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BACKGROUND the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are(More)
High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data,(More)
The method of exchangeable pairs has emerged as an important tool in proving limit theorems for Poisson, normal and other classical approximations. Here the method is used in a simulation context. We estimate transition probabilitites from the simulations and use these to reduce variances. Exchangeable pairs are used as control variates. Finally, a general(More)
Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete. We conducted a case-control study of 49 pregnant women, 15 of whom delivered preterm. From 40 of these women, we analyzed bacterial taxonomic composition of 3,767 specimens collected prospectively and(More)
The rich w orld of permutation tests can be supplemented by a variety of applications where only some permutations are permitted. We consider two examples: testing independence with truncated data and testing extra-sensory perception with feedback. We review relevant literature on permanents, rook polynomials and complexity. The statistical applications(More)
Truncated data plays an important role in the statistical analysis of astronomical observations as well as in survival analysis. The motivating example for this paper concerns a set of measurements on quasars in which there is double truncation. That is, the quasars are only observed if their luminosity occurs within a certain finite interval, bounded at(More)
Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with(More)
The indigenous microbiota of the nasal cavity plays important roles in human health and disease. Patterns of spatial variation in microbiota composition may help explain Staphylococcus aureus colonization and reveal interspecies and species-host interactions. To assess the biogeography of the nasal microbiota, we sampled healthy subjects, representing both(More)
We analyse the convergence to stationarity of a simple non-reversible Markov chain that serves as a model for several non-reversible Markov chain sampling methods that are used in practice. Our theoretical and numerical results show that non-reversibility can indeed lead to improvements over the diiusive behavior of simple Markov chain sampling schemes. The(More)
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and(More)