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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- E. Bolyen, J. Rideout, +109 authors J. Caporaso
- Engineering, Medicine
- Nature Biotechnology
- 1 August 2019
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and… Expand
Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis.
Bacillus anthracis is one of the most genetically homogeneous pathogens described, making strain discrimination particularly difficult. In this paper, we present a novel molecular typing system based… Expand
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. Expand
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
ABSTRACT Since its discovery in the early 2000s, methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often… Expand
Molecular Epidemiology, Evolution, and Ecology of Francisella
- P. Keim, Anders Johansson, D. Wagner
- Biology, Medicine
- Annals of the New York Academy of Sciences
- 1 June 2007
Abstract: Tularemia is a disease caused by several subspecies of Francisella tularensis, although the severity of the disease varies greatly from subspecies to subspecies. Currently, there are four… Expand
Global Genetic Population Structure of Bacillus anthracis
Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and… Expand
Universal method for producing ROX-labeled size standards suitable for automated genotyping.
- J. A. DeWoody, J. Schupp, L. Kenefic, J. Busch, L. Murfitt, P. Keim
- Biology, Medicine
- 1 September 2004
It ROX! Fluorescently labeled size standards are required for automated genotyping assays but are remarkably expensive. Recent publications for in-house production of fluorescently labeled size sta...
The Epidemic of Extended-Spectrum-β-Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx
ABSTRACT The Escherichia coli sequence type 131 (ST131) clone is notorious for extraintestinal infections, fluoroquinolone resistance, and extended-spectrum beta-lactamase (ESBL) production,… Expand
Cleavage of amyloid beta peptide during constitutive processing of its precursor.
The amyloid beta peptide (A beta P) is a small fragment of the much larger, broadly distributed amyloid precursor protein (APP). Abundant A beta P deposition in the brains of patients with… Expand
A detailed linkage map of rainbow trout produced using doubled haploids.
We report the first detailed genetic linkage map of rainbow trout (Oncorhynchus mykiss). The segregation analysis was performed using 76 doubled haploid rainbow trout produced by androgenesis from a… Expand