A5067783602- Genomics and Phylogenetic Studies
- Nuclear physics research studies
- Microbial Community Ecology and Physiology
- Astronomical and nuclear sciences
- Advanced Fiber Laser Technologies
- Atomic and Subatomic Physics Research
- Photonic and Optical Devices
- Analytical Chemistry and Sensors
- Gut microbiota and health
- Atomic and Molecular Physics
- Quantum Chromodynamics and Particle Interactions
- Cold Atom Physics and Bose-Einstein Condensates
- Advanced Frequency and Time Standards
- Sensor Technology and Measurement Systems
- Scientific Measurement and Uncertainty Evaluation
- Nuclear Physics and Applications
- Arsenic contamination and mitigation
- Machine Learning in Bioinformatics
- Particle physics theoretical and experimental studies
- Gene expression and cancer classification
- Mass Spectrometry Techniques and Applications
- Environmental DNA in Biodiversity Studies
- Laser-Matter Interactions and Applications
- Helicobacter pylori-related gastroenterology studies
- Plant Pathogenic Bacteria Studies
University of Chicago
2012-2021
Argonne National Laboratory
2007-2021
Texas A&M University
2010
University of Maryland, College Park
2010
Yale University
2010
University of Manitoba
2010
McGill University
2010
University of Washington
2005
University of Central Florida
1998-2002
MG-RAST (http://metagenomics.anl.gov) is an open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200 000 datasets continuously updated. volume of submissions has increased 4-fold the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes analysis workflow technologies used scale pipeline up required throughput levels. To show possible uses from MG-RAST,...
The most feared complication following intestinal resection is anastomotic leakage. In high risk areas (esophagus/rectum) where neoadjuvant chemoradiation used, the incidence of leaks remains unacceptably (≈ 10%) even when performed by specialist surgeons in volume centers. aims this study were to test hypothesis that leakage develops pathogens colonizing sites become vivo transformed express a tissue destroying phenotype. We developed novel model leak which rats exposed pre-operative...
Abstract As technologies change, MG-RAST is adapting. Newly available software being included to improve accuracy and performance. a computational service constantly running large volume scientific workflows, the right location perform benchmarking implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity run-time cost. The work [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1–3] an example; we use existing well-studied data...
We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess quality (alternatively referred as "noise" or "error") within and/or between samples. provides positional estimates that can be used inform trimming sample. It also global (whole sample) identify samples with high varying levels of may confound downstream analyses, particularly in the case studies utilize data from multiple For shotgun metagenomic data, we believe are more accurate and less...
We reconstructed the complete 2.4 Mb-long genome of a previously uncultivated epsilonproteobacterium, Candidatus Sulfuricurvum sp. RIFRC-1, via assembly short-read shotgun metagenomic data using complexity reduction approach. Genome-based comparisons indicate bacterium is novel species within genus, which contains one cultivated representative, S. kujiense. Divergence between appears due in part to extensive genomic rearrangements, gene loss and chromosomal versus plasmid encoding certain...
Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. is a ubiquitous step in analysis pipelines; it reduces the volume of data by identifying most likely reading frame fragment, permitting out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms—FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal—for accuracy on short (75–1000 bp) fragments containing...
Mass measurements of 68Ge, 68As, and 68Se have been obtained with the Canadian Penning Trap mass spectrometer. The results determine excess as -54 232(19) keV, first measurement a precision reliability sufficient to address light-curve energy output x-ray bursts well abundances elements synthesized. Under typical conditions used for modeling bursts, is found cause significant delay in rp process nucleosynthesis.
A bstract Background The numerous classes of repeats often impede the assembly genome sequences from short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain repeat structure total size bacterial or archaeal without need for directly analyzing abundances distinct k -mers among reads. Results sensitivity this procedure resolve variation within species is demonstrated: sizes five environmental strains E. coli Illumina were estimated method,...
The Canadian Penning Trap mass spectrometer has been used to determine the excesses of $^{64}\mathrm{Ge}$ and $^{64}\mathrm{Ga}$ as \ensuremath{-}54344(30) keV \ensuremath{-}58832.5(39) keV, respectively. Under typical conditions for modeling x-ray bursts, is confirmed a waiting-point nuclide can contribute up 35.5 s timescale $\mathit{rp}$ process at peak burst temperature 1.5 GK.
ABSTRACT Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity dynamics ecologically structured host populations the wild remain poorly understood. Here, we show that natural of marine Vibrionaceae bacteria large numbers families episomes, consisting a surprisingly high fraction plasmid-like temperate phages. Episomes unevenly distributed populations, contrary to notion high-density communities biofilms act hot spots...
We present the genomic sequence of human pathogen Legionella pneumophila serogroup 12 strain 570-CO-H (ATCC 43290), a clinical isolate from Colorado Department Health, Denver, CO. This is first example genome L. other than 1. highlight similarities and differences relative to six sequences that have been reported for 1 strains.
ABSTRACT Alcaligenes faecalis subsp. NCIB 8687, the betaproteobacterium from which arsenite oxidase had its structure solved and first “arsenate gene island” identified, provided a draft genome of 3.9 Mb in 186 contigs (with largest 15 comprising 90% total) for this opportunistic pathogen species.
The masses of the radioactive nuclei and have been measured with Canadian Penning trap on-line mass spectrometer to a precision , respectively. A value for superallowed decay is obtained from difference these two masses. With this precise value, determined improved found be consistent existing data set Fermi emitters. This provides an important test isospin symmetry-breaking corrections. If here used in calibration recent measurement, part discrepancy observed that measurement removed.
We demonstrate a technique for transferring ${}^{226}$Ra atoms from three-dimensional magneto-optical trap (MOT) into standing wave optical dipole (ODT) in an adjacent chamber. The resulting small trapping volume (120 $\ensuremath{\mu}$m diameter) allows high control of the electric and magnetic fields applied to atoms. are first transferred traveling-wave trap, which is then translated 46 cm science subsequently orthogonal standing-wave ODT by application one-dimensional MOT along axis. For...
Halomonas strain GFAJ-1 was reported in Science magazine to be a remarkable microbe for which there "arsenate macromolecules that normally contain phosphate, most notably nucleic acids." The draft genome of the bacterium determined (NCBI accession numbers AHBC01000001 through AHBC01000103). It appears typical gamma proteobacterium.
Abstract Background The MG-RAST API provides search capabilities and delivers organism function data as well raw or annotated sequence via the web interface its RESTful API. For casual users, however, APIs are hard to learn work with. Results We created graphical explorer help researchers more easily build export queries; understand abstractions indices available in MG-RAST; use results presented in-browser for exploration, development, debugging. Conclusions lowers barrier entry occasional...
Summary A novel type of Baeyer–Villiger monooxygenase (BVMO) has been found in a marine strain Stenotrophomonas maltophila PML168 that was isolated from temperate intertidal zone. The enzyme is able to use NADH as the source reducing power necessary accept atom diatomic oxygen not incorporated into oxyfunctionalized substrate. Growth studies have establish inducible, appears serve catabolic role, and specifically induced by one or more unidentified components seawater well various...