Multitable Methods for Microbiome Data Integration

by Kris Sankaran, Susan P. Holmes
Published 2019-08-01

HIV-1 subtype B protease and reverse transcriptase amino acid covariation.

by Soo-Yon Rhee, Tommy F Liu, Susan P Holmes, Robert W Shafer
Published 2007-05-01

Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; referees: 2 approved]

by Ben J. Callahan, Kris Sankaran, Julia A. Fukuyama, Paul J. McMurdie, Susan P. Holmes
Published 2016-06-01

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses [version 2; referees: 3 approved]

by Ben J. Callahan, Kris Sankaran, Julia A. Fukuyama, Paul J. McMurdie, Susan P. Holmes
Published 2016-11-01

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

by Nicole M. Davis, Diana M. Proctor, Susan P. Holmes, David A. Relman, Benjamin J. Callahan
Published 2018-12-01

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.

by Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A Relman, Susan P Holmes
Published 2017-08-01

Down-regulation of the interferon signaling pathway in T lymphocytes from patients with metastatic melanoma.

by Rebecca J Critchley-Thorne, Ning Yan, Serban Nacu, Jeffrey Weber, Susan P Holmes, Peter P Lee
Published 2007-05-01

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

by Alison F Feder, Soo-Yon Rhee, Susan P Holmes, Robert W Shafer, Dmitri A Petrov, Pleuni S Pennings
Published 2017-01-01

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

by Alison F Feder, Soo-Yon Rhee, Susan P Holmes, Robert W Shafer, Dmitri A Petrov, Pleuni S Pennings
Published 2016-02-01

Diversity and recognition efficiency of T cell responses to cancer.

by Tor B Stuge, Susan P Holmes, Sahdev Saharan, Andrea Tuettenberg, Mario Roederer, Jeffrey S Weber, Peter P Lee
Published 2004-11-01

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

by Philip L Tzou, Sergei L Kosakovsky Pond, Santiago Avila-Rios, Susan P Holmes, Rami Kantor, Robert W Shafer
Published 2020-01-01

Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon

by Daniel D. Sprockett, Melanie Martin, Elizabeth K. Costello, Adam R. Burns, Susan P. Holmes, Michael D. Gurven, David A. Relman
Published 2020-07-01

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

by Yana Emmy Hoy, Elisabeth M Bik, Trevor D Lawley, Susan P Holmes, Denise M Monack, Julie A Theriot, David A Relman
Published 2015-01-01

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow

by Diana M. Proctor, Julia A. Fukuyama, Peter M. Loomer, Gary C. Armitage, Stacey A. Lee, Nicole M. Davis, Mark I. Ryder, Susan P. Holmes, David A. Relman
Published 2018-02-01

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea

by Elisabeth M. Bik, Elizabeth K. Costello, Alexandra D. Switzer, Benjamin J. Callahan, Susan P. Holmes, Randall S. Wells, Kevin P. Carlin, Eric D. Jensen, Stephanie Venn-Watson, David A. Relman
Published 2016-02-01

PRC2/EED-EZH2 complex is up-regulated in breast cancer lymph node metastasis compared to primary tumor and correlates with tumor proliferation in situ.

by Hongxiang Yu, Diana L Simons, Ilana Segall, Valeria Carcamo-Cavazos, Erich J Schwartz, Ning Yan, Neta S Zuckerman, Frederick M Dirbas, Denise L Johnson, Susan P Holmes, Peter P Lee
Published 2012-01-01

Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis

by Jennifer G. Wilson, Laura J. Simpson, Anne-Maud Ferreira, Arjun Rustagi, Jonasel Roque, Adijat Asuni, Thanmayi Ranganath, Philip M. Grant, Aruna Subramanian, Yael Rosenberg-Hasson, Holden T. Maecker, Susan P. Holmes, Joseph E. Levitt, Catherine A. Blish, Angela J. Rogers
Published 2020-09-01

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration

by Soo-Yon Rhee, Vici Varghese, Susan P. Holmes, Gert U. Van Zyl, Kim Steegen, Mark A. Boyd, David A. Cooper, Sabin Nsanzimana, Shanmugam Saravanan, Charlotte Charpentier, Tulio de Oliveira, Mary-Ann A. Etiebet, Federico Garcia, Dominique Goedhals, Perpetua Gomes, Huldrych F. Günthard, Raph L. Hamers, Christopher J Hoffmann, Gillian Hunt, Awachana Jiamsakul, Pontiano Kaleebu, Phyllis Kanki, Rami Kantor, Bernhard Kerschberger, Vincent C. Marconi, Jean D'amour Ndahimana, Nicaise Ndembi, Nicole Ngo-Giang-Huong, Casper Rokx, Maria M. Santoro, Jonathan M. Schapiro, Daniel Schmidt, Lillian Seu, Kim C.E. Sigaloff, Sunee Sirivichayakul, Lindiwe Skhosana, Henry Sunpath, Michele Tang, Chunfu Yang, Sergio Carmona, Ravindra K. Gupta, Robert W. Shafer
Published 2017-04-01