| # | Title | Journal | Year | Citations |
|---|
| 1 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement | PLoS Medicine | 2009 | 50,671 |
| 2 | Fiji: an open-source platform for biological-image analysis | Nature Methods | 2012 | 47,818 |
| 3 | NIH Image to ImageJ: 25 years of image analysis | Nature Methods | 2012 | 46,756 |
| 4 | Fast gapped-read alignment with Bowtie 2 | Nature Methods | 2012 | 42,357 |
| 5 | QIIME allows analysis of high-throughput community sequencing data | Nature Methods | 2010 | 31,818 |
| 6 | clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters | OMICS A Journal of Integrative Biology | 2012 | 21,237 |
| 7 | DADA2: High-resolution sample inference from Illumina amplicon data | Nature Methods | 2016 | 18,691 |
| 8 | Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities | Applied and Environmental Microbiology | 2009 | 18,390 |
| 9 | SciPy 1.0: fundamental algorithms for scientific computing in Python | Nature Methods | 2020 | 17,539 |
| 10 | Full-length transcriptome assembly from RNA-Seq data without a reference genome | Nature Biotechnology | 2011 | 17,264 |
| 11 | Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy | Applied and Environmental Microbiology | 2007 | 17,125 |
| 12 | HISAT: a fast spliced aligner with low memory requirements | Nature Methods | 2015 | 16,262 |
| 13 | GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism | Journal of Heredity | 1995 | 14,222 |
| 14 | Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation | Nature Biotechnology | 2010 | 13,805 |
| 15 | The PRISMA Statement for Reporting Systematic Reviews and Meta-Analyses of Studies That Evaluate Health Care Interventions: Explanation and Elaboration | PLoS Medicine | 2009 | 13,772 |
| 16 | jModelTest 2: more models, new heuristics and parallel computing | Nature Methods | 2012 | 13,416 |
| 17 | UPARSE: highly accurate OTU sequences from microbial amplicon reads | Nature Methods | 2013 | 13,193 |
| 18 | MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification | Nature Biotechnology | 2008 | 12,966 |
| 19 | Mapping and quantifying mammalian transcriptomes by RNA-Seq | Nature Methods | 2008 | 12,050 |
| 20 | Superior Thermal Conductivity of Single-Layer Graphene | Nano Letters | 2008 | 11,726 |
| 21 | Integrative genomics viewer | Nature Biotechnology | 2011 | 11,708 |
| 22 | A method and server for predicting damaging missense mutations | Nature Methods | 2010 | 11,491 |
| 23 | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 | Nature Biotechnology | 2019 | 11,167 |
| 24 | The RAST Server: Rapid Annotations using Subsystems Technology | BMC Genomics | 2008 | 9,977 |
| 25 | Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA | Applied and Environmental Microbiology | 1993 | 9,925 |
| 26 | Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB | Applied and Environmental Microbiology | 2006 | 9,859 |
| 27 | ModelFinder: fast model selection for accurate phylogenetic estimates | Nature Methods | 2017 | 9,486 |
| 28 | Integrating single-cell transcriptomic data across different conditions, technologies, and species | Nature Biotechnology | 2018 | 8,878 |
| 29 | Fast and sensitive protein alignment using DIAMOND | Nature Methods | 2015 | 8,761 |
| 30 | SignalP 4.0: discriminating signal peptides from transmembrane regions | Nature Methods | 2011 | 8,521 |
| 31 | Robust enumeration of cell subsets from tissue expression profiles | Nature Methods | 2015 | 8,460 |
| 32 | Projections of Global Mortality and Burden of Disease from 2002 to 2030 | PLoS Medicine | 2006 | 8,440 |
| 33 | StringTie enables improved reconstruction of a transcriptome from RNA-seq reads | Nature Biotechnology | 2015 | 8,385 |
| 34 | Enzymatic assembly of DNA molecules up to several hundred kilobases | Nature Methods | 2009 | 8,117 |
| 35 | Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences | Nature Biotechnology | 2013 | 8,049 |
| 36 | The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: Guidelines for Reporting Observational Studies | PLoS Medicine | 2007 | 7,961 |
| 37 | Biodiesel from microalgae | Biotechnology Advances | 2007 | 7,922 |
| 38 | Emerging Photoluminescence in Monolayer MoS2 | Nano Letters | 2010 | 7,897 |
| 39 | Graphene-Based Ultracapacitors | Nano Letters | 2008 | 7,599 |
| 40 | Salmon provides fast and bias-aware quantification of transcript expression | Nature Methods | 2017 | 7,460 |
| 41 | Self-organized formation of topologically correct feature maps | Biological Cybernetics | 1982 | 7,427 |
| 42 | Near-optimal probabilistic RNA-seq quantification | Nature Biotechnology | 2016 | 7,322 |
| 43 | Why Most Published Research Findings Are False | PLoS Medicine | 2005 | 7,171 |
| 44 | UniFrac: a New Phylogenetic Method for Comparing Microbial Communities | Applied and Environmental Microbiology | 2005 | 7,007 |
| 45 | FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics | Journal of Heredity | 1995 | 6,947 |
| 46 | Commentary: The Materials Project: A materials genome approach to accelerating materials innovation | APL Materials | 2013 | 6,913 |
| 47 | Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) | Nature Methods | 2006 | 6,819 |
| 48 | Nanocrystals of Cesium Lead Halide Perovskites (CsPbX3, X = Cl, Br, and I): Novel Optoelectronic Materials Showing Bright Emission with Wide Color Gamut | Nano Letters | 2015 | 6,814 |
| 49 | UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age | PLoS Medicine | 2015 | 6,753 |
| 50 | DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates | Molecular Marine Biology and Biotechnology | 1994 | 6,687 |
| 51 | Universal sample preparation method for proteome analysis | Nature Methods | 2009 | 6,678 |
| 52 | Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype | Nature Biotechnology | 2019 | 6,567 |
| 53 | The Perseus computational platform for comprehensive analysis of (prote)omics data | Nature Methods | 2016 | 6,181 |
| 54 | MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy | Nature Methods | 2017 | 6,166 |
| 55 | Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform | Applied and Environmental Microbiology | 2013 | 5,923 |
| 56 | Local compositions in thermodynamic excess functions for liquid mixtures | AICHE Journal | 1968 | 5,807 |
| 57 | cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination | Nature Methods | 2017 | 5,371 |
| 58 | Large Area, Few-Layer Graphene Films on Arbitrary Substrates by Chemical Vapor Deposition | Nano Letters | 2009 | 5,220 |
| 59 | Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position | Nature Methods | 2013 | 5,209 |
| 60 | 3D bioprinting of tissues and organs | Nature Biotechnology | 2014 | 5,158 |
| 61 | Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites | Protein Engineering, Design and Selection | 1997 | 5,051 |
| 62 | Protein production by auto-induction in high-density shaking cultures | Protein Expression and Purification | 2005 | 4,981 |
| 63 | The I-TASSER Suite: protein structure and function prediction | Nature Methods | 2015 | 4,923 |
| 64 | Principles of nanoparticle design for overcoming biological barriers to drug delivery | Nature Biotechnology | 2015 | 4,868 |
| 65 | Dose translation from animal to human studies revisited | FASEB Journal | 2008 | 4,838 |
| 66 | Social Relationships and Mortality Risk: A Meta-analytic Review | PLoS Medicine | 2010 | 4,743 |
| 67 | Silver nanoparticles as a new generation of antimicrobials | Biotechnology Advances | 2009 | 4,723 |
| 68 | “Neural” computation of decisions in optimization problems | Biological Cybernetics | 1985 | 4,693 |
| 69 | Quantitative analysis of complex protein mixtures using isotope-coded affinity tags | Nature Biotechnology | 1999 | 4,673 |
| 70 | The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells | Nature Biotechnology | 2014 | 4,652 |
| 71 | LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions | Protein Engineering, Design and Selection | 1995 | 4,648 |
| 72 | Large-scale analysis of the yeast proteome by multidimensional protein identification technology | Nature Biotechnology | 2001 | 4,540 |
| 73 | In vivo cancer targeting and imaging with semiconductor quantum dots | Nature Biotechnology | 2004 | 4,460 |
| 74 | TM4: A Free, Open-Source System for Microarray Data Management and Analysis | BioTechniques | 2003 | 4,443 |
| 75 | Correlation of diffusion coefficients in dilute solutions | AICHE Journal | 1955 | 4,321 |
| 76 | A theoretical basis for a biopharmaceutic drug classification: the correlation of in vitro drug product dissolution and in vivo bioavailability | Pharmaceutical Research | 1995 | 4,287 |
| 77 | Spatial reconstruction of single-cell gene expression data | Nature Biotechnology | 2015 | 4,254 |
| 78 | Determining the Size and Shape Dependence of Gold Nanoparticle Uptake into Mammalian Cells | Nano Letters | 2006 | 4,242 |
| 79 | Transparent, Conductive Graphene Electrodes for Dye-Sensitized Solar Cells | Nano Letters | 2008 | 4,164 |
| 80 | Nitric oxide as a secretory product of mammalian cells | FASEB Journal | 1992 | 4,161 |
| 81 | Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations | Biotechnology Letters | 2004 | 4,156 |
| 82 | Use of nuclepore filters for counting bacteria by fluorescence microscopy | Applied and Environmental Microbiology | 1977 | 4,148 |
| 83 | Chemical Management for Colorful, Efficient, and Stable Inorganic–Organic Hybrid Nanostructured Solar Cells | Nano Letters | 2013 | 4,144 |
| 84 | Statistical thermodynamics of liquid mixtures: A new expression for the excess Gibbs energy of partly or completely miscible systems | AICHE Journal | 1975 | 4,138 |
| 85 | Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein | Nature Biotechnology | 2004 | 4,135 |
| 86 | Synthetic biomaterials as instructive extracellular microenvironments for morphogenesis in tissue engineering | Nature Biotechnology | 2005 | 4,068 |
| 87 | Improved vectors and genome-wide libraries for CRISPR screening | Nature Methods | 2014 | 4,032 |
| 88 | Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data | Nature Methods | 2013 | 4,029 |
| 89 | Raman Spectra of Graphite Oxide and Functionalized Graphene Sheets | Nano Letters | 2008 | 3,995 |
| 90 | CHARMM36m: an improved force field for folded and intrinsically disordered proteins | Nature Methods | 2017 | 3,959 |
| 91 | Molecular Beacons: Probes that Fluoresce upon Hybridization | Nature Biotechnology | 1996 | 3,956 |
| 92 | DNA targeting specificity of RNA-guided Cas9 nucleases | Nature Biotechnology | 2013 | 3,953 |
| 93 | Electrospinning: A fascinating fiber fabrication technique | Biotechnology Advances | 2010 | 3,936 |
| 94 | Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples | Nature Biotechnology | 2013 | 3,934 |
| 95 | Renal clearance of quantum dots | Nature Biotechnology | 2007 | 3,789 |
| 96 | GREAT improves functional interpretation of cis-regulatory regions | Nature Biotechnology | 2010 | 3,789 |
| 97 | Neocognitron: A self-organizing neural network model for a mechanism of pattern recognition unaffected by shift in position | Biological Cybernetics | 1980 | 3,764 |
| 98 | Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material | BioTechniques | 1991 | 3,740 |
| 99 | Lead- and drug-like compounds: the rule-of-five revolution | Drug Discovery Today: Technologies | 2004 | 3,723 |
| 100 | Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations | Applied and Environmental Microbiology | 1990 | 3,720 |
