Search Results - "HOLMES, Susan"

Ten quick tips for effective dimensionality reduction by Nguyen, Lan Huong, Holmes, Susan

“…Both a means of denoising and simplification, it can be beneficial for the majority of modern biological datasets, in which it’s not uncommon to have hundreds…”
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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…”
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phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data by McMurdie, Paul J, Holmes, Susan

“…the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology,…”
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Waste not, want not: why rarefying microbiome data is inadmissible by McMurdie, Paul J, Holmes, Susan

“…Current practice in the normalization of microbiome count data is inefficient in the statistical sense. For apparently historical reasons, the common approach…”
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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…”
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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…”
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Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle by Gorvitovskaia, Anastassia, Holmes, Susan P, Huse, Susan M

“…In a series of studies of the gut microbiome, "enterotypes" have been used to classify gut microbiome samples that cluster together in ordination analyses…”
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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…”
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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…”
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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…”
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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…”
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Frontal fibrosing alopecia: A review of 60 cases by MacDonald, Alison, MRCP, Clark, Colin, FRCP, Holmes, Susan, FRCP, MD

“…Background Frontal fibrosing alopecia (FFA) is a variant of lichen planopilaris primarily affecting postmenopausal women, with a predilection for the…”
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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…”
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Profiling the human intestinal environment under physiological conditions by Shalon, Dari, Culver, Rebecca Neal, Grembi, Jessica A., Folz, Jacob, Treit, Peter V., Shi, Handuo, Rosenberger, Florian A., Dethlefsen, Les, Meng, Xiandong, Yaffe, Eitan, Aranda-Díaz, Andrés, Geyer, Philipp E., Mueller-Reif, Johannes B., Spencer, Sean, Patterson, Andrew D., Triadafilopoulos, George, Holmes, Susan P., Mann, Matthias, Fiehn, Oliver, Relman, David A., Huang, Kerwyn Casey

“…The spatiotemporal structure of the human microbiome 1 , 2 , proteome 3 and metabolome 4 , 5 reflects and determines regional intestinal physiology and may…”
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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…”
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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…”
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A Statistical Perspective on the Challenges in Molecular Microbial Biology by Jeganathan, Pratheepa, Holmes, Susan P.

“…High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial…”
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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…”
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Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations by Nguyen, Lan Huong, Holmes, Susan

“…Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning…”
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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…”
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