Center-Authored Papers

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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
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Matsen FA, Evans SN.  2012.  Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials.. Algorithms for molecular biology : AMB. 7(1):14. Abstract
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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
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Dinh V, Matsen FA.  2017.  THE SHAPE OF THE ONE-DIMENSIONAL PHYLOGENETIC LIKELIHOOD FUNCTION.. ANNALS OF APPLIED PROBABILITY. 27(3):1646-1677. Abstract
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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
Matsen FA, Gallagher A.  2012.  Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots.. Algorithms for molecular biology : AMB. 7(1):8. 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
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Whidden C, Matsen FA.  2015.  Quantifying MCMC Exploration of Phylogenetic Tree Space.. Systematic biology. 64(3):472-91. 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
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Gilmer BB, Comstock BA, Jette JL, Warme WJ, Jackins SE, Matsen FA.  2012.  The Prognosis for Improvement in Comfort and Function After the Ream-and-Run Arthroplasty for Glenohumeral Arthritis: An Analysis of 176 Consecutive Cases.. The Journal of bone and joint surgery. American volume. 94(14):e1021-9. Abstract
Matsen FA, Kodner RB, Armbrust VE.  2010.  pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.. BMC bioinformatics. 11:538. 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
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
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.
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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
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
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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
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
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
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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
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
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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
Ralph DK, Matsen FA.  2016.  Likelihood-Based Inference of B Cell Clonal Families.. PLoS computational biology. 12(10):e1005086. Abstract
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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