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Connor McCoy
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Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria
S Srinivasan, NG Hoffman, MT Morgan, FA Matsen, TL Fiedler, RW Hall, ...
PloS one 7 (6), e37818, 2012
6152012
The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx
ES Lim, OI Fregoso, CO McCoy, FA Matsen, HS Malik, M Emerman
Cell host & microbe 11 (2), 194-204, 2012
2782012
Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections
SJ Salipante, DJ Sengupta, C Rosenthal, G Costa, J Spangler, EH Sims, ...
PloS one 8 (5), e65226, 2013
2032013
Risk of drug resistance among persons acquiring HIV within a randomized clinical trial of single-or dual-agent preexposure prophylaxis
DA Lehman, JM Baeten, CO McCoy, JF Weis, D Peterson, G Mbara, ...
The Journal of infectious diseases 211 (8), 1211-1218, 2015
1322015
Bacterial composition of the human upper gastrointestinal tract microbiome is dynamic and associated with genomic instability in a Barrett’s esophagus cohort
A Gall, J Fero, C McCoy, BC Claywell, CA Sanchez, PL Blount, X Li, ...
PloS one 10 (6), e0129055, 2015
1002015
Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
CO McCoy, FA Matsen IV
PeerJ 1, e157, 2013
642013
HIV-1 superinfection occurs less frequently than initial infection in a cohort of high-risk Kenyan women
K Ronen, CO McCoy, FA Matsen, DF Boyd, S Emery, K Odem-Davis, ...
PLoS pathogens 9 (8), e1003593, 2013
572013
Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial
PT Edlefsen, M Rolland, T Hertz, S Tovanabutra, AJ Gartland, ...
PLoS computational biology 11 (2), e1003973, 2015
532015
Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family
MT Levine, C McCoy, D Vermaak, YCG Lee, MA Hiatt, FA Matsen, ...
PLoS genetics 8 (6), e1002729, 2012
472012
Quantifying evolutionary constraints on B-cell affinity maturation
CO McCoy, T Bedford, VN Minin, P Bradley, H Robins, FA Matsen IV
Philosophical Transactions of the Royal Society B: Biological Sciences 370 …, 2015
362015
Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment
DA Lehman, DC Wanalwa, CO McCoy, FA Matsen, A Langat, BH Chohan, ...
Journal of acquired immune deficiency syndromes (1999) 60 (3), 225, 2012
342012
Prep-selected drug resistance decays rapidly after drug cessation
JF Weis, JM Baeten, CO McCoy, C Warth, D Donnell, KK Thomas, ...
AIDS (London, England) 30 (1), 31, 2016
312016
Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals
M Fourment, BC Claywell, V Dinh, C McCoy, FA Matsen IV, AE Darling
Systematic biology 67 (3), 490-502, 2018
232018
Minimizing the average distance to a closest leaf in a phylogenetic tree
FA Matsen IV, A Gallagher, CO McCoy
Systematic Biology 62 (6), 824-836, 2013
112013
nestly—a framework for running software with nested parameter choices and aggregating results
CO McCoy, A Gallagher, NG Hoffman, FA Matsen
Bioinformatics 29 (3), 387-388, 2013
102013
PrEP exposure and the risk of low-frequency drug resistance
D Lehman, JM Baeten, C McCoy, J Weis, D Peterson, C Celum, N Mugo, ...
Abstract presented at: 21st Conference on Retroviruses and Opportunistic …, 2014
52014
A surrogate function for one-dimensional phylogenetic likelihoods
BC Claywell, V Dinh, M Fourment, CO McCoy, FA Matsen IV
Molecular biology and evolution 35 (1), 242-246, 2018
32018
Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial
PT Edlefsen, M Rolland, T Hertz, S Tovanabutra, AJ Gartland, ...
AIDS Research and Human Retroviruses 30 (S1), A25-A26, 2014
22014
SUBSTITUTION AND SITE-SPECIFIC SELECTION DRIVING B CELL AFFINITY MATURATION IS CONSISTENT ACROSS INDIVIDUALS
CO MCCOY, T BEDFORD, VN MININ, H ROBINS, FA MATSEN IV
arXiv preprint arXiv:1403.3066, 2014
2014
BASIC AND TRANSLATIONAL SCIENCE Low-Frequency Nevirapine Resistance at Multiple Sites May Predict Treatment Failure in Infants on Nevirapine-Based Treatment
DA Lehman, DC Wamalwa, CO Mccoy, FA Matsen, A Langat, BH Chohan, ...
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