Citation Impact
Citing Papers
PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
2019 Standout
Active learning increases student performance in science, engineering, and mathematics
2014 Standout
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”
2009 Standout
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
2020 Standout
Limits of long-term selection against Neandertal introgression
2019 StandoutNobel
Resolution of ray-finned fish phylogeny and timing of diversification
2012 Standout
One thousand plant transcriptomes and the phylogenomics of green plants
2019 StandoutNature
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
2010
Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides × P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence
2010
iGTP: A software package for large-scale gene tree parsimony analysis
2010
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
2013 Standout
Phylogenomics Revives Traditional Views on Deep Animal Relationships
2009 Standout
OrthoFinder: phylogenetic orthology inference for comparative genomics
2019 Standout
Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe
2018 StandoutNobel
Fast and accurate methods for phylogenomic analyses
2011
Early evolution of symmetry and polarity in metazoan body plans
2008
The biogeography of mitochondrial and nuclear discordance in animals
2012 Standout
Coalescent methods for estimating phylogenetic trees
2009
The evolution of bat pollination: a phylogenetic perspective
2009
SpedeSTEM: a rapid and accurate method for species delimitation
2010
A new genus of miniaturized and pug-nosed gecko from South America (Sphaerodactylidae: Gekkota)
2011
Ultrafast Approximation for Phylogenetic Bootstrap
2013 Standout
Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
2018 Standout
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
2007
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
2015
The Colletotrichum gloeosporioides species complex
2012 Standout
Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America’s open biomes
2011
A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root
2012
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
2012 Standout
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
2015 Standout
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
2010
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
2016 Standout
Ecosystem services provided by bats
2011 Standout
Determining species tree topologies from clade probabilities under the coalescent
2011
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
2012 Standout
The integrative future of taxonomy
2010 Standout
Gene tree discordance, phylogenetic inference and the multispecies coalescent
2009
Bayesian Inference of Species Trees from Multilocus Data
2009 Standout
Dynamics of Genome Rearrangement in Bacterial Populations
2008
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
2016
ABGD, Automatic Barcode Gap Discovery for primary species delimitation
2011 Standout
Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core Methods
2012 Standout
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
2015 StandoutNature
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
2010 Standout
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
2018 Standout
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
2014
Recent Trends in Molecular Phylogenetic Analysis: Where to Next?
2010
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
2012 Standout
A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates
2011
Mechanisms of plant defense against insect herbivores
2012 Standout
Harnessing genomics for evolutionary insights
2009
Congruence between nuclear and mitochondrial DNA: Combination of multiple nuclear introns resolves a well-supported phylogeny of New World orioles (Icterus)
2010
Inferring Phylogenies from RAD Sequence Data
2012
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
2012 Standout
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
2010 Standout
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
2008
Mining museums for historical DNA: advances and challenges in museomics
2021 Standout
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets
2017 Standout
Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples
2009
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
2013 Standout
Fine-Scale Phylogenetic Discordance across the House Mouse Genome
2009
Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
2018 Standout
Phytozome: a comparative platform for green plant genomics
2011 Standout
NeatMap - non-clustering heat map alternatives in R
2010
Integrative taxonomy, or iterative taxonomy?
2010
Active Learning Not Associated with Student Learning in a Random Sample of College Biology Courses
2011
Identifying Hybridization Events in the Presence of Coalescence via Model Selection
2009
Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa
2015 StandoutScience
raxmlGUI: a graphical front-end for RAxML
2011 Standout
Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes
2009
Problem-based learning: Creative thinking skills, problem-solving skills, and learning outcome of seventh grade students
2018 Standout
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
2009
Stacks: an analysis tool set for population genomics
2013 Standout
Current trends in the evolutionary ecology of plant defence
2010
Evolutionary history of mycorrhizal symbioses and global host plant diversity
2018 Standout
Estimating Species Trees from Unrooted Gene Trees
2011
Impact of whole‐genome duplication events on diversification rates in angiosperms
2018
2014
Benefits of jasmonate-dependent defenses against vertebrate herbivores in nature
2016
High-Throughput Genomic Data in Systematics and Phylogenetics
2013
How should we teach tree-thinking? An experimental test of two hypotheses
2013
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
2012
Motivation and cognitive load in the flipped classroom: definition, rationale and a call for research
2014 Standout
Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations
2018 StandoutScienceNobel
Revised Classification, Nomenclator and Typification of Gastropod and Monoplacophoran Families
2017 Standout
Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution
2019
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
2010
High-resolution species trees without concatenation
2007
PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES
2013
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
2012 Standout
Properties of Consensus Methods for Inferring Species Trees from Gene Trees
2009
Naive binning improves phylogenomic analyses
2013
Testing Congruence in Phylogenomic Analysis
2008
Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer
2011
Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis
2016
BEST: Bayesian estimation of species trees under the coalescent model
2008 Standout
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
2011
Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats
2010
A general species delimitation method with applications to phylogenetic placements
2013 Standout
Breaking family ties: taxon sampling and molecular phylogeny of chromodorid nudibranchs (Mollusca, Gastropoda)
2010
Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework
2009
Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)
2009
Phylogenetic Inference Using Whole Genomes
2008
Active Learning and Student-centered Pedagogy Improve Student Attitudes and Performance in Introductory Biology
2009
Bayesian Phylogenetics and Its Influence on Insect Systematics
2009
ASTRAL: genome-scale coalescent-based species tree estimation
2014 Standout
Works of Stacey D. Smith being referenced
Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics
2012
Bayesian Estimation of Concordance among Gene Trees
2006
Phylogenetics of the florally diverse Andean clade Iochrominae (Solanaceae)
2006
Plant sex and the evolution of plant defenses against herbivores
2009
How traits shape trees: new approaches for detecting character state‐dependent lineage diversification
2014
Convergent Evolution at the Pathway Level: Predictable Regulatory Changes during Flower Color Transitions
2018
The Tree-Thinking Challenge
2005 Science