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Top Articles

1Fiji: an open-source platform for biological-image analysisNature Methods201247,818
2NIH Image to ImageJ: 25 years of image analysisNature Methods201246,756
3Fast gapped-read alignment with Bowtie 2Nature Methods201242,357
4QIIME allows analysis of high-throughput community sequencing dataNature Methods201031,818
5DADA2: High-resolution sample inference from Illumina amplicon dataNature Methods201618,691
6SciPy 1.0: fundamental algorithms for scientific computing in PythonNature Methods202017,539
7HISAT: a fast spliced aligner with low memory requirementsNature Methods201516,262
8jModelTest 2: more models, new heuristics and parallel computingNature Methods201213,416
9UPARSE: highly accurate OTU sequences from microbial amplicon readsNature Methods201313,193
10Mapping and quantifying mammalian transcriptomes by RNA-SeqNature Methods200812,050
11A method and server for predicting damaging missense mutationsNature Methods201011,491
12ModelFinder: fast model selection for accurate phylogenetic estimatesNature Methods20179,486
13Fast and sensitive protein alignment using DIAMONDNature Methods20158,761
14SignalP 4.0: discriminating signal peptides from transmembrane regionsNature Methods20118,521
15Robust enumeration of cell subsets from tissue expression profilesNature Methods20158,460
16Enzymatic assembly of DNA molecules up to several hundred kilobasesNature Methods20098,117
17Salmon provides fast and bias-aware quantification of transcript expressionNature Methods20177,460
18Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)Nature Methods20066,819
19Universal sample preparation method for proteome analysisNature Methods20096,678
20The Perseus computational platform for comprehensive analysis of (prote)omics dataNature Methods20166,181
21MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopyNature Methods20176,166
22cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determinationNature Methods20175,371
23Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome positionNature Methods20135,209
24The I-TASSER Suite: protein structure and function predictionNature Methods20154,923
25Improved vectors and genome-wide libraries for CRISPR screeningNature Methods20144,032
26Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing dataNature Methods20134,029
27CHARMM36m: an improved force field for folded and intrinsically disordered proteinsNature Methods20173,959
28Deep tissue two-photon microscopyNature Methods20053,641
29Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometryNature Methods20073,547
30Fast, sensitive and accurate integration of single-cell data with HarmonyNature Methods20193,494
31Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencingNature Methods20133,402
32Quantum dots versus organic dyes as fluorescent labelsNature Methods20083,331
33ColabFold: making protein folding accessible to allNature Methods20223,242
34MutationTaster2: mutation prediction for the deep-sequencing ageNature Methods20143,203
35SCENIC: single-cell regulatory network inference and clusteringNature Methods20173,086
36Orchestrating high-throughput genomic analysis with BioconductorNature Methods20153,070
37Large-scale automated synthesis of human functional neuroimaging dataNature Methods20112,993
38mRNA-Seq whole-transcriptome analysis of a single cellNature Methods20092,736
39Reversed graph embedding resolves complex single-cell trajectoriesNature Methods20172,691
40A guide to choosing fluorescent proteinsNature Methods20052,642
41MutationTaster evaluates disease-causing potential of sequence alterationsNature Methods20102,538
42nnU-Net: a self-configuring method for deep learning-based biomedical image segmentationNature Methods20212,456
43ChromHMM: automating chromatin-state discovery and characterizationNature Methods20122,127
44Simultaneous epitope and transcriptome measurement in single cellsNature Methods20172,124
45Direct observation of individual endogenous protein complexes in situ by proximity ligationNature Methods20062,103
46Smart-seq2 for sensitive full-length transcriptome profiling in single cellsNature Methods20132,022
47Semi-supervised learning for peptide identification from shotgun proteomics datasetsNature Methods20072,010
48Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopyNature Methods20082,008
49CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomicsNature Methods20122,006
50MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysisNature Methods20151,955