Bioinformatics Commons^™

Draft Genome Sequence Of Enterobacter Asburiae Ufmg-H9, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Enterobacter asburiae is part of the Enterobacter cloacae complex, related to nosocomial opportunistic infections in humans. Here, we report the draft genome of E. asburiae strain UFMG-H9, an isolate from urine from a healthy Gyr heifer.

Draft Genome Sequence Of Clinical Isolate Alcaligenaceae Sp. Strain 429, Catherine Putonti, Michael Zilliox, Paul Schreckenberger

Bioinformatics Faculty Publications

Here, we present the 3.53-Mb genome for Alcaligenaceae sp. strain 429, isolated from a patient with unknown etiology. While the 16S rRNA gene most closely resembles Paenalcaligenes species, average amino acid identity (AAI) analysis did not meet the threshold to classify our strain as a species of this family.

Draft Genome Sequence Of The Siderophore-Degrading Soil Bacterium Mesorhizobium Loti Strain Lu, Domenic Castignetti, Nathaniel Polley, Catherine Putonti

Bioinformatics Faculty Publications

Here, we present the draft genome of Mesorhizobium loti strain LU, a soil bacterium capable of degrading the trihydroxamate siderophore deferrioxamine B to its constituent monohydroxamic acids. Genome size was 6,399,828 bp, with a GC content of 61.5%. This draft genome consists of 35 scaffolds, with an N50 of 389,921 bp.

Pharmacogenetic Discovery In Calgb (Alliance) 90401 And Mechanistic Validation Of A Vac14 Polymorphism That Increases Risk Of Docetaxel-Induced Neuropathy, Heather E. Wheeler

Bioinformatics Faculty Publications

Purpose: Discovery of SNPs that predict a patient's risk of docetaxel-induced neuropathy would enable treatment individualization to maximize efficacy and avoid unnecessary toxicity. The objectives of this analysis were to discover SNPs associated with docetaxel-induced neuropathy and mechanistically validate these associations in preclinical models of drug-induced neuropathy.

Experimental Design: A genome-wide association study was conducted in metastatic castrate-resistant prostate cancer patients treated with docetaxel, prednisone and randomized to bevacizumab or placebo on CALGB 90401. SNPs were genotyped on the Illumina HumanHap610-Quad platform followed by rigorous quality control. The inference was conducted on the cumulative dose at occurrence of grade 3+ …

Cbdb: The Codon Bias Database, Adam Hilterbrand, Joseph Saelens, Catherine Putonti

Bioinformatics Faculty Publications

Background

In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their viral pathogens have been observed for a myriad of host-virus systems. As such, numerous studies have investigated codon usage and codon bias in an effort to better understand how species evolve. Numerous metrics have been developed to identify biases in codon usage. In addition, a few data repositories of codon bias data are available, …