the Chemical Checker compound universe	23
Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2)	23
Generation of quality-controlled SARS-CoV-2 variant stocks	23
Proteome-wide profiling of S-nitrosylated proteins using the SNOTRAP probe and mass spectrometry-based detection	23
The OBSERVE guidelines provide refinement criteria for rodent oncology models	23
Generation and characterization of vestibular inner ear organoids from human pluripotent stem cells	23
Preparing and characterizing environmentally aged microplastics	23
The use of methanol as a C1 building block	22
Ultra-fast supercritically solvothermal polymerization for large single-crystalline covalent organic frameworks	22
Visualizing infection by single positive-sense RNA viruses using virus infection real-time imaging (VIRIM)	22
Molecular recording using DNA Typewriter	22
Facile synthesis of mesoporous TiO2 architectures with tunable configurations and nanometer precision	22
In vivo ultrasound-induced luminescence imaging via trianthracene derivatives nanomaterials	22
Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection	22
Precise mutagenesis in zebrafish using cytosine base editors	22
Scanorama: integrating large and diverse single-cell transcriptomic datasets	22
In vivo Raman spectroscopy for real-time biochemical assessment of tissue pathology and physiology	22
A guide to reverse metabolomics—a framework for big data discovery strategy	22
INFOGEST Quant: standardized in vitro determination of digestibility and DIAAS of dietary proteins based on the INFOGEST static digestion model	22
A versatile toolkit for drug metabolism studies with GNPS2: from drug development to clinical monitoring	22
Reprogramming fibroblast into human iBlastoids	21
Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters	21
Author Correction: Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging	21
A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification	21
In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation	21
Formulation of two lipid-based membrane–core nanoparticles for FOLFOX combination therapy	20
A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues	20
Retina-specific laminin-based generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions	20
A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure	20
Detection of intramolecular protein dynamics on nanosecond-to-microsecond timescales by nanoparticle-assisted NMR spin relaxation (NASR)	20
Optimizing the Cell Painting assay for image-based profiling	20
Click chemistry: a transformative technology in nuclear medicine	19
Scale-up approach for the preparation of magnetic ferrite nanocubes and other shapes with benchmark performance for magnetic hyperthermia applications	19
Preparation of ENBSe-based photoredox catalysts for O2-independent phototherapy in living systems	19
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units	19
Reply to: Byproducts in the synthesis of [68Ga]Ga-PSMA-11	19
Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq)	19
Precise kilobase-scale genomic insertions in mammalian cells using PASTE	19
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy	18
Report Approval for Transcranial Electrical Stimulation (RATES): expert recommendation based on a Delphi consensus study	18
Correlative light and electron microscopy for human brain and other biological models	18
Real-time imaging of axonal membrane protein life cycles	18
Selecting aminoacyl-tRNA synthetase/tRNA pairs for efficient genetic encoding of noncanonical amino acids into proteins	18
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection	18
XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models	18
Fabrication and characterization of optoelectronic in-sensor computing devices	17
Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes	17
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples	17
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors	17
Multichannel genomic recording of biological information with ENGRAM	17
Author Correction: Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells	17
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds	17
Extracting and characterizing microplastics and nanoplastics from environmental samples	17
A multimodal imaging pipeline to decipher cell-specific metabolic functions and tissue microenvironment dynamics	17
Transcriptomic profiling of individual bacteria by MATQ-seq	17
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq	17
Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures	16
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control	16
Controlled synthesis of noble metal aerogels mediated by salts	16
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells	16
Modeling heart rhythm using human engineered heart tissues	16
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin	16
Isolation, purification and characterization of lipocartilage in mice	16
Streamlining spatial omics data analysis with Pysodb	16
Induction of human trophoblast stem cells	16
An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction	16
Multidimensional analysis of host–virus interactions using the virus-encoded CRISPR-based direct readout system (VECOS)	16
Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing	16