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Search: authors:"Andrey Tovchigrechko"

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Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure

curation: Meghan H. Shilts, Andrey Tovchigrechko, Chunlin Wang, Suman R. Das, Jo?rn-Hendrik Weitkamp. Formal analysis: Joann Romano-Keeler, Meghan H. Shilts, Chunlin Wang, Daniel J. Moore, Christopher ... Fonnesbeck, Shufang Meng, Suman R. Das. Funding acquisition: Joann Romano-Keeler, Jo?rn-Hendrik Weitkamp. Investigation: Joann Romano-Keeler, Jo?rn-Hendrik Weitkamp. Methodology: Joann Romano-Keeler, Andrey

Characterization of circulating RSV strains among subjects in the OUTSMART-RSV surveillance program during the 2016-17 winter viral season in the United States

Tovchigrechko, Bin Lu, Yanping Qi, Hui Liu, Hong Jin, Judith Hackett, Tonya Villafana, Mark T. Esser. Methodology: Alexey Ruzin, Jon Fryzek, Andrey Tovchigrechko, Mark T. Esser. Project administration: Alexey ... . Writing ? review & editing: Alexey Ruzin, Susan T. Pastula, Elizabeth Levin-Sparenberg, Andrey Tovchigrechko, Bin Lu, Yanping Qi, Hui Liu, Hong Jin, Li Yu, Judith Hackett, Tonya Villafana, Mark T. Esser. 13

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations

Summary: We present the first public release of our proteogenomic annotation pipeline. We have previously used our original unreleased implementation to improve the annotation of 46 diverse prokaryotic genomes by discovering novel genes, post-translational modifications and correcting the erroneous annotations by analyzing proteomic mass-spectrometry data. This public version has...

A Novel Class of Small Molecule Agonists with Preference for Human over Mouse TLR4 Activation

The best-characterized Toll-like receptor 4 (TLR4) ligands are lipopolysaccharide (LPS) and its chemically modified and detoxified variant, monophosphoryl lipid A (MPL). Although both molecules are active for human TLR4, they demonstrate a potency preference for mouse TLR4 based on data from transfected cell lines and primary cells of both species. After a high throughput...

GRAMM-X public web server for protein–protein docking

Protein docking software GRAMM-X and its web interface (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx) extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large...

Metagenomic Exploration of Viruses throughout the Indian Ocean

The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra...

RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors

The YbeB (DUF143) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea. While they have been shown to be associated with ribosomes, their molecular function remains unclear. Here we show that YbeB is a ribosomal silencing factor (RsfA) in the stationary growth phase and during the transition from rich to poor media. A knock...

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

Zeigler Allen Martin Ekman Andrew J. Lucas A ke Hagstro m Mathangi Thiagarajan Bjo rn Brindefalk Alexander R. Richter Anders F. Andersson Aaron Tenney Daniel Lundin Andrey Tovchigrechko Johan A. A. Nylander