Matchings and phylogenetic trees

Por Diaconis, Persi W., Holmes, Susan P.
Publicado em 1998

Adaptive importance sampling for network growth models

Por Guetz, Adam N., Holmes, Susan P.
Publicado no Ann Oper Res (2011)

HIV-1 Transmission Networks in a Small World

Por Pennings, Pleuni S., Holmes, Susan P., Shafer, Robert W.
Publicado em 2014

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

Por Gorvitovskaia, Anastassia, Holmes, Susan P., Huse, Susan M.
Publicado no Microbiome (2016)

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

Por Callahan, Benjamin J, McMurdie, Paul J, Holmes, Susan P
Publicado no ISME J (2017)

Denoising PCR-amplified metagenome data

Por Rosen, Michael J, Callahan, Benjamin J, Fisher, Daniel S, Holmes, Susan P
Publicado em 2012

HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation

Por Rhee, Soo-Yon, Liu, Tommy F, Holmes, Susan P, Shafer, Robert W
Publicado em 2007

Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations

Por Reuman, Elizabeth C., Rhee, Soo-Yon, Holmes, Susan P., Shafer, Robert W.
Publicado em 2010

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

Por Callahan, Ben J., Sankaran, Kris, Fukuyama, Julia A., McMurdie, Paul J., Holmes, Susan P.
Publicado no F1000Res (2016)

Down-Regulation of the Interferon Signaling Pathway in T Lymphocytes from Patients with Metastatic Melanoma

Por Critchley-Thorne, Rebecca J, Yan, Ning, Nacu, Serban, Weber, Jeffrey, Holmes, Susan P, Lee, Peter P
Publicado em 2007

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

Por Fukuyama, Julia, Rumker, Laurie, Sankaran, Kris, Jeganathan, Pratheepa, Dethlefsen, Les, Relman, David A., Holmes, Susan P.
Publicado no PLoS Comput Biol (2017)

Diversity and Recognition Efficiency of T Cell Responses to Cancer

Por Stuge, Tor B, Holmes, Susan P, Saharan, Sahdev, Tuettenberg, Andrea, Roederer, Mario, Weber, Jeffrey S, Lee, Peter P
Publicado em 2004

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

Por Feder, Alison F, Rhee, Soo-Yon, Holmes, Susan P, Shafer, Robert W, Petrov, Dmitri A, Pennings, Pleuni S
Publicado no eLife (2016)

Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

Por Feder, Alison F, Rhee, Soo-Yon, Holmes, Susan P, Shafer, Robert W, Petrov, Dmitri A, Pennings, Pleuni S
Publicado no eLife (2017)

Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitors

Por Rhee, Soo-Yon, Liu, Tommy F, Kiuchi, Mark, Zioni, Rafael, Gifford, Robert J, Holmes, Susan P, Shafer, Robert W
Publicado em 2008

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

Por Doherty, Kathleen M, Nakka, Priyanka, King, Bracken M, Rhee, Soo-Yon, Holmes, Susan P, Shafer, Robert W, Radhakrishnan, Mala L
Publicado em 2011

DADA2: High resolution sample inference from Illumina amplicon data

Por Callahan, Benjamin J, McMurdie, Paul J, Rosen, Michael J, Han, Andrew W, Johnson, Amy Jo A, Holmes, Susan P
Publicado no Nat Methods (2016)

Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time

Por Hoy, Yana Emmy, Bik, Elisabeth M., Lawley, Trevor D., Holmes, Susan P., Monack, Denise M., Theriot, Julie A., Relman, David A.
Publicado no PLoS One (2015)

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads

Por Reuman, Elizabeth C., Margeridon-Thermet, Severine, Caudill, Harrison B., Liu, Tommy, Borroto-Esoda, Katyna, Svarovskaia, Evguenia S., Holmes, Susan P., Shafer, Robert W.
Publicado em 2010

Detection of Cytomegalovirus Drug Resistance Mutations by Next-Generation Sequencing

Por Sahoo, Malaya K., Lefterova, Martina I., Yamamoto, Fumiko, Waggoner, Jesse J., Chou, Sunwen, Holmes, Susan P., Anderson, Matthew W., Pinsky, Benjamin A.
Publicado em 2013