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Published on Dec 20, 2012in PLOS ONE2.78
Patricio S. La Rosa10
Estimated H-index: 10
(WashU: Washington University in St. Louis),
J. Paul Brooks14
Estimated H-index: 14
(VCU: Virginia Commonwealth University)
+ 6 AuthorsWilliam D. Shannon50
Estimated H-index: 50
(WashU: Washington University in St. Louis)
This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches...
Published on Sep 20, 2012in PLOS Computational Biology
Jonathan Friedman15
Estimated H-index: 15
(MIT: Massachusetts Institute of Technology),
Eric J. Alm55
Estimated H-index: 55
(MIT: Massachusetts Institute of Technology)
High-throughput sequencing based techniques, such as 16S rRNA gene profiling, have the potential to elucidate the complex inner workings of natural microbial communities - be they from the world's oceans or the human gut. A key step in exploring such data is the identification of dependencies between members of these communities, which is commonly achieved by correlation analysis. However, it has been known since the days of Karl Pearson that the analysis of the type of data generated by such te...
Published on Aug 1, 2012in Nature Methods28.47
Nicola Segata35
Estimated H-index: 35
Levi Waldron24
Estimated H-index: 24
+ 3 AuthorsCurtis Huttenhower68
Estimated H-index: 68
(Harvard University)
MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and accurate identification of microbial species and higher clades from shotgun sequencing data.
Published on Jul 12, 2012in PLOS Computational Biology
Karoline Faust19
Estimated H-index: 19
(Vrije Universiteit Brussel),
J. Fah Sathirapongsasuti6
Estimated H-index: 6
(Harvard University)
+ 4 AuthorsCurtis Huttenhower68
Estimated H-index: 68
(Broad Institute)
The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unp...
Published on Jun 14, 2012in Nature43.07
Barbara A. Methé5
Estimated H-index: 5
(JCVI: J. Craig Venter Institute),
Karen E. Nelson71
Estimated H-index: 71
(JCVI: J. Craig Venter Institute)
+ 245 AuthorsJonathan H. Badger32
Estimated H-index: 32
(JCVI: J. Craig Venter Institute)
The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.
Published on Jun 13, 2012in PLOS ONE2.78
Susan M. Huse42
Estimated H-index: 42
(MBL: Marine Biological Laboratory),
Yuzhen Ye29
Estimated H-index: 29
(IU: Indiana University Bloomington)
+ 1 AuthorsAnthony A. Fodor29
Estimated H-index: 29
(UNCC: University of North Carolina at Charlotte)
We explore the microbiota of 18 body sites in over 200 individuals using sequences amplified V1–V3 and the V3–V5 small subunit ribosomal RNA (16S) hypervariable regions as part of the NIH Common Fund Human Microbiome Project. The body sites with the greatest number of core OTUs, defined as OTUs shared amongst 95% or more of the individuals, were the oral sites (saliva, tongue, cheek, gums, and throat) followed by the nose, stool, and skin, while the vaginal sites had the fewest number of OTUs sh...
Published on Jun 13, 2012in PLOS ONE2.78
Kelvin Li24
Estimated H-index: 24
(JCVI: J. Craig Venter Institute),
Monika Bihan8
Estimated H-index: 8
(JCVI: J. Craig Venter Institute)
+ 1 AuthorsBarbara A. Methé5
Estimated H-index: 5
(JCVI: J. Craig Venter Institute)
Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the applicat...
Published on Jun 13, 2012in PLOS ONE2.78
Doyle V. Ward30
Estimated H-index: 30
(Broad Institute),
Dirk Gevers66
Estimated H-index: 66
(Broad Institute)
+ 64 AuthorsCesar Arze12
Estimated H-index: 12
(UMB: University of Maryland, Baltimore)
Published on Mar 1, 2012in Oral Diseases2.63
Maria Fernanda Zarco1
Estimated H-index: 1
(Duke University),
T Vess2
Estimated H-index: 2
(Duke University),
Geoffrey S. Ginsburg55
Estimated H-index: 55
(Duke University)
Oral Diseases (2012) 18, 109–120 Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The oral microbiome is particularly imperative to health because it can cause both oral and systemic disease. The oral microbiome rests within biofilms throughout the oral cavity, forming an ecosystem that maintains health when in equilibrium. However, certain ecological shifts in the microbiome allow pathogens to manifest and cause diseas...
Published on Feb 3, 2012in PLOS ONE2.78
Ian Holmes27
Estimated H-index: 27
(University of California, Berkeley),
Keith Harris6
Estimated H-index: 6
(Glas.: University of Glasgow),
Christopher Quince42
Estimated H-index: 42
(Glas.: University of Glasgow)
We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features. We describe each community by a vector of taxa probabilities. These ve...
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