A5013526952- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Salmonella and Campylobacter epidemiology
- Escherichia coli research studies
- Plant Pathogenic Bacteria Studies
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Vibrio bacteria research studies
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- Legume Nitrogen Fixing Symbiosis
- SARS-CoV-2 and COVID-19 Research
- Genomics and Chromatin Dynamics
- Plant-Microbe Interactions and Immunity
- Biofuel production and bioconversion
- CRISPR and Genetic Engineering
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Resistance in Staphylococcus
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
University of Arkansas for Medical Sciences
2016-2025
University of Arkansas at Fayetteville
2024
Molecular Microbiology and Genomics Consultants (Germany)
2017-2018
Kunming University of Science and Technology
2018
Siriraj Hospital
2018
Mahidol University
2018
Oak Ridge National Laboratory
2011-2017
Technical University of Denmark
2007-2016
University of Tennessee at Knoxville
2014-2015
Joint Institute for Computational Sciences
2014-2015
The publication of a complete genome sequence is usually accompanied by annotations its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA difficult. We have therefore created computational predictors the major species from all kingdoms life and compiled them into program called RNAmmer. uses hidden Markov models trained data 5S database European project. A pre-screening step...
ABSTRACT Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) considered the “gold standard” of typing, but it traditionally performed in an expensive and time-consuming manner. As costs whole-genome sequencing (WGS) continue to decline, becomes increasingly available scientists routine diagnostic laboratories. Currently, cost below that traditional MLST. The new challenges will be how extract relevant information...
The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for production of enzymes and organic acids, particularly citric acid. We sequenced 33.9-megabase genome A. CBS 513.88, ancestor currently used enzyme strains. A high level synteny was observed with other aspergilli sequenced. Strong function predictions were made 6,506 14,165 open reading frames identified. detailed description components protein secretion pathway striking differences in hydrolytic...
More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography gene expression required for infection, basic genetic information such as global locations transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques two sequencing platforms to generate robust picture S....
One of the first issues that emerges when a prokaryotic organism interest is encountered question what it is--that is, which species is. The 16S rRNA gene formed basis method for sequence-based taxonomy and has had tremendous impact on field microbiology. Nevertheless, been found to have number shortcomings. In current study, we trained benchmarked five methods whole-genome identification common data set complete genomes: (i) SpeciesFinder, based gene; (ii) Reads2Type searches...
Abstract Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct of native using Oxford Nanopore Technologies (ONT) can allow for directly detecting the base modifications, although these modifications might appear as errors. The percent Error Specific Bases (%ESB) was higher than...
A vast and rich body of information has grown up as a result the world's enthusiasm for 'omics technologies. Finding ways to describe make available this that maximise its usefulness become major effort across world. At heart is Genomic Standards Consortium (GSC), an open-membership organization drives community-based standardization activities, Here we provide short history GSC, overview range current call scientific community join forces improve quality quantity contextual about our public...
Arcobacter butzleri is a member of the epsilon subdivision Proteobacteria and close taxonomic relative established pathogens, such as Campylobacter jejuni Helicobacter pylori. Here we present complete genome sequence human clinical isolate, A. strain RM4018.Arcobacter Campylobacteraceae, but majority its proteome most similar to those Sulfuromonas denitrificans Wolinella succinogenes, both members Helicobacteraceae, deep-sea vent Epsilonproteobacteria Sulfurovum Nitratiruptor. In addition,...
Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene can be studied detail, including number mutations found for any given gene. This knowledge will useful creating better phylogenies, determination molecular clocks improved typing techniques. We find 3,051 clusters/families present at least 95% genomes 1,702 clusters 100% genomes. The former 'soft core' about 3,000 families is perhaps...
Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different levels, such as species and genera) from 32 genome sequences of vibrio species. We use variety tools explore the relationship between sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, Genome BLAST atlases. Our aim is analyse usefulness these for...
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along chromosomes and short read lengths second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism cell factory, was selected for this study to demonstrate superior capability very long sequence reads de novo genome assembly. We generated using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) Pacific Biosciences...
The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to smaller, more refined ordered list having specific properties. relationship Azotobacter vinelandii is examined using three genomic sequence-based methods. First, 16S rRNA trees, it shown that A. groups within close aeruginosa. Genomes other related organisms (Acinetobacter, Psychrobacter, Cellvibrio) are outside cluster. Second, pan genome family...