The First Darwinian Phylogenetic Tree of Plants.
Sign Up to like & getrecommendations! Published in 2017 at "Trends in plant science"
DOI: 10.1016/j.tplants.2016.12.002
Abstract: In 1866, the German zoologist Ernst Haeckel (1834-1919) published the first Darwinian trees of life in the history of biology in his book General Morphology of Organisms. We take a specific look at the first… read more here.
Keywords: first darwinian; biology; tree plants; darwinian phylogenetic ... See more keywords
Phylogenetic tree of Litopterna and Perissodactyla indicates a complex early history of hoofed mammals
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-70287-5
Abstract: The Litopterna is an extinct clade of endemic South American ungulates that range from Paleocene up to late Pleistocene times. Because of their unique anatomy, litopterns are of uncertain phylogenetic affinities. However, some nineteenth century… read more here.
Keywords: litopterna perissodactyla; tree litopterna; hoofed mammals; hoofed ... See more keywords
A novel deep learning method for predictive modeling of microbiome data
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbaa073
Abstract: With the development and decreasing cost of next-generation sequencing technologies, the study of the human microbiome has become a rapid expanding research field, which provides an unprecedented opportunity in various clinical applications such as drug… read more here.
Keywords: microbiome data; phylogenetic tree; method; deep learning ... See more keywords
Tumor phylogeny inference using tree-constrained importance sampling
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx270
Abstract: Motivation: A tumor arises from an evolutionary process that can be modeled as a phylogenetic tree. However, reconstructing this tree is challenging as most cancer sequencing uses bulk tumor tissue containing heterogeneous mixtures of cells.… read more here.
Keywords: tree; importance sampling; phylogenetic tree; inference ... See more keywords
Phylogenetic tree-based microbiome association test
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz686
Abstract: MOTIVATION Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals. To overcome these issues, non-parametric approaches, such as the Mann-Whitney U-test and Wilcoxon rank-sum test,… read more here.
Keywords: test; association; tree based; based microbiome ... See more keywords
A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree
Sign Up to like & getrecommendations! Published in 2020 at "Botanical Journal of the Linnean Society"
DOI: 10.1093/botlinnean/boaa042
Abstract: The field of systematics is experiencing a new molecular revolution driven by the increased availability of high-throughput sequencing technologies. As these techniques become more affordable, the increased genomic resources have increasingly far-reaching implications for our… read more here.
Keywords: carex; subgenera; kit; cyperaceae ... See more keywords
Robust analysis of phylogenetic tree space.
Sign Up to like & getrecommendations! Published in 2021 at "Systematic biology"
DOI: 10.1093/sysbio/syab100
Abstract: Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in 'tree space' can illuminate the behaviour and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different data… read more here.
Keywords: robust analysis; tree space; analysis phylogenetic; phylogenetic tree ... See more keywords
A Metric on Phylogenetic Tree Shapes
Sign Up to like & getrecommendations! Published in 2018 at "Systematic Biology"
DOI: 10.1093/sysbio/syx046
Abstract: Abstract. The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a… read more here.
Keywords: characterization; shapes metric; tree; phylogenetic tree ... See more keywords
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Sign Up to like & getrecommendations! Published in 2019 at "Systematic biology"
DOI: 10.1093/sysbio/syz047
Abstract: Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the… read more here.
Keywords: tree topologies; high likelihood; topology; likelihood set ... See more keywords
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1101/2022.01.12.475688
Abstract: Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the COVID-19 pandemic. One transformative approach, online… read more here.
Keywords: online phylogenetics; tree optimization; phylogenetic tree; optimization ... See more keywords
Scalable and Fast Algorithm for Constructing Phylogenetic Trees With Application to IoT Malware Clustering
Sign Up to like & getrecommendations! Published in 2023 at "IEEE Access"
DOI: 10.1109/access.2023.3238711
Abstract: With the development of IoT devices, there is a rapid increase in new types of IoT malware and variants, causing social problems. The malware’s phylogenetic tree has been used in many studies for malware clustering… read more here.
Keywords: phylogenetic tree; iot malware; constructing phylogenetic; malware ... See more keywords