| # | Title | Journal | Year | Citations |
|---|
| 1 | Estimates of the severity of coronavirus disease 2019: a model-based analysis | Lancet Infectious Diseases, The | 2020 | 3,036 |
| 2 | Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2) | Science | 2020 | 2,940 |
| 3 | How will country-based mitigation measures influence the course of the COVID-19 epidemic? | Lancet, The | 2020 | 2,738 |
| 4 | adegenet 1.3-1: new tools for the analysis of genome-wide SNP data | Bioinformatics | 2011 | 2,514 |
| 5 | BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis | PLoS Computational Biology | 2019 | 2,484 |
| 6 | Emerging fungal threats to animal, plant and ecosystem health | Nature | 2012 | 2,478 |
| 7 | The effect of malaria control on Plasmodium falciparum in Africa between 2000 and 2015 | Nature | 2015 | 2,140 |
| 8 | Strategies for mitigating an influenza pandemic | Nature | 2006 | 1,863 |
| 9 | eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data | Journal of Bacteriology | 2004 | 1,697 |
| 10 | Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings | Science | 2009 | 1,665 |
| 11 | Strategies for containing an emerging influenza pandemic in Southeast Asia | Nature | 2005 | 1,592 |
| 12 | Re-evaluating prokaryotic species | Nature Reviews Microbiology | 2005 | 1,019 |
| 13 | Transmission Dynamics of the Etiological Agent of SARS in Hong Kong: Impact of Public Health Interventions | Science | 2003 | 1,004 |
| 14 | Factors that make an infectious disease outbreak controllable | Proceedings of the National Academy of Sciences of the United States of America | 2004 | 1,000 |
| 15 | ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes | PLoS Computational Biology | 2015 | 841 |
| 16 | Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong | Lancet, The | 2003 | 840 |
| 17 | Rapid Pneumococcal Evolution in Response to Clinical Interventions | Science | 2011 | 828 |
| 18 | How to measure and test phylogenetic signal | Methods in Ecology and Evolution | 2012 | 759 |
| 19 | Heterosexual risk of HIV-1 infection per sexual act: systematic review and meta-analysis of observational studies | Lancet Infectious Diseases, The | 2009 | 725 |
| 20 | The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries | Science | 2020 | 718 |
| 21 | The exceptional value of intact forest ecosystems | Nature Ecology and Evolution | 2018 | 681 |
| 22 | A global map of travel time to cities to assess inequalities in accessibility in 2015 | Nature | 2018 | 672 |
| 23 | Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes | PLoS Genetics | 2006 | 661 |
| 24 | Global hotspots and correlates of emerging zoonotic diseases | Nature Communications | 2017 | 645 |
| 25 | Future challenges for clinical care of an ageing population infected with HIV: a modelling study | Lancet Infectious Diseases, The | 2015 | 634 |
| 26 | The effect of public health measures on the 1918 influenza pandemic in U.S. cities | Proceedings of the National Academy of Sciences of the United States of America | 2007 | 627 |
| 27 | Risk Factors for Severe Outcomes following 2009 Influenza A (H1N1) Infection: A Global Pooled Analysis | PLoS Medicine | 2011 | 581 |
| 28 | Ecological and immunological determinants of influenza evolution | Nature | 2003 | 580 |
| 29 | HIV-1 Transmission, by Stage of Infection | Journal of Infectious Diseases | 2008 | 575 |
| 30 | HIV transmission risk through anal intercourse: systematic review, meta-analysis and implications for HIV prevention | International Journal of Epidemiology | 2010 | 574 |
| 31 | Modeling targeted layered containment of an influenza pandemic in the United States | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 570 |
| 32 | Global Emergence ofBatrachochytrium dendrobatidisand Amphibian Chytridiomycosis in Space, Time, and Host | Annual Review of Microbiology | 2009 | 564 |
| 33 | How Clonal Is Staphylococcus aureus ? | Journal of Bacteriology | 2003 | 560 |
| 34 | Batrachochytrium salamandrivorans sp. nov. causes lethal chytridiomycosis in amphibians | Proceedings of the National Academy of Sciences of the United States of America | 2013 | 528 |
| 35 | Mathematical models of infectious disease transmission | Nature Reviews Microbiology | 2008 | 527 |
| 36 | Recombination and the Nature of Bacterial Speciation | Science | 2007 | 512 |
| 37 | Multilocus Sequence Typing System for Group B Streptococcus | Journal of Clinical Microbiology | 2003 | 509 |
| 38 | The genome of a Late Pleistocene human from a Clovis burial site in western Montana | Nature | 2014 | 500 |
| 39 | Factors determining the occurrence of submicroscopic malaria infections and their relevance for control | Nature Communications | 2012 | 490 |
| 40 | Global and National Burden of Diseases and Injuries Among Children and Adolescents Between 1990 and 2013 | JAMA Pediatrics | 2016 | 479 |
| 41 | Phandango: an interactive viewer for bacterial population genomics | Bioinformatics | 2018 | 468 |
| 42 | The global distribution and spread of the mobilized colistin resistance gene mcr-1 | Nature Communications | 2018 | 464 |
| 43 | Hitting Hotspots: Spatial Targeting of Malaria for Control and Elimination | PLoS Medicine | 2012 | 460 |
| 44 | Multilocus Sequence Typing and Evolutionary Relationships among the Causative Agents of Melioidosis and Glanders, Burkholderia pseudomallei and Burkholderia mallei | Journal of Clinical Microbiology | 2003 | 459 |
| 45 | Geographic Distribution of Staphylococcus aureus Causing Invasive Infections in Europe: A Molecular-Epidemiological Analysis | PLoS Medicine | 2010 | 456 |
| 46 | Closure of schools during an influenza pandemic | Lancet Infectious Diseases, The | 2009 | 448 |
| 47 | Challenges in creating herd immunity to SARS-CoV-2 infection by mass vaccination | Lancet, The | 2020 | 447 |
| 48 | Global circulation patterns of seasonal influenza viruses vary with antigenic drift | Nature | 2015 | 445 |
| 49 | Submicroscopic Infection inPlasmodium falciparum–Endemic Populations: A Systematic Review and Meta‐Analysis | Journal of Infectious Diseases | 2009 | 444 |
| 50 | Suppression of a Field Population of Aedes aegypti in Brazil by Sustained Release of Transgenic Male Mosquitoes | PLoS Neglected Tropical Diseases | 2015 | 441 |
