Center-Authored Papers

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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
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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.
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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
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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
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
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
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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
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
Matsen, FA, Hoffman NG, Gallagher A, Stamatakis A.  2012.  A format for phylogenetic placements.. PloS one. 7(2):e31009. Abstract
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
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
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, 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