Nature Protocols

Papers
(The median citation count of Nature Protocols is 10. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-06-01 to 2025-06-01.)
ArticleCitations
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo1046
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA493
Cytosine and adenosine base editing in human pluripotent stem cells using transient reporters for editing enrichment457
Open thoracic surgical implantation of cardiac pacemakers in rats360
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis358
Purification and functional characterization of novel human skeletal stem cell lineages332
Design and application of the transformer base editor in mammalian cells and mice284
Generation of heart-forming organoids from human pluripotent stem cells276
Isoform-specific RNA structure determination using Nano-DMS-MaP238
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ235
Routine culture and study of adult human brain cells from neurosurgical specimens218
Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline204
Generating human bone marrow organoids for disease modeling and drug discovery202
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution196
Reproducible strategy for excisional skin-wound-healing studies in mice194
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling188
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration186
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses183
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing168
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice167
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input165
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy152
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy152
How to isolate channel-forming membrane proteins using the E. coli expression system150
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag140
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants140
Precise tracking of nanoparticles in plant roots137
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination134
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells134
Chromatin accessibility profiling by ATAC-seq132
Implantation of Neuropixels probes for chronic recording of neuronal activity in freely behaving mice and rats123
Small RNA structural biochemistry in a post-sequencing era122
Tutorial: using nanoneedles for intracellular delivery120
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue120
Quantitative molecular imaging using deep magnetic resonance fingerprinting118
Stable isotope tracing to assess tumor metabolism in vivo117
Fabrication of electron tunneling probes for measuring single-protein conductance113
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry111
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance110
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids106
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds106
Achieving transient and reversible optical transparency in live mice with tartrazine101
Gene expression and chromatin state mapped in space97
Collections from Nature Protocols96
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract91
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts91
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data91
Honey bee functional genomics using symbiont-mediated RNAi89
mRNA lipid nanoparticle formulation, characterization and evaluation89
Large-scale growth of C. elegans and isolation of membrane protein complexes88
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells87
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging86
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases86
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia86
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility83
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography82
Preparation and quantitative analysis of multicenter luminescence materials for sensing function80
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene79
Fibrous polyisocyanide hydrogels for 3D cell culture applications79
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery79
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes77
Author Correction: Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells72
Inverse electron demand Diels–Alder click chemistry for pretargeted PET imaging and radioimmunotherapy71
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points71
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting68
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures68
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development68
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system68
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics67
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling66
Scalable tissue labeling and clearing of intact human organs66
All-optical interrogation of neural circuits in behaving mice66
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction66
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding65
An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality64
Web-based multi-omics integration using the Analyst software suite62
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals61
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture61
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells61
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data60
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D58
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments55
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues54
Profiling native pulmonary basement membrane stiffness using atomic force microscopy54
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM53
Enhancing consistency in brain imaging research for population neuroimaging53
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression53
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder52
Integrating optical neuroscience tools into touchscreen operant systems52
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid51
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView51
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents51
Easy and accurate protein structure prediction using ColabFold51
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS51
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations50
Construction of complex bacteriogenic protocells from living material assembly49
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout49
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells48
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification48
Outcome devaluation as a method for identifying goal-directed behaviors in rats47
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes47
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience47
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz46
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy46
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq45
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells45
Analyzing somatic mutations by single-cell whole-genome sequencing45
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data45
In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability44
Annotating genetic variants to target genes using H-MAGMA44
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries43
Capture of the newly transcribed RNA interactome using click chemistry43
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents43
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 editing43
High-speed laser-scanning biological microscopy using FACED42
Thrombin generation test based on a 96-channel pipettor for evaluation of FXIa procoagulant activity in pharmaceuticals42
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity42
Stabilization and structure determination of integral membrane proteins by termini restraining42
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice41
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding41
RNA sample optimization for cryo-EM analysis41
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles40
Whole-brain functional ultrasound imaging in awake head-fixed mice40
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes40
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair40
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells39
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks39
YCharOS protocol for antibody validation39
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice39
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device38
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq37
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo37
Direct analysis of biotransformations with mass spectrometry—DiBT-MS36
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics36
Simultaneous ribosome profiling of hundreds of microbes from the human microbiome36
m6A-SAC-seq for quantitative whole transcriptome m6A profiling36
Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING35
Synthesis of N-heterocycles through alcohol dehydrogenative coupling35
A multi-glycomic platform for the analysis of food carbohydrates35
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain35
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector34
Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo34
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity34
A consensus platform for antibody characterization33
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)33
Tutorial: a guide to diffusion MRI and structural connectomics33
Purification of mammalian telomeric DNA for single-molecule analysis33
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys32
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations32
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP32
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells32
Protocols and risks: when less is more32
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale31
Determining chromatin architecture with Micro Capture-C31
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach30
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules30
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes30
A new era begins at Nature Protocols30
Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry30
Generic acquisition protocol for quantitative MRI of the spinal cord29
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells29
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection28
Testing physiologically relevant conditions in minimal inhibitory concentration assays28
High spatial and temporal resolution Ca2+ imaging of myocardial strips from human, pig and rat28
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS28
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging28
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties28
The GFP thermal shift assay for screening ligand and lipid interactions to solute carrier transporters28
A practical guide to large-scale docking28
Translation of 11C-labeled tracer synthesis to a CGMP environment as exemplified by [11C]ER176 for PET imaging of human TSPO27
Designing and executing prime editing experiments in mammalian cells27
Generation of quality-controlled SARS-CoV-2 variant stocks27
Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2)26
A guide to reverse metabolomics—a framework for big data discovery strategy26
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes26
Precise mutagenesis in zebrafish using cytosine base editors26
The use of methanol as a C1 building block26
The OBSERVE guidelines provide refinement criteria for rodent oncology models26
Integration of diverse bioactivity data into the Chemical Checker compound universe26
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)25
Facile synthesis of mesoporous TiO2 architectures with tunable configurations and nanometer precision25
Molecular recording using DNA Typewriter25
Scanorama: integrating large and diverse single-cell transcriptomic datasets25
Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection25
Ultra-fast supercritically solvothermal polymerization for large single-crystalline covalent organic frameworks24
Large-scale preparation of fluorescence multiplex host cell reactivation (FM-HCR) reporters24
Publisher Correction: Precision genome editing using cytosine and adenine base editors in mammalian cells24
Retina-specific laminin-based generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions24
Precise kilobase-scale genomic insertions in mammalian cells using PASTE24
Reply to: Byproducts in the synthesis of [68Ga]Ga-PSMA-1123
Reprogramming fibroblast into human iBlastoids23
A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues23
A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification23
In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation23
Correlative light and electron microscopy for human brain and other biological models23
Author Correction: Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging23
Native MS-guided lipidomics to define endogenous lipid microenvironments of eukaryotic receptors and transporters22
Click chemistry: a transformative technology in nuclear medicine22
Pooled genetic perturbation screens with image-based phenotypes22
Scale-up approach for the preparation of magnetic ferrite nanocubes and other shapes with benchmark performance for magnetic hyperthermia applications22
Real-time imaging of axonal membrane protein life cycles22
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection22
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses22
A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure22
Formulation of two lipid-based membrane–core nanoparticles for FOLFOX combination therapy22
Optimizing the Cell Painting assay for image-based profiling22
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy22
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units22
Publisher Correction: A practical guide to large-scale docking21
Author Correction: Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells21
Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures21
Integrative structural modeling of macromolecular complexes using Assembline21
Assembly of a stem cell-derived human postimplantation embryo model21
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors20
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds20
Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR20
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq20
Subretinal injection in mice to study retinal physiology and disease20
Induction of human trophoblast stem cells20
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors20
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples20
Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq20
A multimodal imaging pipeline to decipher cell-specific metabolic functions and tissue microenvironment dynamics20
Generation of mouse–human chimeric embryos20
Transcriptomic profiling of individual bacteria by MATQ-seq20
Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry20
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments20
An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction19
Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids19
Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes19
Expression and characterization of SARS-CoV-2 spike proteins19
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin19
Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test19
Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells18
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V18
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control18
High-resolution topographic surveying and change detection with the iPhone LiDAR18
Multiplexed single-cell analysis of organoid signaling networks18
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain18
Preparation of single-cell suspensions of mouse glomeruli for high-throughput analysis18
Streamlining spatial omics data analysis with Pysodb18
Metagenome-assembled genome extraction and analysis from microbiomes using KBase17
Creating hierarchical pores in metal–organic frameworks via postsynthetic reactions17
Prototype mouse models for researching SEND-based mRNA delivery and gene therapy17
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport17
A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues17
Pair correlation microscopy of intracellular molecular transport17
Using clusterProfiler to characterize multiomics data17
A practical guide to machine-learning scoring for structure-based virtual screening17
Multigram synthesis of N-alkyl bis-ureas for asymmetric hydrogen bonding phase-transfer catalysis17
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