A5086477052- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Listeria monocytogenes in Food Safety
- Microbial Inactivation Methods
- Salmonella and Campylobacter epidemiology
- Biochemical and Structural Characterization
- Molecular Biology Techniques and Applications
- Malaria Research and Control
- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
- CRISPR and Genetic Engineering
- Antibiotic Resistance in Bacteria
- Advanced biosensing and bioanalysis techniques
- Bacterial Identification and Susceptibility Testing
- RNA and protein synthesis mechanisms
- Plant Disease Resistance and Genetics
- vaccines and immunoinformatics approaches
- HIV/AIDS drug development and treatment
Oak Ridge Institute for Science and Education
2022
Oak Ridge Associated Universities
2022
University of Georgia
2016-2021
Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in getting the smallest possible amount of data from a run); (3) sample preparation. Reducing preparation costs is commonly addressed, are rarely addressed. We present dual-indexing systems to address all three these issues. By breaking library construction process into universal, re-usable, combinatorial components, we...
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions the from many individuals (e.g., RADseq, GBS). However, researchers often find existing methods expensive initiate and/or difficult implement consistently, especially because it is multiplex sufficient numbers samples fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for construction dual-digest RADseq...
Next-generation sequencing (NGS) of amplicons is used in a wide variety contexts. In many cases, NGS amplicon remains overly expensive and inflexible, with library preparation strategies relying upon the fusion locus-specific primers to full-length adapter sequences single identifying sequence or ligating adapters onto PCR products. Adapterama I, we presented universal stubs produce thousands unique index combinations modifiable system for incorporating them into Illumina libraries. Here,...
Abstract Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing for the first time); 2) buy-in getting smallest possible amount of data from a run); and 3) sample preparation. Reducing preparation is commonly addressed, are rarely addressed. We present dual-indexing systems to address all three these issues. By breaking library construction process into universal, re-usable, combinatorial components, we...
Crocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, gene regulation in the clade, we generated a high-quality de novo assembly of saltwater crocodile, Crocodylus porosus, from Illumina short read data genomic libraries vitro proximity-ligation libraries. The assembled is 2,123.5 Mb, with N50 scaffold size 17.7 Mb N90 3.8 Mb. We then annotated this new assembly, increasing number genes by 74%. In...
The western mosquitofish,
Abstract Next-generation sequencing (NGS) of amplicons is used in a wide variety contexts. Most NGS amplicon remains overly expensive and inflexible, with library preparation strategies relying upon the fusion locus-specific primers to full-length adapter sequences single identifying sequence or ligating adapters onto PCR products. In Adapterama I , we presented universal stubs produce thousands unique index combinations modifiable system for incorporating them into Illumina libraries. Here,...
The song sparrow,
Abstract Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions the from many individuals (e.g., RADseq, GBS). However, researchers often find existing methods expensive initiate and/or difficult implement consistently, especially due inability highly-multiplex samples fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for construction dual-digest RADseq...
A reliable and standardized classification of Listeria monocytogenes is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS)-based approaches characterization are either difficult to standardize, rendering them less suitable data exchange, or not freely available. Thus, we developed a portable open-source tool, Haplo-ST, improve standardization provide maximum discriminatory potential WGS tied multilocus sequence typing (MLST)...
Abstract The song sparrow, Melospiza melodia , is one of the most widely distributed species songbirds found in North America. It has been used a wide range behavioral and ecological studies. This species’ pronounced morphological diversity across populations makes it favorable candidate several areas biomedical research. We have generated high-quality de novo genome assembly M. using Illumina short read sequences from genomic vitro proximity-ligation libraries. assembled 978.3 Mb, with...
Sequencing large numbers of individual samples is often needed for countrywide antimalarial drug resistance surveillance. Pooling DNA from several an alternative cost and time saving approach providing allele frequency (AF) estimates at a population level. Using 100 patient dried blood spots 2017 nationwide surveillance study in Haiti, we compared codon coverage resistance-conferring mutations four Plasmodium falciparum genes ( crt , dhps dhfr mdr1 ), the same deep sequenced run individually...
Abstract Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, gene regulation in the clade, we generated a high-quality de novo assembly of saltwater crocodile, Crocodylus porosus , from Illumina short read data genomic libraries vitro proximity-ligation libraries. The assembled is 2,123.5 Mb, with N50 scaffold size 17.7 Mb N90 3.8 Mb. We then annotated this new assembly, increasing number genes...
We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical temporal origins. The subtyping data was used characterizing genetic variation evaluating patterns linkage disequilibrium the pan-genome L . Our analysis revealed presence strong , with ~99% showing significant non-random associations majority other genome. Twenty-seven loci lower levels association were considered to be...
ABSTRACT A reliable and standardized classification of Listeria monocytogenes ( Lm ) is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS) based approaches characterization either lack standardization, rendering them less suitable data exchange, or are not freely available. Thus, we developed a portable open-source tool Haplo-ST to improve standardization provide maximum discriminatory potential WGS tied an MLST (multi locus...
Abstract We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical temporal origins. The subtyping data was used characterizing genetic variation evaluating patterns linkage disequilibrium the pan-genome L. . Our analysis revealed presence strong , with ∼99% showing significant non-random associations majority other genome. Twenty-seven loci lower levels association were considered...