Jeremy Widmann

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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)
By combining crystallographic and NMR structural data for RNA-bound amino acids within riboswitches, aptamers, and RNPs, chemical principles governing specific RNA interaction with amino acids can be deduced. Such principles, which we summarize in a “polar profile”, are useful in explaining newly selected specific RNA binding sites for free amino acids(More)
We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with(More)
Seven new arginine binding motifs have been selected from a heterogeneous RNA pool containing 17, 25, and 50mer randomized tracts, yielding 131 independently derived binding sites that are multiply isolated. The shortest 17mer random region is sufficient to build varied arginine binding sites using five different conserved motifs (motifs 1a, 1b, 1c, 2, and(More)
Many studies have suggested that the modern cloverleaf structure of tRNA may have arisen through duplication of a primordial hairpin, but the timing of this duplication event has been unclear. Here we measure the level of sequence identity between the two halves of each of a large sample of tRNAs and compare this level to that of chimeric tRNAs constructed(More)
tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life(More)
SUMMARY The explosion of interest in non-coding RNAs, together with improvements in RNA X-ray crystallography, has led to a rapid increase in RNA structures at atomic resolution from 847 in 2005 to 1900 in 2010. The success of whole-genome sequencing has led to an explosive growth of unaligned homologous sequences. Consequently, there is a compelling and(More)
The fine structural characteristics and phagocytic properties of peroxidase-positive and peroxidase-negative cells in rat hepatic sinusoids were investigated. Cells with a positive peroxidase reaction in the endoplasmic reticulum and the nuclear envelope make up approximately 40% of cells in rat hepatic sinusoids and have abundant cytoplasm containing(More)
Reported here is a case of hereditary myeloperoxidase deficinecy in a diabetic patient suffering from a Candida albicans liver abscess. Peroxidase activity is completely absent from the neutrophils and monocytes although it is present in the eosinophils. The different forms of myeloperoxidase deficiency are discussed.