| 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 | 745 | 2012 |
| 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 | 299 | 2012 |
| 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 | 245 | 2013 |
| 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 | 147 | 2015 |
| 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 | 129 | 2015 |
| Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth CO McCoy, FA Matsen IV PeerJ 1, e157, 2013 | 73 | 2013 |
| 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 | 65 | 2013 |
| 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 | 61 | 2015 |
| 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 | 58 | 2012 |
| 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 | 47 | 2015 |
| 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, ... JAIDS Journal of Acquired Immune Deficiency Syndromes 60 (3), 225-233, 2012 | 45 | 2012 |
| 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 | 36 | 2018 |
| Preexposure prophylaxis-selected drug resistance decays rapidly after drug cessation JF Weis, JM Baeten, CO McCoy, C Warth, D Donnell, KK Thomas, ... Aids 30 (1), 31-35, 2016 | 36 | 2016 |
| 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 | 12 | 2013 |
| 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 | 10 | 2013 |
| 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 | 5 | 2014 |
| 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 | 4 | 2018 |
| 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 | 2 | 2014 |
| 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 |
