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
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	159
Quantitative molecular imaging using deep magnetic resonance fingerprinting	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
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
Stable isotope tracing to assess tumor metabolism in vivo	108
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	100
Chromatin accessibility profiling by ATAC-seq	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
Collections from Nature Protocols	86
Gene expression and chromatin state mapped in space	86
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	86
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	85
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	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 and quantitative analysis of multicenter luminescence materials for sensing function	78
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	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
Inverse electron demand Diels–Alder click chemistry for pretargeted PET imaging and radioimmunotherapy	69
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	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
Scalable tissue labeling and clearing of intact human organs	65
All-optical interrogation of neural circuits in behaving mice	65
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	65
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	64
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
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
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	61
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	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
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	54
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	54
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	52
Easy and accurate protein structure prediction using ColabFold	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