| # | Title | Journal | Year | Citations |
|---|
| 1 | Fiji: an open-source platform for biological-image analysis | Nature Methods | 2012 | 47,818 |
| 2 | NIH Image to ImageJ: 25 years of image analysis | Nature Methods | 2012 | 46,756 |
| 3 | Fast gapped-read alignment with Bowtie 2 | Nature Methods | 2012 | 42,357 |
| 4 | QIIME allows analysis of high-throughput community sequencing data | Nature Methods | 2010 | 31,818 |
| 5 | DADA2: High-resolution sample inference from Illumina amplicon data | Nature Methods | 2016 | 18,691 |
| 6 | SciPy 1.0: fundamental algorithms for scientific computing in Python | Nature Methods | 2020 | 17,539 |
| 7 | HISAT: a fast spliced aligner with low memory requirements | Nature Methods | 2015 | 16,262 |
| 8 | jModelTest 2: more models, new heuristics and parallel computing | Nature Methods | 2012 | 13,416 |
| 9 | UPARSE: highly accurate OTU sequences from microbial amplicon reads | Nature Methods | 2013 | 13,193 |
| 10 | Mapping and quantifying mammalian transcriptomes by RNA-Seq | Nature Methods | 2008 | 12,050 |
| 11 | A method and server for predicting damaging missense mutations | Nature Methods | 2010 | 11,491 |
| 12 | ModelFinder: fast model selection for accurate phylogenetic estimates | Nature Methods | 2017 | 9,486 |
| 13 | Fast and sensitive protein alignment using DIAMOND | Nature Methods | 2015 | 8,761 |
| 14 | SignalP 4.0: discriminating signal peptides from transmembrane regions | Nature Methods | 2011 | 8,521 |
| 15 | Robust enumeration of cell subsets from tissue expression profiles | Nature Methods | 2015 | 8,460 |
| 16 | Enzymatic assembly of DNA molecules up to several hundred kilobases | Nature Methods | 2009 | 8,117 |
| 17 | Salmon provides fast and bias-aware quantification of transcript expression | Nature Methods | 2017 | 7,460 |
| 18 | Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) | Nature Methods | 2006 | 6,819 |
| 19 | Universal sample preparation method for proteome analysis | Nature Methods | 2009 | 6,678 |
| 20 | The Perseus computational platform for comprehensive analysis of (prote)omics data | Nature Methods | 2016 | 6,181 |
| 21 | MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy | Nature Methods | 2017 | 6,166 |
| 22 | cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination | Nature Methods | 2017 | 5,371 |
| 23 | Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position | Nature Methods | 2013 | 5,209 |
| 24 | The I-TASSER Suite: protein structure and function prediction | Nature Methods | 2015 | 4,923 |
| 25 | Improved vectors and genome-wide libraries for CRISPR screening | Nature Methods | 2014 | 4,032 |
| 26 | Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data | Nature Methods | 2013 | 4,029 |
| 27 | CHARMM36m: an improved force field for folded and intrinsically disordered proteins | Nature Methods | 2017 | 3,959 |
| 28 | Deep tissue two-photon microscopy | Nature Methods | 2005 | 3,641 |
| 29 | Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry | Nature Methods | 2007 | 3,547 |
| 30 | Fast, sensitive and accurate integration of single-cell data with Harmony | Nature Methods | 2019 | 3,494 |
| 31 | Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing | Nature Methods | 2013 | 3,402 |
| 32 | Quantum dots versus organic dyes as fluorescent labels | Nature Methods | 2008 | 3,331 |
| 33 | ColabFold: making protein folding accessible to all | Nature Methods | 2022 | 3,242 |
| 34 | MutationTaster2: mutation prediction for the deep-sequencing age | Nature Methods | 2014 | 3,203 |
| 35 | SCENIC: single-cell regulatory network inference and clustering | Nature Methods | 2017 | 3,086 |
| 36 | Orchestrating high-throughput genomic analysis with Bioconductor | Nature Methods | 2015 | 3,070 |
| 37 | Large-scale automated synthesis of human functional neuroimaging data | Nature Methods | 2011 | 2,993 |
| 38 | mRNA-Seq whole-transcriptome analysis of a single cell | Nature Methods | 2009 | 2,736 |
| 39 | Reversed graph embedding resolves complex single-cell trajectories | Nature Methods | 2017 | 2,691 |
| 40 | A guide to choosing fluorescent proteins | Nature Methods | 2005 | 2,642 |
| 41 | MutationTaster evaluates disease-causing potential of sequence alterations | Nature Methods | 2010 | 2,538 |
| 42 | nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation | Nature Methods | 2021 | 2,456 |
| 43 | ChromHMM: automating chromatin-state discovery and characterization | Nature Methods | 2012 | 2,127 |
| 44 | Simultaneous epitope and transcriptome measurement in single cells | Nature Methods | 2017 | 2,124 |
| 45 | Direct observation of individual endogenous protein complexes in situ by proximity ligation | Nature Methods | 2006 | 2,103 |
| 46 | Smart-seq2 for sensitive full-length transcriptome profiling in single cells | Nature Methods | 2013 | 2,022 |
| 47 | Semi-supervised learning for peptide identification from shotgun proteomics datasets | Nature Methods | 2007 | 2,010 |
| 48 | Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy | Nature Methods | 2008 | 2,008 |
| 49 | CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics | Nature Methods | 2012 | 2,006 |
| 50 | MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis | Nature Methods | 2015 | 1,955 |
