Frederick A Matsen

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. pmc Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
    Frederick A Matsen
    Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 8:e56859. 2013
  2. pmc Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
    Frederick A Matsen
    Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Algorithms Mol Biol 7:8. 2012
  3. pmc Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Algorithms Mol Biol 7:14. 2012
  4. pmc A format for phylogenetic placements
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 7:e31009. 2012
  5. doi request reprint constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center 1100, Seattle, Washington 98109 1024, USA
    J Comput Biol 17:799-818. 2010
  6. pmc pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    Frederick A Matsen
    Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    BMC Bioinformatics 11:538. 2010
  7. pmc More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis
    Sujatha Srinivasan
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 8:e78633. 2013
  8. pmc Nestly--a framework for running software with nested parameter choices and aggregating results
    Connor O McCoy
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Bioinformatics 29:387-8. 2013
  9. pmc Minimizing the average distance to a closest leaf in a phylogenetic tree
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 91802, USA
    Syst Biol 62:824-36. 2013
  10. pmc Gene loss and adaptation to hominids underlie the ancient origin of HIV-1
    Lucie Etienne
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell Host Microbe 14:85-92. 2013

Detail Information

Publications18

  1. pmc Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
    Frederick A Matsen
    Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 8:e56859. 2013
    ..We present these methods and illustrate their use with data from the human microbiome...
  2. pmc Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
    Frederick A Matsen
    Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Algorithms Mol Biol 7:8. 2012
    ..abstract:..
  3. pmc Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Algorithms Mol Biol 7:14. 2012
    ..abstract:..
  4. pmc A format for phylogenetic placements
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 7:e31009. 2012
    ....
  5. doi request reprint constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center 1100, Seattle, Washington 98109 1024, USA
    J Comput Biol 17:799-818. 2010
    ..constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints...
  6. pmc pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    Frederick A Matsen
    Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    BMC Bioinformatics 11:538. 2010
    ....
  7. pmc More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis
    Sujatha Srinivasan
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 8:e78633. 2013
    ..Gram-negative rods designated Mobiluncus morphotypes on Gram stain are more likely BVAB1. These findings provide a clearer picture of the bacteria associated with morphotypes on vaginal Gram stain. ..
  8. pmc Nestly--a framework for running software with nested parameter choices and aggregating results
    Connor O McCoy
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Bioinformatics 29:387-8. 2013
    ..We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds...
  9. pmc Minimizing the average distance to a closest leaf in a phylogenetic tree
    Frederick A Matsen
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 91802, USA
    Syst Biol 62:824-36. 2013
    ..These algorithms have been implemented in publicly available software...
  10. pmc Gene loss and adaptation to hominids underlie the ancient origin of HIV-1
    Lucie Etienne
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell Host Microbe 14:85-92. 2013
    ..Thus, HIV-1 originated through a series of gene loss and adaptation events that generated its chimpanzee precursor and lowered the species barrier to human infection. ..
  11. pmc Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria
    Sujatha Srinivasan
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 7:e37818. 2012
    ..We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV...
  12. pmc HIV-1 superinfection occurs less frequently than initial infection in a cohort of high-risk Kenyan women
    Keshet Ronen
    Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Pathog 9:e1003593. 2013
    ..The observation that superinfection risk changes with time implies a window of protection that coincides with the maturation of HIV-specific immunity...
  13. pmc Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections
    Stephen J Salipante
    Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
    PLoS ONE 8:e65226. 2013
    ..The described method is sufficiently rapid (theoretically compatible with same-day turnaround times) and inexpensive for routine clinical use...
  14. pmc Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family
    Mia T Levine
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Genet 8:e1002729. 2012
    ....
  15. pmc A novel bayesian method for detection of APOBEC3-mediated hypermutation and its application to zoonotic transmission of simian foamy viruses
    Frederick A Matsen
    Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003493. 2014
    ..We find that human APOBEC3G can induce genetic changes that may prevent SFV replication in infected humans in vivo. ..
  16. pmc The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx
    Efrem S Lim
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    Cell Host Microbe 11:194-204. 2012
    ..We conclude that vpr neofunctionalized to degrade SAMHD1 even prior to the birth of a separate vpx gene, thereby initiating an evolutionary arms race with SAMHD1...
  17. pmc Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment
    Dara A Lehman
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    J Acquir Immune Defic Syndr 60:225-33. 2012
    ..It remains unclear whether specific NVP resistance mutations or combinations of mutations predict virologic failure in infants when present at low frequencies before NVP-based treatment...