| # | Title | Journal | Year | Citations |
|---|
| 1 | phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data | PLoS ONE | 2013 | 13,960 |
| 2 | FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments | PLoS ONE | 2010 | 11,284 |
| 3 | Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement | PLoS ONE | 2014 | 6,781 |
| 4 | A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species | PLoS ONE | 2011 | 5,470 |
| 5 | REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms | PLoS ONE | 2011 | 5,347 |
| 6 | Leishmaniasis Worldwide and Global Estimates of Its Incidence | PLoS ONE | 2012 | 4,058 |
| 7 | progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement | PLoS ONE | 2010 | 3,652 |
| 8 | Plastic Pollution in the World's Oceans: More than 5 Trillion Plastic Pieces Weighing over 250,000 Tons Afloat at Sea | PLoS ONE | 2014 | 3,144 |
| 9 | BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics | PLoS ONE | 2013 | 3,003 |
| 10 | Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers | PLoS ONE | 2008 | 2,972 |
| 11 | Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species | PLoS ONE | 2012 | 2,836 |
| 12 | NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data | PLoS ONE | 2012 | 2,732 |
| 13 | Predicting the Functional Effect of Amino Acid Substitutions and Indels | PLoS ONE | 2012 | 2,465 |
| 14 | SoilGrids250m: Global gridded soil information based on machine learning | PLoS ONE | 2017 | 2,385 |
| 15 | The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets | PLoS ONE | 2015 | 2,354 |
| 16 | Global Prevalence of Chronic Kidney Disease – A Systematic Review and Meta-Analysis | PLoS ONE | 2016 | 2,336 |
| 17 | Yield Trends Are Insufficient to Double Global Crop Production by 2050 | PLoS ONE | 2013 | 2,328 |
| 18 | On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation | PLoS ONE | 2015 | 2,319 |
| 19 | Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults | PLoS ONE | 2010 | 2,309 |
| 20 | Dose-Response Analysis Using R | PLoS ONE | 2015 | 2,265 |
| 21 | Source Partitioning Using Stable Isotopes: Coping with Too Much Variation | PLoS ONE | 2010 | 2,255 |
| 22 | An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets | PLoS ONE | 2007 | 2,236 |
| 23 | More than 75 percent decline over 27 years in total flying insect biomass in protected areas | PLoS ONE | 2017 | 2,176 |
| 24 | Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types | PLoS ONE | 2012 | 2,088 |
| 25 | Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies | PLoS ONE | 2011 | 1,891 |
| 26 | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation | PLoS ONE | 2010 | 1,883 |
| 27 | A One Pot, One Step, Precision Cloning Method with High Throughput Capability | PLoS ONE | 2008 | 1,867 |
| 28 | Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps | PLoS ONE | 2015 | 1,801 |
| 29 | Mental health problems and social media exposure during COVID-19 outbreak | PLoS ONE | 2020 | 1,749 |
| 30 | ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software | PLoS ONE | 2014 | 1,733 |
| 31 | Graphical Tools for Network Meta-Analysis in STATA | PLoS ONE | 2013 | 1,714 |
| 32 | REST: A Toolkit for Resting-State Functional Magnetic Resonance Imaging Data Processing | PLoS ONE | 2011 | 1,710 |
| 33 | Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach | PLoS ONE | 2012 | 1,685 |
| 34 | Future Coastal Population Growth and Exposure to Sea-Level Rise and Coastal Flooding - A Global Assessment | PLoS ONE | 2015 | 1,613 |
| 35 | A Meta-Analysis of Global Urban Land Expansion | PLoS ONE | 2011 | 1,601 |
| 36 | A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System | PLoS ONE | 2013 | 1,562 |
| 37 | Racism as a Determinant of Health: A Systematic Review and Meta-Analysis | PLoS ONE | 2015 | 1,537 |
| 38 | SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation | PLoS ONE | 2016 | 1,527 |
| 39 | TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline | PLoS ONE | 2014 | 1,511 |
| 40 | Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer | PLoS ONE | 2013 | 1,502 |
| 41 | Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review | PLoS ONE | 2012 | 1,465 |
| 42 | The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats | PLoS ONE | 2010 | 1,439 |
| 43 | Disordered Microbial Communities in Asthmatic Airways | PLoS ONE | 2010 | 1,436 |
| 44 | Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results | PLoS ONE | 2013 | 1,399 |
| 45 | Generation of Breast Cancer Stem Cells through Epithelial-Mesenchymal Transition | PLoS ONE | 2008 | 1,389 |
| 46 | Inferring Regulatory Networks from Expression Data Using Tree-Based Methods | PLoS ONE | 2010 | 1,381 |
| 47 | The Human Serum Metabolome | PLoS ONE | 2011 | 1,378 |
| 48 | Where Is Current Research on Blockchain Technology?—A Systematic Review | PLoS ONE | 2016 | 1,367 |
| 49 | pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels | PLoS ONE | 2014 | 1,363 |
| 50 | Paracrine Factors of Mesenchymal Stem Cells Recruit Macrophages and Endothelial Lineage Cells and Enhance Wound Healing | PLoS ONE | 2008 | 1,350 |
