| # | Title | Journal | Year | Citations |
|---|
| 1 | Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources | Nature Protocols | 2009 | 31,831 |
| 2 | Analyzing real-time PCR data by the comparative CT method | Nature Protocols | 2008 | 21,086 |
| 3 | Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks | Nature Protocols | 2012 | 11,433 |
| 4 | Genome engineering using the CRISPR-Cas9 system | Nature Protocols | 2013 | 9,114 |
| 5 | The Phyre2 web portal for protein modeling, prediction and analysis | Nature Protocols | 2015 | 8,366 |
| 6 | De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis | Nature Protocols | 2013 | 7,054 |
| 7 | Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm | Nature Protocols | 2009 | 6,149 |
| 8 | I-TASSER: a unified platform for automated protein structure and function prediction | Nature Protocols | 2010 | 5,594 |
| 9 | Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols | 2016 | 4,743 |
| 10 | Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances | Nature Protocols | 2008 | 4,289 |
| 11 | In-gel digestion for mass spectrometric characterization of proteins and proteomes | Nature Protocols | 2006 | 4,265 |
| 12 | Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis | Nature Protocols | 2007 | 4,224 |
| 13 | Protein structure prediction on the Web: a case study using the Phyre server | Nature Protocols | 2009 | 3,815 |
| 14 | Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips | Nature Protocols | 2007 | 3,693 |
| 15 | In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro | Nature Protocols | 2007 | 3,638 |
| 16 | Morris water maze: procedures for assessing spatial and related forms of learning and memory | Nature Protocols | 2006 | 3,377 |
| 17 | The MaxQuant computational platform for mass spectrometry-based shotgun proteomics | Nature Protocols | 2016 | 3,353 |
| 18 | Full-length RNA-seq from single cells using Smart-seq2 | Nature Protocols | 2014 | 3,308 |
| 19 | Clonogenic assay of cells in vitro | Nature Protocols | 2006 | 3,193 |
| 20 | Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt | Nature Protocols | 2009 | 3,084 |
| 21 | Locating proteins in the cell using TargetP, SignalP and related tools | Nature Protocols | 2007 | 2,940 |
| 22 | Using circular dichroism spectra to estimate protein secondary structure | Nature Protocols | 2006 | 2,926 |
| 23 | Sulforhodamine B colorimetric assay for cytotoxicity screening | Nature Protocols | 2006 | 2,788 |
| 24 | High-resolution in situ hybridization to whole-mount zebrafish embryos | Nature Protocols | 2008 | 2,282 |
| 25 | Large-scale gene function analysis with the PANTHER classification system | Nature Protocols | 2013 | 2,276 |
| 26 | Integration of biological networks and gene expression data using Cytoscape | Nature Protocols | 2007 | 2,275 |
| 27 | Materials fabrication from Bombyx mori silk fibroin | Nature Protocols | 2011 | 2,265 |
| 28 | Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry | Nature Protocols | 2011 | 2,236 |
| 29 | Tricine–SDS-PAGE | Nature Protocols | 2006 | 2,194 |
| 30 | The use of the elevated plus maze as an assay of anxiety-related behavior in rodents | Nature Protocols | 2007 | 2,116 |
| 31 | High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method | Nature Protocols | 2007 | 2,082 |
| 32 | The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability | Nature Protocols | 2007 | 2,069 |
| 33 | Estimation of total phenolic content and other oxidation substrates in plant tissues using Folin–Ciocalteu reagent | Nature Protocols | 2007 | 2,034 |
| 34 | The ClusPro web server for protein–protein docking | Nature Protocols | 2017 | 1,959 |
| 35 | Soft lithography for micro- and nanoscale patterning | Nature Protocols | 2010 | 1,904 |
| 36 | INFOGEST static in vitro simulation of gastrointestinal food digestion | Nature Protocols | 2019 | 1,873 |
| 37 | Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts | Nature Protocols | 2007 | 1,830 |
| 38 | Gas chromatography mass spectrometry–based metabolite profiling in plants | Nature Protocols | 2006 | 1,808 |
| 39 | Quantification of mRNA using real-time RT-PCR | Nature Protocols | 2006 | 1,780 |
| 40 | CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes | Nature Protocols | 2020 | 1,768 |
| 41 | Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method | Nature Protocols | 2006 | 1,758 |
| 42 | Assay for quantitative determination of glutathione and glutathione disulfide levels using enzymatic recycling method | Nature Protocols | 2006 | 1,700 |
| 43 | The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on | Nature Protocols | 2006 | 1,642 |
| 44 | Neutral red uptake assay for the estimation of cell viability/cytotoxicity | Nature Protocols | 2008 | 1,639 |
| 45 | Cytokinesis-block micronucleus cytome assay | Nature Protocols | 2007 | 1,613 |
| 46 | A protocol for generating a high-quality genome-scale metabolic reconstruction | Nature Protocols | 2010 | 1,568 |
| 47 | Immunodesign of experimental sepsis by cecal ligation and puncture | Nature Protocols | 2009 | 1,535 |
| 48 | Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants | Nature Protocols | 2006 | 1,534 |
| 49 | Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 | Nature Protocols | 2008 | 1,516 |
| 50 | Blue native PAGE | Nature Protocols | 2006 | 1,502 |
