F
Frederick A. Matsen
Researcher at Fred Hutchinson Cancer Research Center
Publications - 159
Citations - 7055
Frederick A. Matsen is an academic researcher from Fred Hutchinson Cancer Research Center. The author has contributed to research in topics: Phylogenetic tree & Tree (data structure). The author has an hindex of 37, co-authored 158 publications receiving 5905 citations. Previous affiliations of Frederick A. Matsen include University of Canterbury & University of Washington.
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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
TL;DR: Pplacer as discussed by the authors is a software package for phylogenetic placement and subsequent visualization, which can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, and is easy to run in parallel.
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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
TL;DR: Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.
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PhyloSift: phylogenetic analysis of genomes and metagenomes.
Aaron E. Darling,Aaron E. Darling,Guillaume Jospin,Eric Lowe,Frederick A. Matsen,Holly M. Bik,Jonathan A. Eisen +6 more
TL;DR: This work presents an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample and applies new tools to analyze the phylogenetic diversity of microbial communities.
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Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
Sujatha Srinivasan,Noah G. Hoffman,Martin Morgan,Frederick A. Matsen,Tina L. Fiedler,Robert W. Hall,Frederick J. Ross,Connor O. McCoy,Roger E. Bumgarner,Jeanne M. Marrazzo,David N. Fredricks,David N. Fredricks +11 more
TL;DR: The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present.
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The Ability of Primate Lentiviruses to Degrade the Monocyte Restriction Factor SAMHD1 Preceded the Birth of the Viral Accessory Protein Vpx
Efrem S. Lim,Oliver I. Fregoso,Connor O. McCoy,Frederick A. Matsen,Harmit S. Malik,Michael Emerman +5 more
TL;DR: It is concluded that vpr neofunctionalized to degrade SAM HD1 even prior to the birth of a separate vpx gene, thereby initiating an evolutionary arms race with SAMHD1.