Nature Protocols

Article	Citations
An accessible workflow for high-sensitivity proteomics using parallel accumulation–serial fragmentation (PASEF)	993
A multimodal imaging pipeline to decipher cell-specific metabolic functions and tissue microenvironment dynamics	468
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	422
Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics	342
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors	306
Induction of human trophoblast stem cells	296
Reproducible strategy for excisional skin-wound-healing studies in mice	259
Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts	246
Stabilization and structure determination of integral membrane proteins by termini restraining	232
Snapshot photoacoustic topography through an ergodic relay of optical absorption in vivo	220
An LC-MS/MS assay and complementary web-based tool to quantify and predict compound accumulation in E. coli	218
Subretinal injection in mice to study retinal physiology and disease	190
Design and application of the transformer base editor in mammalian cells and mice	184
fMRI data acquisition and analysis for task-free, anesthetized rats	182
Scalable single-cell profiling of chromatin modifications with sciCUT&Tag	176
Modified Neuropixels probes for recording human neurophysiology in the operating room	171
Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes	165
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments	165
Purification and functional characterization of novel human skeletal stem cell lineages	161
In situ label-free X-ray imaging for visualizing the localization of nanomedicines and subcellular architecture in intact single cells	154
Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays	154
Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry	152
Bacterial genome engineering using CRISPR-associated transposases	150
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	143
Genetic recording of in vivo cell proliferation by ProTracer	138

Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	132
Advances in mass spectrometry to unravel the structure and function of protein condensates	131
Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements)	128
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	125
QurvE: user-friendly software for the analysis of biological growth and fluorescence data	124
Generation of proximal tubule-enhanced kidney organoids from human pluripotent stem cells	123
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	122
Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting	121
BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS	114
Measuring carbohydrate recognition profile of lectins on live cells using liquid glycan array (LiGA)	112
OBSERVE: guidelines for the refinement of rodent cancer models	112
Assembly of a stem cell-derived human postimplantation embryo model	109
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	106
Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors	106
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	105
Generating human bone marrow organoids for disease modeling and drug discovery	104
Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice	104
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins	103
Publisher Correction: Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	97
Generation of mouse–human chimeric embryos	95
RNA sample optimization for cryo-EM analysis	95
Capture of the newly transcribed RNA interactome using click chemistry	93
dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy	92
Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D	89
Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research	85
Open thoracic surgical implantation of cardiac pacemakers in rats	83
Genetic manipulation and immortalized culture of ex vivo primary human germinal center B cells	83
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents	83
Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment	82
Thrombin generation test based on a 96-channel pipettor for evaluation of FXIa procoagulant activity in pharmaceuticals	82
Cytosine and adenosine base editing in human pluripotent stem cells using transient reporters for editing enrichment	82
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	80
Publisher Correction: A practical guide to large-scale docking	80
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors	78
Generation of heart-forming organoids from human pluripotent stem cells	78
Precise motor mapping with transcranial magnetic stimulation	74
Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline	73
Microtiter plate assays to assess antibiofilm activity against bacteria	73
Full-length circular RNA profiling by nanopore sequencing with CIRI-long	72
CRISPR–Cas9-mediated chromosome engineering in Arabidopsis thaliana	71
FIND-seq: high-throughput nucleic acid cytometry for rare single-cell transcriptomics	70
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq	70
Biolayer interferometry for measuring the kinetics of protein–protein interactions and nanobody binding	69
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	68
Routine culture and study of adult human brain cells from neurosurgical specimens	68
A mouse model of volumetric muscle loss and therapeutic scaffold implantation	68
From whole-slide image to biomarker prediction: end-to-end weakly supervised deep learning in computational pathology	66
Isoform-specific RNA structure determination using Nano-DMS-MaP	66
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds	64
Raman spectral cytopathology for cancer diagnostic applications	64

In situ electrochemical Raman spectroscopy and ab initio molecular dynamics study of interfacial water on a single-crystal surface	63
Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq	62
Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel	61
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	60
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	60
Optimized single-nucleus transcriptional profiling by combinatorial indexing	59
Whole-brain functional ultrasound imaging in awake head-fixed mice	59
High-speed laser-scanning biological microscopy using FACED	58
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	58
Precise genome engineering in Pseudomonas using phage-encoded homologous recombination and the Cascade–Cas3 system	58
Author Correction: Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells	58
A dynamic DNA tetrahedron framework for active targeting	57
iBEAT V2.0: a multisite-applicable, deep learning-based pipeline for infant cerebral cortical surface reconstruction	57
Algorithmic assessment of cellular senescence in experimental and clinical specimens	56
rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data	54
The normative modeling framework for computational psychiatry	54
Affinity-based profiling of endogenous phosphoprotein phosphatases by mass spectrometry	52
A distal lung organoid model to study interstitial lung disease, viral infection and human lung development	51
Analysis of clonogenic growth in vitro	51
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	49
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	48
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	48
Enzyme immobilization on covalent organic framework supports	48
Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures	48
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples	47
Protocols for clinical use at Nature Protocols	47
Assembly of complete mouse embryo models from embryonic and induced stem cell types in vitro	46
A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues	46
Genetic circuit design automation with Cello 2.0	46
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	46
A practical guide to machine-learning scoring for structure-based virtual screening	45
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	45
Small RNA structural biochemistry in a post-sequencing era	45
Laser microsurgery for presynaptic interrogation	44
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	43
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	43
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	43
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	42
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	42
Fabrication of electron tunneling probes for measuring single-protein conductance	42
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	41
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	41
Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids	41
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	40
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	40
Molecular profiling of enteric nervous system cell lineages	40
A nanobody-based strategy for rapid and scalable purification of human protein complexes	40
Expression and characterization of SARS-CoV-2 spike proteins	40
Isolation of ready-made rat microvessels and its applications in effective in vivo vascularization and in angiogenic studies in vitro	39
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	39
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	38
YCharOS protocol for antibody validation	38
Selected ion flow tube mass spectrometry for targeted analysis of volatile organic compounds in human breath	38
Growing and making nano- and microcrystals	38
Simultaneous ribosome profiling of hundreds of microbes from the human microbiome	38
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	38
Precise tracking of nanoparticles in plant roots	38
Preparation of single-cell suspensions of mouse glomeruli for high-throughput analysis	38
iDRiP for the systematic discovery of proteins bound directly to noncoding RNA	38
Multiplexed bioluminescence-mediated tracking of DNA double-strand break repairs in vitro and in vivo	38
In vitro culture of cynomolgus monkey embryos from blastocyst to early organogenesis	37
Structural characterization of protein-material interfacial interactions using lysine reactivity profiling-mass spectrometry	37
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin	37
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	37
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	36
Single-cell RNA-seq of maize meiocytes and pollen grains	36
Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test	36
Characterizing the structure of mouse behavior using Motion Sequencing	35
Construction and utilization of a new generation of bacteriophage-based particles, or TPA, for guided systemic delivery of nucleic acids to tumors	35
How to isolate channel-forming membrane proteins using the E. coli expression system	34
Proximity sequencing for the detection of mRNA, extracellular proteins and extracellular protein complexes in single cells	34
Preparing submicrometer crystals for electron diffraction	34
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	34
An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction	34
Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models	34
Multiplexed single-cell analysis of organoid signaling networks	33
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells	32
Implantation of Neuropixels probes for chronic recording of neuronal activity in freely behaving mice and rats	32
Intestinal organoid cocultures with microbes	32
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control	32

Interrogating the configurational stability of atropisomers	32
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	32
Chromatin accessibility profiling by ATAC-seq	32
A multi-glycomic platform for the analysis of food carbohydrates	31
3D bioprinted silk fibroin hydrogels for tissue engineering	31
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	31
Self-assembled ultraflexible probes for long-term neural recordings and neuromodulation	31
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	30
High-resolution topographic surveying and change detection with the iPhone LiDAR	30
Rapid biosynthesis of glycoprotein therapeutics and vaccines from freeze-dried bacterial cell lysates	30
Host circuit engagement of human cortical organoids transplanted in rodents	30
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance	30