| # | Title | Journal | Year | Citations |
|---|
|
| 1 | A method and server for predicting damaging missense mutations | Nature Methods | 2010 | 11,805 |
| 2 | Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi | Proceedings of the National Academy of Sciences of the United States of America | 2012 | 4,186 |
| 3 | Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level | Molecular Biology and Evolution | 2005 | 1,681 |
| 4 | Phylogenetic distribution and evolution of mycorrhizas in land plants | Mycorrhiza | 2006 | 1,586 |
| 5 | A REVIEW OF TRAIT-MEDIATED INDIRECT INTERACTIONS IN ECOLOGICAL COMMUNITIES | Ecology | 2003 | 1,362 |
| 6 | Three keys to the radiation of angiosperms into freezing environments | Nature | 2014 | 1,362 |
| 7 | Phylotranscriptomic analysis of the origin and early diversification of land plants | Proceedings of the National Academy of Sciences of the United States of America | 2014 | 1,171 |
| 8 | A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data | Mycologia | 2016 | 1,151 |
| 9 | Scaling environmental change through the community‐level: a trait‐based response‐and‐effect framework for plants | Global Change Biology | 2008 | 1,008 |
| 10 | Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes | Journal of Eukaryotic Microbiology | 2019 | 985 |
| 11 | Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence | Nature Reviews Genetics | 2012 | 978 |
| 12 | Inferring Phylogeny Despite Incomplete Lineage Sorting | Systematic Biology | 2006 | 973 |
| 13 | Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees | PLoS ONE | 2014 | 964 |
| 14 | The neural basis of puberty and adolescence | Nature Neuroscience | 2004 | 912 |
| 15 | rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development | Nucleic Acids Research | 2015 | 867 |
| 16 | geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees | Bioinformatics | 2014 | 798 |
| 17 | BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees | Methods in Ecology and Evolution | 2014 | 790 |
| 18 | Constructing a broadly inclusive seed plant phylogeny | American Journal of Botany | 2018 | 723 |
| 19 | Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses | Nature | 2016 | 686 |
| 20 | ADZE: a rarefaction approach for counting alleles private to combinations of populations | Bioinformatics | 2008 | 679 |
| 21 | Multispecies coalescent delimits structure, not species | Proceedings of the National Academy of Sciences of the United States of America | 2017 | 675 |
| 22 | Delimiting Species without Monophyletic Gene Trees | Systematic Biology | 2007 | 669 |
| 23 | Organic agriculture and the global food supply | Renewable Agriculture and Food Systems | 2007 | 667 |
| 24 | Why Do Hubs Tend to Be Essential in Protein Networks? | PLoS Genetics | 2006 | 643 |
| 25 | Individual recognition: it is good to be different | Trends in Ecology and Evolution | 2007 | 641 |
| 26 | Strong and Consistent Social Bonds Enhance the Longevity of Female Baboons | Current Biology | 2010 | 632 |
| 27 | Synthesis of phylogeny and taxonomy into a comprehensive tree of life | Proceedings of the National Academy of Sciences of the United States of America | 2015 | 619 |
| 28 | An inverse latitudinal gradient in speciation rate for marine fishes | Nature | 2018 | 618 |
| 29 | The changing landscape: ecosystem responses to urbanization and pollution across climatic and societal gradients | Frontiers in Ecology and the Environment | 2008 | 615 |
| 30 | Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution | Genetics | 2005 | 610 |
| 31 | The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms | Nature Reviews Genetics | 2011 | 605 |
| 32 | treePL: divergence time estimation using penalized likelihood for large phylogenies | Bioinformatics | 2012 | 605 |
| 33 | Angiosperm phylogeny: 17 genes, 640 taxa | American Journal of Botany | 2011 | 598 |
| 34 | The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution | Science | 2013 | 598 |
| 35 | The deepest divergences in land plants inferred from phylogenomic evidence | Proceedings of the National Academy of Sciences of the United States of America | 2006 | 586 |
| 36 | Data access for the 1,000 Plants (1KP) project | GigaScience | 2014 | 586 |
| 37 | Ecological Lessons from Free-Air CO2 Enrichment (FACE) Experiments | Annual Review of Ecology, Evolution, and Systematics | 2011 | 572 |
| 38 | Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers | MBio | 2019 | 563 |
| 39 | The biology of color | Science | 2017 | 550 |
| 40 | Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 539 |
| 41 | Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation | Nature Communications | 2013 | 539 |
| 42 | The agroecological matrix as alternative to the land-sparing/agriculture intensification model | Proceedings of the National Academy of Sciences of the United States of America | 2010 | 534 |
| 43 | The benefits of social capital: close social bonds among female baboons enhance offspring survival | Proceedings of the Royal Society B: Biological Sciences | 2009 | 532 |
| 44 | Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae | Proceedings of the National Academy of Sciences of the United States of America | 2002 | 527 |
| 45 | Local fitness landscape of the green fluorescent protein | Nature | 2016 | 480 |
| 46 | Minimum Information about an Uncultivated Virus Genome (MIUViG) | Nature Biotechnology | 2019 | 463 |
| 47 | The impacts of climate change on ecosystem structure and function | Frontiers in Ecology and the Environment | 2013 | 462 |
| 48 | Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix | PLoS ONE | 2012 | 454 |
| 49 | Subspecific origin and haplotype diversity in the laboratory mouse | Nature Genetics | 2011 | 451 |
| 50 | Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation | Systematic Biology | 2015 | 446 |
