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line built using the PyCogent toolkit6, to address the problem of taking sequencing data from raw sequences to interpretation and database deposition. QIIME, available at http://qiime.sourceforge. net/, supports a wide range of microbial community analyses and visualizations that have been central to several recent high-profile studies, including network(More)
Do bacterial taxa demonstrate clear endemism, like macroorganisms, or can one site's bacterial community recapture the total phylogenetic diversity of the world's oceans? Here we compare a deep bacterial community characterization from one site in the English Channel (L4-DeepSeq) with 356 datasets from the International Census of Marine Microbes (ICoMM)(More)
BACKGROUND As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the(More)
Large-scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of "Western diseases" may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial(More)
MOTIVATION Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies. RESULTS TopiaryExplorer supports the visualization of very large phylogenetic trees, including(More)
Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic(More)
The ability to construct domain specific knowledge graphs (KG) and perform question-answering or hypothesis generation is a transformative capability. Despite their value, automated construction of knowledge graphs remains an expensive technical challenge that is beyond the reach for most enterprises and academic institutions. We propose an end-toend(More)
Social media can provide a resource for characterizing communities and small populations through activities and content shared online. For instance, studying the language use in social media within military populations may provide insights into their health and well-being. In this paper, we address three research questions: (1) How do military populations(More)
Summary FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable(More)
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