| pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree FA Matsen, RB Kodner, EV Armbrust BMC bioinformatics 11, 1-16, 2010 | 1074 | 2010 |
| 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 | 770 | 2012 |
| PhyloSift: phylogenetic analysis of genomes and metagenomes AE Darling, G Jospin, E Lowe, FA Matsen IV, HM Bik, JA Eisen PeerJ 2, e243, 2014 | 679* | 2014 |
| 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 | 307 | 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 | 254 | 2013 |
| The phylogenetic Kantorovich–Rubinstein metric for environmental sequence samples SN Evans, FA Matsen Journal of the Royal Statistical Society Series B: Statistical Methodology …, 2012 | 154 | 2012 |
| 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 | 152 | 2015 |
| Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation DK Ralph, FA Matsen IV PLoS computational biology 12 (1), e1004409, 2016 | 139 | 2016 |
| Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity WS DeWitt III, A Smith, G Schoch, JA Hansen, FA Matsen IV, P Bradley Elife 7, e38358, 2018 | 136 | 2018 |
| 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 | 135 | 2015 |
| Gene loss and adaptation to hominids underlie the ancient origin of HIV-1 L Etienne, BH Hahn, PM Sharp, FA Matsen, M Emerman Cell host & microbe 14 (1), 85-92, 2013 | 127 | 2013 |
| Quantifying MCMC exploration of phylogenetic tree space C Whidden, FA Matsen IV Systematic biology 64 (3), 472-491, 2015 | 111 | 2015 |
| Likelihood-based inference of B cell clonal families DK Ralph, FA Matsen IV PLoS computational biology 12 (10), e1005086, 2016 | 103 | 2016 |
| Reproducibility and reuse of adaptive immune receptor repertoire data F Breden, ET Luning Prak, B Peters, F Rubelt, CA Schramm, CE Busse, ... Frontiers in immunology 8, 1418, 2017 | 101 | 2017 |
| Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison FA Matsen IV, SN Evans PloS one 8 (3), e56859, 2013 | 95 | 2013 |
| Phylogenetic mixtures on a single tree can mimic a tree of another topology FA Matsen, M Steel Systematic Biology 56 (5), 767-775, 2007 | 86 | 2007 |
| Non-human primates harbor diverse mammalian and avian astroviruses including those associated with human infections EA Karlsson, CT Small, P Freiden, MM Feeroz, FA Matsen IV, S San, ... PLoS pathogens 11 (11), e1005225, 2015 | 85 | 2015 |
| More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis S Srinivasan, MT Morgan, C Liu, FA Matsen, NG Hoffman, TL Fiedler, ... PloS one 8 (10), e78633, 2013 | 85 | 2013 |
| AIRR community standardized representations for annotated immune repertoires JA Vander Heiden, S Marquez, N Marthandan, SAC Bukhari, CE Busse, ... Frontiers in immunology 9, 2206, 2018 | 82 | 2018 |
| A format for phylogenetic placements FA Matsen, NG Hoffman, A Gallagher, A Stamatakis PLoS One 7 (2), e31009, 2012 | 80 | 2012 |
Connor McCoyFred Hutchinson Cancer Research CenterVerified email at fhcrc.org
