Tracy K. Teal

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Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords(More)
Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. Although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. It is commonly thought that large subpopulations of cells within biofilms are not actively(More)
We present a set of computing tools and techniques that every researcher can and should adopt. These recommendations synthesize inspiration from our own work, from the experiences of the thousands of people who have taken part in Software Carpentry and Data Carpentry workshops over the past six years, and from a variety of other guides. Unlike some other(More)
BACKGROUND The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities across individuals with and without enteric infections are useful for identifying microbes that support or impede intestinal health. RESULTS(More)
Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow includes quality control of reads, mapping to a reference, counting transcript abundance, and statistical tests for differentially expressed genes. In(More)
We developed an information retrieval and extraction system that processes the full text of biological papers. The system, called Textpresso, separates text into sentences, labels words and phrases according to an ontology (an organized lexicon), and allows queries to be performed on a database of labeled sentences. The current ontology comprises(More)
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