| # | Title | Journal | Year | Citations |
|---|
| 1 | BEAST: Bayesian evolutionary analysis by sampling trees | BMC Evolutionary Biology | 2007 | 11,072 |
| 2 | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 | Systematic Biology | 2018 | 6,726 |
| 3 | BEAST 2: A Software Platform for Bayesian Evolutionary Analysis | PLoS Computational Biology | 2014 | 5,301 |
| 4 | The proximal origin of SARS-CoV-2 | Nature Medicine | 2020 | 3,871 |
| 5 | SARS-CoV-2 variants, spike mutations and immune escape | Nature Reviews Microbiology | 2021 | 2,650 |
| 6 | BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis | PLoS Computational Biology | 2019 | 2,484 |
| 7 | Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 | Virus Evolution | 2018 | 2,401 |
| 8 | A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology | Nature Microbiology | 2020 | 2,291 |
| 9 | Genome-wide genetic marker discovery and genotyping using next-generation sequencing | Nature Reviews Genetics | 2011 | 2,198 |
| 10 | Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic | Nature | 2009 | 1,870 |
| 11 | Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings | Science | 2009 | 1,665 |
| 12 | Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) | Virus Evolution | 2016 | 1,638 |
| 13 | Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection | Journal of Evolutionary Biology | 2007 | 1,541 |
| 14 | Bayesian Phylogeography Finds Its Roots | PLoS Computational Biology | 2009 | 1,519 |
| 15 | Heritability in the genomics era — concepts and misconceptions | Nature Reviews Genetics | 2008 | 1,496 |
| 16 | Effective population size and patterns of molecular evolution and variation | Nature Reviews Genetics | 2009 | 1,339 |
| 17 | The distribution of fitness effects of new mutations | Nature Reviews Genetics | 2007 | 1,234 |
| 18 | Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa | Nature | 2022 | 1,210 |
| 19 | Real-time, portable genome sequencing for Ebola surveillance | Nature | 2016 | 1,179 |
| 20 | Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil | Science | 2021 | 1,125 |
| 21 | Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak | Science | 2014 | 1,083 |
| 22 | Adaptive Phenotypic Plasticity in Response to Climate Change in a Wild Bird Population | Science | 2008 | 1,057 |
| 23 | Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England | Nature | 2021 | 1,001 |
| 24 | Social evolution theory for microorganisms | Nature Reviews Microbiology | 2006 | 993 |
| 25 | Chromosome Inversions, Local Adaptation and Speciation | Genetics | 2006 | 984 |
| 26 | BlobToolKit – Interactive Quality Assessment of Genome Assemblies | G3: Genes, Genomes, Genetics | 2020 | 883 |
| 27 | An ecologist’s guide to the animal model | Journal of Animal Ecology | 2010 | 849 |
| 28 | Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity | Cell | 2021 | 843 |
| 29 | Genome partitioning of genetic variation for complex traits using common SNPs | Nature Genetics | 2011 | 834 |
| 30 | Steps in the evolution of heteromorphic sex chromosomes | Heredity | 2005 | 827 |
| 31 | The genomic and epidemiological dynamics of human influenza A virus | Nature | 2008 | 824 |
| 32 | Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits | PLoS Genetics | 2008 | 823 |
| 33 | Evolutionary Explanations for Cooperation | Current Biology | 2007 | 815 |
| 34 | Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool | Virus Evolution | 2021 | 774 |
| 35 | Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic | Nature Microbiology | 2020 | 772 |
| 36 | Cooperation and conflict in quorum-sensing bacterial populations | Nature | 2007 | 737 |
| 37 | Defining operational taxonomic units using DNA barcode data | Philosophical Transactions of the Royal Society B: Biological Sciences | 2005 | 729 |
| 38 | The evolutionary ecology of individual phenotypic plasticity in wild populations | Journal of Evolutionary Biology | 2007 | 719 |
| 39 | Phenological sensitivity to climate across taxa and trophic levels | Nature | 2016 | 705 |
| 40 | General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters | Journal of Evolutionary Biology | 2010 | 691 |
| 41 | SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout | Nature Genetics | 2008 | 678 |
| 42 | Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity | Nature Communications | 2014 | 640 |
| 43 | The Social Lives of Microbes | Annual Review of Ecology, Evolution, and Systematics | 2007 | 636 |
| 44 | Current issues in fish welfare | Journal of Fish Biology | 2006 | 627 |
| 45 | Identification of 100 fundamental ecological questions | Journal of Ecology | 2013 | 605 |
| 46 | BlobTools: Interrogation of genome assemblies | F1000Research | 0 | 600 |
| 47 | Selection on Heritable Phenotypic Plasticity in a Wild Bird Population | Science | 2005 | 571 |
| 48 | Balancing Selection and Its Effects on Sequences in Nearby Genome Regions | PLoS Genetics | 2006 | 560 |
| 49 | Senescence in natural populations of animals: Widespread evidence and its implications for bio-gerontology | Ageing Research Reviews | 2013 | 548 |
| 50 | Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity | Cell | 2021 | 541 |
