Nature Protocols

Article	Citations
Tutorial: a guide to performing polygenic risk score analyses	893
The HDOCK server for integrated protein–protein docking	639
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data	571
A scalable SCENIC workflow for single-cell gene regulatory network analysis	495
Reproducible molecular networking of untargeted mass spectrometry data using GNPS	338
Establishment of patient-derived cancer organoids for drug-screening applications	310
The trRosetta server for fast and accurate protein structure prediction	293
Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay	287
Tutorial: design and fabrication of nanoparticle-based lateral-flow immunoassays	238
CODEX multiplexed tissue imaging with DNA-conjugated antibodies	226
Design, fabrication and applications of tetrahedral DNA nanostructure-based multifunctional complexes in drug delivery and biomedical treatment	212
A practical guide to large-scale docking	209
Isolation and characterization of extracellular vesicle subpopulations from tissues	194
Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays	192
Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results	190
Efficient low-cost chromatin profiling with CUT&Tag	178
Tutorial: multivariate classification for vibrational spectroscopy in biological samples	177
Proximity labeling in mammalian cells with TurboID and split-TurboID	169
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data	167
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2	145
Tutorial: guidelines for standardized performance tests for electrodes intended for neural interfaces and bioelectronics	142
MOF-derived nanoporous carbons with diverse tunable nanoarchitectures	131
Engineering SARS-CoV-2 using a reverse genetic system	131
Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography–mass spectrometry	129
Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development	125

Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles	120
Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking	116
Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation	115
Optimization of metabolomic data processing using NOREVA	113
Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography	112
Metagenome analysis using the Kraken software suite	112
Standardized bacteriophage purification for personalized phage therapy	110
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction	108
High-yield production of mono- or few-layer transition metal dichalcogenide nanosheets by an electrochemical lithium ion intercalation-based exfoliation method	104
Multiplexed single-cell proteomics using SCoPE2	104
Chromatin accessibility profiling by ATAC-seq	104
Generation of synthetic nanobodies against delicate proteins	103
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods	99
Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA	98
3D bioprinted silk fibroin hydrogels for tissue engineering	97
Intestinal organoid cocultures with microbes	97
Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids	96
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	94
High-throughput cultivation and identification of bacteria from the plant root microbiota	92
Precision genome editing using cytosine and adenine base editors in mammalian cells	92
Ligand binding free-energy calculations with funnel metadynamics	91
Jointly defining cell types from multiple single-cell datasets using LIGER	91
Algorithmic assessment of cellular senescence in experimental and clinical specimens	90
An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality	89
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	89
Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR T cell testing	88
A standardized social preference protocol for measuring social deficits in mouse models of autism	86
RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19	85
High-yield, green and scalable methods for producing MOF-303 for water harvesting from desert air	84
Establishment and differentiation of long-term trophoblast organoid cultures from the human placenta	84
Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	83
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	81
Measuring DNA modifications with the comet assay: a compendium of protocols	80
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	80
Microfluidic integration of regeneratable electrochemical affinity-based biosensors for continual monitoring of organ-on-a-chip devices	79
Analyzing high-dimensional cytometry data using FlowSOM	78
Cellular thermal shift assay for the identification of drug–target interactions in the Plasmodium falciparum proteome	75
Analysis of task-based functional MRI data preprocessed with fMRIPrep	75
Generation of insulin-producing pancreatic β cells from multiple human stem cell lines	73
A dynamic DNA tetrahedron framework for active targeting	73
Combined proximity labeling and affinity purification−mass spectrometry workflow for mapping and visualizing protein interaction networks	72
Establishment of human fetal hepatocyte organoids and CRISPR–Cas9-based gene knockin and knockout in organoid cultures from human liver	71
Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap	70
Rolling circle amplification (RCA)-based DNA hydrogel	70
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	69
Identifying unknown metabolites using NMR-based metabolic profiling techniques	69
3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert	67
Engineering brain assembloids to interrogate human neural circuits	64
Measuring the elastic modulus of soft culture surfaces and three-dimensional hydrogels using atomic force microscopy	64
Generic acquisition protocol for quantitative MRI of the spinal cord	63

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements	63
The normative modeling framework for computational psychiatry	63
Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome	62
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging	62
Fabrication, characterization and applications of graphene electronic tattoos	61
Microtiter plate assays to assess antibiofilm activity against bacteria	59
Simultaneous noninvasive recording of electrocardiogram and skin sympathetic nerve activity (neuECG)	58
A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei	56
Rapid (30-second), equipment-free purification of nucleic acids using easy-to-make dipsticks	55
Tools for experimental and computational analyses of off-target editing by programmable nucleases	55
Genetic circuit design automation with Cello 2.0	55
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	55
Solid-state 31P NMR mapping of active centers and relevant spatial correlations in solid acid catalysts	54
Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction	54
A well plate–based multiplexed platform for incorporation of organoids into an organ-on-a-chip system with a perfusable vasculature	54
Detection of aberrant gene expression events in RNA sequencing data	54
Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages	54
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport	54
Synthesis of N-heterocyclic carbene gold(I) complexes	53
Norovirus detection in water samples at the level of single virus copies per microliter using a smartphone-based fluorescence microscope	52
Antigen retrieval and clearing for whole-organ immunofluorescence by FLASH	52
Digital postprocessing and image segmentation for objective analysis of colorimetric reactions	52
Tutorial: practical considerations for tissue clearing and imaging	52
CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes	51
Whole-brain functional ultrasound imaging in awake head-fixed mice	51
Generation, functional analysis and applications of isogenic three-dimensional self-aggregating cardiac microtissues from human pluripotent stem cells	50
Tutorial: using nanoneedles for intracellular delivery	49
Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy	49
Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq	48
Comparative analysis of assays to measure CAR T-cell-mediated cytotoxicity	47
Combined whole-mount fluorescence in situ hybridization and antibody staining in zebrafish embryos and larvae	47
A complete pupillometry toolbox for real-time monitoring of locus coeruleus activity in rodents	47
Analysis of clonogenic growth in vitro	46
Raman spectroscopy for real-time and in situ monitoring of mechanochemical milling reactions	46
Inducible mouse models of colon cancer for the analysis of sporadic and inflammation-driven tumor progression and lymph node metastasis	45
A universal approach for the synthesis of mesoporous gold, palladium and platinum films for applications in electrocatalysis	45
Stem-cell-derived human microglia transplanted into mouse brain to study human disease	45
Comprehensive structural glycomic characterization of the glycocalyxes of cells and tissues	44
Characterization of connective tissues using near-infrared spectroscopy and imaging	44
Evaluation of the effects of cold atmospheric plasma and plasma-treated liquids in cancer cell cultures	43
Nanocarriers based on bacterial membrane materials for cancer vaccine delivery	43
Culture and analysis of kidney tubuloids and perfused tubuloid cells-on-a-chip	43
Cargo loading within ferritin nanocages in preparation for tumor-targeted delivery	43
CRISPR off-target detection with DISCOVER-seq	42
Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release	42
Tutorial: a computational framework for the design and optimization of peripheral neural interfaces	41
COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2	41
Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq	41
Stable isotope tracing to assess tumor metabolism in vivo	41
Use of deep learning to develop continuous-risk models for adverse event prediction from electronic health records	41
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane	41
Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions	41
Mapping mechanical properties of biological materials via an add-on Brillouin module to confocal microscopes	41
Transplantation of intestinal organoids into a mouse model of colitis	40
In vitro generation of self-renewing human intestinal epithelia over planar and shaped collagen hydrogels	40
Design, assembly, and characterization of membrane-spanning DNA nanopores	40
Phage-assisted continuous and non-continuous evolution	40
Spooling electrochemiluminescence spectroscopy: development, applications and beyond	40
A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility	39
Statistical analysis in metabolic phenotyping	39
IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues	38
Organotypic culture assays for murine and human primary and metastatic-site tumors	38
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	37
Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles	36
A generalized workflow for conducting electric field–optimized, fMRI-guided, transcranial magnetic stimulation	36
Chronic, cortex-wide imaging of specific cell populations during behavior	36
Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry	35
A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes	35
Designing and executing prime editing experiments in mammalian cells	35
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	35
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes	35
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit	34
Protein higher-order-structure determination by fast photochemical oxidation of proteins and mass spectrometry analysis	34
Composable microfluidic spinning platforms for facile production of biomimetic perfusable hydrogel microtubes	34
High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery	33
Smart-RRBS for single-cell methylome and transcriptome analysis	33
Engineering DNA nanostructures for siRNA delivery in plants	33
An optimized comet-based in vitro DNA repair assay to assess base and nucleotide excision repair activity	33
Expression and characterization of SARS-CoV-2 spike proteins	33
The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies	32

Label-free capacitive assaying of biomarkers for molecular diagnostics	32
Macrophage phagocytosis assay with reconstituted target particles	32
A comprehensive guide to studying inflammasome activation and cell death	32
Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture	31
Isolation of mitochondria-derived mitovesicles and subpopulations of microvesicles and exosomes from brain tissues	31
Implantation of Neuropixels probes for chronic recording of neuronal activity in freely behaving mice and rats	31
Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures	31
Monomicellar assembly to synthesize structured and functional mesoporous carbonaceous nanomaterials	31
Graphene- and metal-induced energy transfer for single-molecule imaging and live-cell nanoscopy with (sub)-nanometer axial resolution	31
Subzero non-frozen preservation of human livers in the supercooled state	31
Integrative structural modeling of macromolecular complexes using Assembline	31
Responsive and activable nanomedicines for remodeling the tumor microenvironment	31
Selected ion flow tube mass spectrometry for targeted analysis of volatile organic compounds in human breath	31