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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis
A novel molecular typing system based on rapidly evolving variable-number tandem repeat (VNTR) loci is presented and six genetically distinct groups that appear to be derived from clones are identified.
Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
The results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA, which appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance.
Molecular Epidemiology, Evolution, and Ecology of Francisella
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…
RFLP analysis of soybean seed protein and oil content
- B. Diers, P. Keim, W. Fehr, R. Shoemaker
- Biology, MedicineTheoretical and Applied Genetics
- 1 March 1992
An expanded soybean RFLP map and quantitative trait loci (QTL) in soybean [Glycine max (L.) Merr.] for seed protein and oil content were presented and G. soja alleles at significant loci for protein content were associated with greater protein content than G. max alleles.
Universal method for producing ROX-labeled size standards suitable for automated genotyping.
- J. DeWoody, James A. Schupp, L. Kenefic, J. Busch, L. Murfitt, P. Keim
- 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...
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity
The phylogenetic analysis suggests that Y. pestis evolved in or near China and spread through multiple radiations to Europe, South America, Africa and Southeast Asia, leading to country-specific lineages that can be traced by lineage-specific SNPs.
Global Genetic Population Structure of Bacillus anthracis
Findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease.
Microevolution and history of the plague bacillus, Yersinia pestis.
- M. Achtman, G. Morelli, P. Keim
- BiologyProceedings of the National Academy of Sciences…
- 21 December 2004
An evolutionary tree is proposed for these populations, rooted on Yersinia pseudotuberculosis, which invokes microevolution over millennia, during which enzootic pestoides isolates evolved and led to populations that are more frequently associated with human disease.