Susan P Holmes
Susan P Holmes
Professor of Statistics, Stanford University
Verified email at - Homepage
Cited by
Cited by
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
PJ McMurdie, S Holmes
PloS one 8 (4), e61217, 2013
DADA2: high-resolution sample inference from Illumina amplicon data
BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJA Johnson, ...
Nature methods 13 (7), 581-583, 2016
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, CC Abnet, GA Al-Ghalith, ...
Nature biotechnology 37 (8), 852-857, 2019
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.
PJ McMurdie, S Holmes
PLOS Computational Biology 10 (4), 2014
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
BJ Callahan, PJ McMurdie, SP Holmes
The ISME Journal, 1-5, 2017
Bootstrap confidence levels for phylogenetic trees
B Efron, E Halloran, S Holmes
Proceedings of the National Academy of Sciences 93 (23), 13429-13429, 1996
Temporal and spatial variation of the human microbiota during pregnancy
DB DiGiulio, BJ Callahan, PJ McMurdie, EK Costello, DJ Lyell, ...
Proceedings of the National Academy of Sciences 112 (35), 11060-11065, 2015
Geometry of the space of phylogenetic trees
LJ Billera, SP Holmes, K Vogtmann
Advances in Applied Mathematics 27 (4), 733-767, 2001
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ...
PeerJ Preprints, 2018
A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes
F Cruciani, P Santolamazza, P Shen, V Macaulay, P Moral, A Olckers, ...
American journal of human genetics 70 (5), 1197, 2002
Advancing our understanding of the human microbiome using QIIME
JA Navas-Molina, JM Peralta-Sánchez, A González, PJ McMurdie, ...
Methods in enzymology 531, 371-444, 2013
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
NM Davis, D Proctor, SP Holmes, DA Relman, BJ Callahan
biorxiv, 2018
Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
BJ Callahan, K Sankaran, JA Fukuyama, PJ McMurdie, SP Holmes
F1000Research 5, 2016
50 years of data science
D Donoho
Journal of Computational and Graphical Statistics 26 (4), 745-766, 2017
Colonic contribution to uremic solutes
PA Aronov, FJG Luo, NS Plummer, Z Quan, S Holmes, TH Hostetter, ...
Journal of the American Society of Nephrology 22 (9), 1769-1776, 2011
Sequential Monte Carlo methods for statistical analysis of tables
Y Chen, P Diaconis, SP Holmes, JS Liu
Journal of the American Statistical Association 100 (469), 109-120, 2005
Analysis of a nonreversible Markov chain sampler
P Diaconis, S Holmes, RM Neal
Annals of Applied Probability, 726-752, 2000
Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage
M Yan, SJ Pamp, J Fukuyama, PH Hwang, DY Cho, S Holmes, ...
Cell host & microbe 14 (6), 631-640, 2013
The molecular architecture of the eukaryotic chaperonin TRiC/CCT
A Leitner, LA Joachimiak, A Bracher, L Mönkemeyer, T Walzthoeni, ...
Structure 20 (5), 814-825, 2012
Profile of immune cells in axillary lymph nodes predicts disease-free survival in breast cancer
HE Kohrt, N Nouri, K Nowels, D Johnson, S Holmes, PP Lee
PLoS Med 2 (9), e284, 2005
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