Search Results - "HOLMES, Susan P"

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis by Callahan, Benjamin J, McMurdie, Paul J, Holmes, Susan P

“…Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular…”
Get full text

DADA2: High-resolution sample inference from Illumina amplicon data by Callahan, Benjamin J, McMurdie, Paul J, Rosen, Michael J, Han, Andrew W, Johnson, Amy Jo A, Holmes, Susan P

“…DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample…”
Get full text

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data by Davis, Nicole M, Proctor, Diana M, Holmes, Susan P, Relman, David A, Callahan, Benjamin J

“…The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not…”
Get full text

Latent variable modeling for the microbiome by Sankaran, Kris, Holmes, Susan P

“…The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both…”
Get full text

Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; peer review: 3 approved] by Callahan, Ben J, Sankaran, Kris, Fukuyama, Julia A, McMurdie, Paul J, Holmes, Susan P

“…High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities…”
Get full text

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women by Callahan, Benjamin J., DiGiulio, Daniel B., Goltsman, Daniela S. Aliaga, Sun, Christine L., Costello, Elizabeth K., Jeganathan, Pratheepa, Biggio, Joseph R., Wong, Ronald J., Druzin, Maurice L., Shaw, Gary M., Stevenson, David K., Holmes, Susan P., Relman, David A.

“…Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. Previous studies have suggested that the maternal vaginal microbiota contributes…”
Get full text

Temporal and spatial variation of the human microbiota during pregnancy by DiGiulio, Daniel B., Callahan, Benjamin J., McMurdie, Paul J., Costello, Elizabeth K., Lyell, Deirdre J., Robaczewska, Anna, Sun, Christine L., Goltsman, Daniela S. A., Wong, Ronald J., Shaw, Gary, Stevenson, David K., Holmes, Susan P., Relman, David A.

“…Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete…”
Get full text

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea by Bik, Elisabeth M., Costello, Elizabeth K., Switzer, Alexandra D., Callahan, Benjamin J., Holmes, Susan P., Wells, Randall S., Carlin, Kevin P., Jensen, Eric D., Venn-Watson, Stephanie, Relman, David A.

“…Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples…”
Get full text

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow by Proctor, Diana M., Fukuyama, Julia A., Loomer, Peter M., Armitage, Gary C., Lee, Stacey A., Davis, Nicole M., Ryder, Mark I., Holmes, Susan P., Relman, David A.

“…Spatial and temporal patterns in microbial communities provide insights into the forces that shape them, their functions and roles in health and disease. Here,…”
Get full text

Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis by Wilson, Jennifer G, Simpson, Laura J, Ferreira, Anne-Maud, Rustagi, Arjun, Roque, Jonasel, Asuni, Adijat, Ranganath, Thanmayi, Grant, Philip M, Subramanian, Aruna, Rosenberg-Hasson, Yael, Maecker, Holden T, Holmes, Susan P, Levitt, Joseph E, Blish, Catherine A, Rogers, Angela J

“…BACKGROUNDElevated levels of inflammatory cytokines have been associated with poor outcomes among COVID-19 patients. It is unknown, however, how these levels…”
Get full text

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota by Kashyap, Purna C., Marcobal, Angela, Ursell, Luke K., Smits, Samuel A., Sonnenburg, Erica D., Costello, Elizabeth K., Higginbottom, Steven K., Domino, Steven E., Holmes, Susan P., Relman, David A., Knight, Rob, Gordon, Jeffrey I., Sonnenburg, Justin L.

“…We investigate how host mucus glycan composition interacts with dietary carbohydrate content to influence the composition and expressed functions of a human…”
Get full text

Multitable Methods for Microbiome Data Integration by Sankaran, Kris, Holmes, Susan P.

“…The simultaneous study of multiple measurement types is a frequently encountered problem in practical data analysis. It is especially common in microbiome…”
Get full text

Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth by Costello, Elizabeth K., DiGiulio, Daniel B., Robaczewska, Anna, Symul, Laura, Wong, Ronald J., Shaw, Gary M., Stevenson, David K., Holmes, Susan P., Kwon, Douglas S., Relman, David A.

“…The vaginal ecosystem is closely tied to human health and reproductive outcomes, yet its dynamics in the wake of childbirth remain poorly characterized. Here,…”
Get full text

Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon by Sprockett, Daniel D., Martin, Melanie, Costello, Elizabeth K., Burns, Adam R., Holmes, Susan P., Gurven, Michael D., Relman, David A.

“…Selective and neutral forces shape human microbiota assembly in early life. The Tsimane are an indigenous Bolivian population with infant care-associated…”
Get full text

Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time by Hoy, Yana Emmy, Bik, Elisabeth M, Lawley, Trevor D, Holmes, Susan P, Monack, Denise M, Theriot, Julie A, Relman, David A

“…Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals…”
Get full text

Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences by Tzou, Philip L, Kosakovsky Pond, Sergei L, Avila-Rios, Santiago, Holmes, Susan P, Kantor, Rami, Shafer, Robert W

“…At low mutation-detection thresholds, next generation sequencing (NGS) for HIV-1 genotypic resistance testing is susceptible to artifactual detection of…”
Get full text

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment by Fukuyama, Julia, Rumker, Laurie, Sankaran, Kris, Jeganathan, Pratheepa, Dethlefsen, Les, Relman, David A, Holmes, Susan P

“…Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like…”
Get full text

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation by Rhee, Soo-Yon, Sankaran, Kris, Varghese, Vici, Winters, Mark A, Hurt, Christopher B, Eron, Joseph J, Parkin, Neil, Holmes, Susan P, Holodniy, Mark, Shafer, Robert W

“…HIV-1 protease (PR), reverse transcriptase (RT), and integrase (IN) variability presents a challenge to laboratories performing genotypic resistance testing…”
Get full text

Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants by Dzanibe, Sonwabile, Wilk, Aaron J., Canny, Susan, Ranganath, Thanmayi, Alinde, Berenice, Rubelt, Florian, Huang, Huang, Davis, Mark M., Holmes, Susan P., Jaspan, Heather B., Blish, Catherine A., Gray, Clive M.

“…While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared…”
Get full text

Microbial biogeography and ecology of the mouth and implications for periodontal diseases by Proctor, Diana M., Shelef, Katie M., Gonzalez, Antonio, Davis, Clara L., Dethlefsen, Les, Burns, Adam R., Loomer, Peter M., Armitage, Gary C., Ryder, Mark I., Millman, Meredith E., Knight, Rob, Holmes, Susan P., Relman, David A.

“…In humans, the composition of microbial communities differs among body sites and between habitats within a single site. Patterns of variation in the…”
Get full text