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	1206
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	676
Inducible CRISPR–Cas9 screening platform to interrogate non-proliferative cellular states	548
Isoform-specific RNA structure determination using Nano-DMS-MaP	520
Design and application of the transformer base editor in mammalian cells and mice	431
Routine culture and study of adult human brain cells from neurosurgical specimens	406
Open thoracic surgical implantation of cardiac pacemakers in rats	396
Spontaneous and experimental models of lymph node metastasis	305
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	305
Reproducible strategy for excisional skin-wound-healing studies in mice	276
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	274
Purification and functional characterization of novel human skeletal stem cell lineages	269
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	206
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	204
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	204
Generating human bone marrow organoids for disease modeling and drug discovery	201
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	190
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	187
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	186
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	183
Preparation and biomedical applications of single-metal atom catalysts	169
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	161
Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing	149
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	146
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	146

Small RNA structural biochemistry in a post-sequencing era	145
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	138
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	133
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	132
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	128
How to isolate channel-forming membrane proteins using the E. coli expression system	123
Precise tracking of nanoparticles in plant roots	116
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	114
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	113
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	108
Fabrication of electron tunneling probes for measuring single-protein conductance	107
Quantitative molecular imaging using deep magnetic resonance fingerprinting	104
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	104
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells	103
Large-scale growth of C. elegans and isolation of membrane protein complexes	97
Chromatin accessibility profiling by ATAC-seq	97
Collections from Nature Protocols	96
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	95
Gene expression and chromatin state mapped in space	94
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	93
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	87
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	85
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	84
mRNA lipid nanoparticle formulation, characterization and evaluation	84
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	82
Achieving transient and reversible optical transparency in live mice with tartrazine	82
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	82
Fibrous polyisocyanide hydrogels for 3D cell culture applications	79
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	78
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	78
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	77
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	76
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	76
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	74
Honey bee functional genomics using symbiont-mediated RNAi	72
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	71
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	70
Identification of immunogenic commensal antigens using phage display	69
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	69
Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy	69
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	69
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	67
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	66
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	64
Scalable tissue labeling and clearing of intact human organs	64
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	63
All-optical interrogation of neural circuits in behaving mice	63
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	63
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	62
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	61

Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	61
Web-based multi-omics integration using the Analyst software suite	60
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	60
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	60
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	59
Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples	59
Enhancing consistency in brain imaging research for population neuroimaging	59
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	56
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	56
Integrating optical neuroscience tools into touchscreen operant systems	56
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	55
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	54
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
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	53
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	53
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	53
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	52
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	52
Easy and accurate protein structure prediction using ColabFold	51
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	51
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	50
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	50
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	50
In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability	50
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	49
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience	48
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	48
Annotating genetic variants to target genes using H-MAGMA	48
Construction of complex bacteriogenic protocells from living material assembly	48
Analyzing somatic mutations by single-cell whole-genome sequencing	47
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	44
CRISPR screens in human neural organoids and assembloids	44
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	44
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	44
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	43
Directional conjugation of monoclonal antibodies to nanoparticles using metal-free click chemistry	43
Outcome devaluation as a method for identifying goal-directed behaviors in rats	41
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	40
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	40
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	39
RNA sample optimization for cryo-EM analysis	39
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	38
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	38
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	38
Microfluidic gradients create a stem cell model of the human central nervous system	38
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	37
Stabilization and structure determination of integral membrane proteins by termini restraining	37
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	36
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	36
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	36
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	36
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	35
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	35
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	35
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	35
YCharOS protocol for antibody validation	34
Using tunable hydrogel microparticles to measure cellular forces	34
Bioengineering mini-colons for ex vivo colorectal cancer research	33
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	33
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	33
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	33
Multilevel characterization of genome editor nuclease activity with BreakTag	33
A multi-glycomic platform for the analysis of food carbohydrates	32
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	32
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	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
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	31
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	30
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	30
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	30
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	30
Determining chromatin architecture with Micro Capture-C	30
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	30
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	30
A consensus platform for antibody characterization	29
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	29
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP	29
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	29
Purification of mammalian telomeric DNA for single-molecule analysis	29

DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	29
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	29
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	29
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	29
Tutorial: a guide to diffusion MRI and structural connectomics	29
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	29
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection	28
NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns	28
scGPT: end-to-end protocol for fine-tuned retinal cell type annotation	28
A new era begins at Nature Protocols	28
Labeling, isolation and characterization of cell-type-specific exosomes derived from mouse skin tissue	28
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties	28
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS	28
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells	28
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging	28
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules	28
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach	28