Frederick "Erick" A. Matsen IV
Frederick "Erick" A. Matsen IV
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Cited by
Cited by
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
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
PhyloSift: phylogenetic analysis of genomes and metagenomes
AE Darling, G Jospin, E Lowe, FA Matsen IV, HM Bik, JA Eisen
PeerJ 2, e243, 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
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
The phylogenetic Kantorovich–Rubinstein metric for environmental sequence samples
SN Evans, FA Matsen
Journal of the Royal Statistical Society Series B: Statistical Methodology …, 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
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
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
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
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
Quantifying MCMC exploration of phylogenetic tree space
C Whidden, FA Matsen IV
Systematic biology 64 (3), 472-491, 2015
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
Likelihood-based inference of B cell clonal families
DK Ralph, FA Matsen IV
PLoS computational biology 12 (10), e1005086, 2016
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
Phylogenetic mixtures on a single tree can mimic a tree of another topology
FA Matsen, M Steel
Systematic Biology 56 (5), 767-775, 2007
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
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
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
A format for phylogenetic placements
FA Matsen, NG Hoffman, A Gallagher, A Stamatakis
PLoS One 7 (2), e31009, 2012
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