Center-Authored Papers

Filters: Author is Matsen, Frederick A  [Clear All Filters]
2017
Dinh V, Matsen FA.  2017.  THE SHAPE OF THE ONE-DIMENSIONAL PHYLOGENETIC LIKELIHOOD FUNCTION.. ANNALS OF APPLIED PROBABILITY. 27(3):1646-1677. 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.
Gavryushkin A, Whidden C, Matsen FA.  2017.  The combinatorics of discrete time-trees: theory and open problems.. Journal of mathematical biology. Abstract
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
2016
Ralph DK, Matsen FA.  2016.  Likelihood-Based Inference of B Cell Clonal Families.. PLoS computational biology. 12(10):e1005086. Abstract
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
2015
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
McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA.  2015.  Quantifying evolutionary constraints on B-cell affinity maturation.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 370(1676) 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
Whidden C, Matsen FA.  2015.  Quantifying MCMC Exploration of Phylogenetic Tree Space.. Systematic biology. 64(3):472-91. Abstract
Lehman DA, Baeten JM, McCoy CO, Weis JF, Peterson D, Mbara G, Donnell D, Thomas KK, Hendrix CW, Marzinke MA et al..  2015.  Risk of drug resistance among persons acquiring HIV within a randomized clinical trial of single- or dual-agent preexposure prophylaxis.. The Journal of infectious diseases. 211(8):1211-8. 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
2014
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
Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA.  2014.  PhyloSift: phylogenetic analysis of genomes and metagenomes.. PeerJ. 2:e243. Abstract
2013
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
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
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
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
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
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
McCoy CO, Matsen FA.  2013.  Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth.. PeerJ. 1:e157. 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
Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT et al..  2013.  Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections.. PloS one. 8(5):e65226. Abstract
Soliven K, Wang X, Small CT, Feeroz MM, Lee E-G, Craig KL, Hasan K, Engel GA, Jones-Engel L, Matsen FA et al..  2013.  Simian Foamy Virus Infection of Rhesus Macaques in Bangladesh: Relationship of latent proviruses and transcriptionally active viruses.. Journal of virology. 87(24):13628-39. Abstract
Engel GA, Small CT, Soliven K, Feeroz MM, Wang X, Hasan MK, Oh G, Alam SMR, Craig KL, Jackson DL et al..  2013.  Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection. Emerging Microbes & Infections. 2 Abstract