Nature Protocols

(The TQCC of Nature Protocols is 31. 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 2020-04-01 to 2024-04-01.)
Tutorial: a guide to performing polygenic risk score analyses893
The HDOCK server for integrated protein–protein docking639
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data571
A scalable SCENIC workflow for single-cell gene regulatory network analysis495
Reproducible molecular networking of untargeted mass spectrometry data using GNPS338
Establishment of patient-derived cancer organoids for drug-screening applications310
The trRosetta server for fast and accurate protein structure prediction293
Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay287
Tutorial: design and fabrication of nanoparticle-based lateral-flow immunoassays238
CODEX multiplexed tissue imaging with DNA-conjugated antibodies226
Design, fabrication and applications of tetrahedral DNA nanostructure-based multifunctional complexes in drug delivery and biomedical treatment212
A practical guide to large-scale docking209
Isolation and characterization of extracellular vesicle subpopulations from tissues194
Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays192
Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results190
Efficient low-cost chromatin profiling with CUT&Tag178
Tutorial: multivariate classification for vibrational spectroscopy in biological samples177
Proximity labeling in mammalian cells with TurboID and split-TurboID169
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data167
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2145
Tutorial: guidelines for standardized performance tests for electrodes intended for neural interfaces and bioelectronics142
MOF-derived nanoporous carbons with diverse tunable nanoarchitectures131
Engineering SARS-CoV-2 using a reverse genetic system131
Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography–mass spectrometry129
Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development125
Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles120
Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking116
Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation115
Optimization of metabolomic data processing using NOREVA113
Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography112
Metagenome analysis using the Kraken software suite112
Standardized bacteriophage purification for personalized phage therapy110
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction108
High-yield production of mono- or few-layer transition metal dichalcogenide nanosheets by an electrochemical lithium ion intercalation-based exfoliation method104
Multiplexed single-cell proteomics using SCoPE2104
Chromatin accessibility profiling by ATAC-seq104
Generation of synthetic nanobodies against delicate proteins103
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods99
Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA98
3D bioprinted silk fibroin hydrogels for tissue engineering97
Intestinal organoid cocultures with microbes97
Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids96
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery94
High-throughput cultivation and identification of bacteria from the plant root microbiota92
Precision genome editing using cytosine and adenine base editors in mammalian cells92
Ligand binding free-energy calculations with funnel metadynamics91
Jointly defining cell types from multiple single-cell datasets using LIGER91
Algorithmic assessment of cellular senescence in experimental and clinical specimens90
An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality89
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling89
Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR T cell testing88
A standardized social preference protocol for measuring social deficits in mouse models of autism86
RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-1985
High-yield, green and scalable methods for producing MOF-303 for water harvesting from desert air84
Establishment and differentiation of long-term trophoblast organoid cultures from the human placenta84
Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing83
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases81
Measuring DNA modifications with the comet assay: a compendium of protocols80
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses80
Microfluidic integration of regeneratable electrochemical affinity-based biosensors for continual monitoring of organ-on-a-chip devices79
Analyzing high-dimensional cytometry data using FlowSOM78
Cellular thermal shift assay for the identification of drug–target interactions in the Plasmodium falciparum proteome75
Analysis of task-based functional MRI data preprocessed with fMRIPrep75
Generation of insulin-producing pancreatic β cells from multiple human stem cell lines73
A dynamic DNA tetrahedron framework for active targeting73
Combined proximity labeling and affinity purification−mass spectrometry workflow for mapping and visualizing protein interaction networks72
Establishment of human fetal hepatocyte organoids and CRISPR–Cas9-based gene knockin and knockout in organoid cultures from human liver71
Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap70
Rolling circle amplification (RCA)-based DNA hydrogel70
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)69
Identifying unknown metabolites using NMR-based metabolic profiling techniques69
3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert67
Engineering brain assembloids to interrogate human neural circuits64
Measuring the elastic modulus of soft culture surfaces and three-dimensional hydrogels using atomic force microscopy64
Generic acquisition protocol for quantitative MRI of the spinal cord63
lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements63
The normative modeling framework for computational psychiatry63
Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome62
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging62
Fabrication, characterization and applications of graphene electronic tattoos61
Microtiter plate assays to assess antibiofilm activity against bacteria59
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 nuclei56
Rapid (30-second), equipment-free purification of nucleic acids using easy-to-make dipsticks55
Tools for experimental and computational analyses of off-target editing by programmable nucleases55
Genetic circuit design automation with Cello 2.055
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations55
Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction54
Solid-state 31P NMR mapping of active centers and relevant spatial correlations in solid acid catalysts54
A well plate–based multiplexed platform for incorporation of organoids into an organ-on-a-chip system with a perfusable vasculature54
Detection of aberrant gene expression events in RNA sequencing data54
Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages54
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport54
Synthesis of N-heterocyclic carbene gold(I) complexes53
Tutorial: practical considerations for tissue clearing and imaging52
Norovirus detection in water samples at the level of single virus copies per microliter using a smartphone-based fluorescence microscope52
Antigen retrieval and clearing for whole-organ immunofluorescence by FLASH52
Digital postprocessing and image segmentation for objective analysis of colorimetric reactions52
Whole-brain functional ultrasound imaging in awake head-fixed mice51
CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes51
Generation, functional analysis and applications of isogenic three-dimensional self-aggregating cardiac microtissues from human pluripotent stem cells50
Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy49
Tutorial: using nanoneedles for intracellular delivery49
Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq48
A complete pupillometry toolbox for real-time monitoring of locus coeruleus activity in rodents47
Comparative analysis of assays to measure CAR T-cell-mediated cytotoxicity47
Combined whole-mount fluorescence in situ hybridization and antibody staining in zebrafish embryos and larvae47
Raman spectroscopy for real-time and in situ monitoring of mechanochemical milling reactions46
Analysis of clonogenic growth in vitro46
Stem-cell-derived human microglia transplanted into mouse brain to study human disease45
Inducible mouse models of colon cancer for the analysis of sporadic and inflammation-driven tumor progression and lymph node metastasis45
A universal approach for the synthesis of mesoporous gold, palladium and platinum films for applications in electrocatalysis45
Comprehensive structural glycomic characterization of the glycocalyxes of cells and tissues44
Characterization of connective tissues using near-infrared spectroscopy and imaging44
Cargo loading within ferritin nanocages in preparation for tumor-targeted delivery43
Evaluation of the effects of cold atmospheric plasma and plasma-treated liquids in cancer cell cultures43
Nanocarriers based on bacterial membrane materials for cancer vaccine delivery43
Culture and analysis of kidney tubuloids and perfused tubuloid cells-on-a-chip43
CRISPR off-target detection with DISCOVER-seq42
Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release42
Mapping mechanical properties of biological materials via an add-on Brillouin module to confocal microscopes41
Tutorial: a computational framework for the design and optimization of peripheral neural interfaces41
COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-241
Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq41
Stable isotope tracing to assess tumor metabolism in vivo41
Use of deep learning to develop continuous-risk models for adverse event prediction from electronic health records41
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane41
Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions41
Phage-assisted continuous and non-continuous evolution40
Spooling electrochemiluminescence spectroscopy: development, applications and beyond40
Transplantation of intestinal organoids into a mouse model of colitis40
In vitro generation of self-renewing human intestinal epithelia over planar and shaped collagen hydrogels40
Design, assembly, and characterization of membrane-spanning DNA nanopores40
Statistical analysis in metabolic phenotyping39
A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility39
IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues38
Organotypic culture assays for murine and human primary and metastatic-site tumors38
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView37
Chronic, cortex-wide imaging of specific cell populations during behavior36
Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles36
A generalized workflow for conducting electric field–optimized, fMRI-guided, transcranial magnetic stimulation36
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes35
Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry35
A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes35
Designing and executing prime editing experiments in mammalian cells35
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity35
Composable microfluidic spinning platforms for facile production of biomimetic perfusable hydrogel microtubes34
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit34
Protein higher-order-structure determination by fast photochemical oxidation of proteins and mass spectrometry analysis34
High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry–based deubiquitylating enzyme assay for drug discovery33
Smart-RRBS for single-cell methylome and transcriptome analysis33
Engineering DNA nanostructures for siRNA delivery in plants33
An optimized comet-based in vitro DNA repair assay to assess base and nucleotide excision repair activity33
Expression and characterization of SARS-CoV-2 spike proteins33
A comprehensive guide to studying inflammasome activation and cell death32
The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies32
Label-free capacitive assaying of biomarkers for molecular diagnostics32
Macrophage phagocytosis assay with reconstituted target particles32
Integrative structural modeling of macromolecular complexes using Assembline31
Responsive and activable nanomedicines for remodeling the tumor microenvironment31
Selected ion flow tube mass spectrometry for targeted analysis of volatile organic compounds in human breath31
Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture31
Isolation of mitochondria-derived mitovesicles and subpopulations of microvesicles and exosomes from brain tissues31
Implantation of Neuropixels probes for chronic recording of neuronal activity in freely behaving mice and rats31
Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures31
Monomicellar assembly to synthesize structured and functional mesoporous carbonaceous nanomaterials31
Graphene- and metal-induced energy transfer for single-molecule imaging and live-cell nanoscopy with (sub)-nanometer axial resolution31
Subzero non-frozen preservation of human livers in the supercooled state31