Multitable Methods for Microbiome Data Integration

por Sankaran, Kris, Holmes, Susan P.
Publicado 2019

HIV-1 Transmission Networks in a Small World

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

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

por Gorvitovskaia, Anastassia, Holmes, Susan P., Huse, Susan M.
Publicado 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 2017

Denoising PCR-amplified metagenome data

por Rosen, Michael J, Callahan, Benjamin J, Fisher, Daniel S, Holmes, Susan P
Publicado 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 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 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 2016

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

por Davis, Nicole M., Proctor, Diana M., Holmes, Susan P., Relman, David A., Callahan, Benjamin J.
Publicado 2018

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 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 2017

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 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 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 2004

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

por Grembi, Jessica A., Nguyen, Lan H., Haggerty, Thomas D., Gardner, Christopher D., Holmes, Susan P., Parsonnet, Julie
Publicado 2020

Author Correction: Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

por Grembi, Jessica A., Nguyen, Lan H., Haggerty, Thomas D., Gardner, Christopher D., Holmes, Susan P., Parsonnet, Julie
Publicado 2020

Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences

por Tzou, Philip L., Kosakovsky Pond, Sergei L., Avila-Rios, Santiago, Holmes, Susan P., Kantor, Rami, Shafer, Robert W.
Publicado 2020

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 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 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 2016