Nature Protocols

(The TQCC of Nature Protocols is 65. The table below lists those papers that are above that threshold based on CrossRef citation counts. The publications cover those that have been published in the past four years, i.e., from 2019-03-01 to 2023-03-01.)
Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants1160
INFOGEST static in vitro simulation of gastrointestinal food digestion1067
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap787
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)677
SHERLOCK: nucleic acid detection with CRISPR nucleases592
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0562
Using DeepLabCut for 3D markerless pose estimation across species and behaviors509
Single-pot, solid-phase-enhanced sample preparation for proteomics experiments480
Reproducible molecular networking of untargeted mass spectrometry data using GNPS216
High-resolution 3D imaging of fixed and cleared organoids212
Asymmetric-flow field-flow fractionation technology for exomere and small extracellular vesicle separation and characterization199
Generation of lung organoids from human pluripotent stem cells in vitro194
Determination of hydroxyl groups in biorefinery resources via quantitative 31P NMR spectroscopy178
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute164
Systemic AAV vectors for widespread and targeted gene delivery in rodents159
Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics153
Cell culture and infection system for hepatitis C virus150
MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing128
Tumor organoid–T-cell coculture systems120
Derivation of self-renewing lung alveolar epithelial type II cells from human pluripotent stem cells106
High-resolution 13C metabolic flux analysis97
High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing95
Development, application and computational analysis of high-dimensional fluorescent antibody panels for single-cell flow cytometry95
Carbon nanotube–mediated DNA delivery without transgene integration in intact plants90
CODEX multiplexed tissue imaging with DNA-conjugated antibodies87
Preparation of paper-based devices for reagentless electrochemical (bio)sensor strips86
Advanced CUBIC tissue clearing for whole-organ cell profiling86
Generation of blood vessel organoids from human pluripotent stem cells85
Ex vivo and in vivo stable isotope labelling of central carbon metabolism and related pathways with analysis by LC–MS/MS81
Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization81
Microfabricated blood vessels for modeling the vascular transport barrier79
Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA79
Solid-state nanopore fabrication by automated controlled breakdown78
High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry77
A practical guide to optimization in X10 expansion microscopy76
High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging74
Engineering of human cardiac muscle electromechanically matured to an adult-like phenotype74
CRISPR–Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV–host factor interactions72
Application of anisotropic NMR parameters to the confirmation of molecular structure71
Temperature imaging using a cationic linear fluorescent polymeric thermometer and fluorescence lifetime imaging microscopy70
Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin70
Facile synthesis to tune size, textural properties and fiber density of dendritic fibrous nanosilica for applications in catalysis and CO2 capture69
Preparation, functionalization and characterization of engineered carbon nanodots67
Life cycle maintenance and drug-sensitivity assays for early drug discovery in Schistosoma mansoni67
Standardization of complex biologically derived spectrochemical datasets67
Creation of CRISPR-based germline-genome-engineered mice without ex vivo handling of zygotes by i-GONAD66
Nanoscale chemical imaging using tip-enhanced Raman spectroscopy65
A nanostructure platform for live-cell manipulation of membrane curvature65
Fabrication and practical applications of molybdenum disulfide nanopores65