Center-Authored Papers

Filters: Author is Matsen, Frederick A  [Clear All Filters]
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Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M.  2012.  The Ability of Primate Lentiviruses to Degrade the Monocyte Restriction Factor SAMHD1 Preceded the Birth of the Viral Accessory Protein Vpx.. Cell host & microbe. 11(2):194-204. Abstract
McCoy CO, Matsen FA.  2013.  Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth.. PeerJ. 1:e157. Abstract
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Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM et al..  2012.  Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.. PloS one. 7(6):e37818. Abstract
Gall A, Fero J, McCoy C, Claywell BC, Sanchez CA, Blount PL, Li X, Vaughan TL, Matsen FA, Reid BJ et al..  2015.  Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort.. PloS one. 10(6):e0129055. Abstract
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Gavryushkin A, Whidden C, Matsen FA.  2017.  The combinatorics of discrete time-trees: theory and open problems.. Journal of mathematical biology. Abstract
Watson CT, Matsen FA, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE.  2017.  Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data".. Journal of immunology (Baltimore, Md. : 1950). 198(9):3371-3373.
Ralph DK, Matsen FA.  2016.  Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.. PLoS computational biology. 12(1):e1004409. Abstract
Matsen FA.  2010.  constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.. Journal of computational biology : a journal of computational molecular cell biology. 17(6):799-818. Abstract
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Cobey S, Wilson P, Matsen FA.  2015.  The evolution within us.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 370(1676) Abstract
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Matsen FA, Hoffman NG, Gallagher A, Stamatakis A.  2012.  A format for phylogenetic placements.. PloS one. 7(2):e31009. Abstract
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Etienne L, Hahn BH, Sharp PM, Matsen FA, Emerman M.  2013.  Gene loss and adaptation to hominids underlie the ancient origin of HIV-1.. Cell host & microbe. 14(1):85-92. Abstract
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Warren EH, Matsen FA, Chou J.  2013.  High-throughput sequencing of B- and T-lymphocyte antigen receptors in hematology.. Blood. 122(1):19-22. Abstract
Ronen K, McCoy CO, Matsen FA, Boyd DF, Emery S, Odem-Davis K, Jaoko W, Mandaliya K, McClelland SR, Richardson BA et al..  2013.  HIV-1 superinfection occurs less frequently than initial infection in a cohort of high-risk Kenyan women.. PLoS pathogens. 9(8):e1003593. Abstract
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Ralph DK, Matsen FA.  2016.  Likelihood-Based Inference of B Cell Clonal Families.. PLoS computational biology. 12(10):e1005086. Abstract
Lehman DA, Wanalwa DC, McCoy CO, Matsen FA, Langat A, Chohan BH, Benki-Nugent S, Custers-Allen R, Bushman FD, John-Stewart GC et al..  2012.  Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment.. Journal of acquired immune deficiency syndromes (1999). Abstract
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Nipperess DA, Matsen FA.  2013.  The mean and variance of phylogenetic diversity under rarefaction.. Methods in ecology and evolution / British Ecological Society. 4(6):566-572. Abstract
Matsen FA, Gallagher A, McCoy CO.  2013.  Minimizing the average distance to a closest leaf in a phylogenetic tree.. Systematic biology. 62(6):824-36. Abstract
Srinivasan S, Morgan MT, Liu C, Matsen FA, Hoffman NG, Fiedler TL, Agnew KJ, Marrazzo JM, Fredricks DN.  2013.  More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis.. PloS one. 8(10):e78633. Abstract
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McCoy CO, Gallagher A, Hoffman NG, Matsen FA.  2013.  nestly--a framework for running software with nested parameter choices and aggregating results.. Bioinformatics (Oxford, England). 29(3):387-8. Abstract
Karlsson EA, Small CT, Freiden P, Feeroz MM, Matsen FA, San S, Hasan KM, Wang D, Jones-Engel L, Schultz-Cherry S.  2015.  Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections.. PLoS pathogens. 11(11):e1005225. Abstract
Matsen FA, Small CT, Soliven K, Engel GA, Feeroz MM, Wang X, Craig KL, Hasan KM, Emerman M, Linial ML et al..  2014.  A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses.. PLoS computational biology. 10(2):e1003493. Abstract
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Billey SC, Konvalinka M, Matsen FA.  2017.  On the enumeration of tanglegrams and tangled chains.. Journal of Combinatorial Theory, Series A. 146:239-263. Abstract
Butler-Wu SM, Burns EM, Pottinger PS, Magaret AS, Rakeman JL, Matsen FA, Cookson BT.  2011.  Optimization of periprosthetic culture for diagnosis of Propionibacterium acnes prosthetic joint infection.. Journal of clinical microbiology. 49(7):2490-5. Abstract
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Evans SN, Matsen FA.  2012.  The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. Journal of the Royal Statistical Society: Series B (Statistical Methodology). 74(3):569-592.
Levine MT, McCoy C, Vermaak D, Lee YCG, Hiatt MA, Matsen FA, Malik HS.  2012.  Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family.. PLoS genetics. 8(6):e1002729. Abstract