A5054369332- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Chromosomal and Genetic Variations
- SARS-CoV-2 detection and testing
- RNA and protein synthesis mechanisms
- Bacterial Identification and Susceptibility Testing
- SARS-CoV-2 and COVID-19 Research
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Probiotics and Fermented Foods
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Antibiotic Resistance in Bacteria
- Antimicrobial Resistance in Staphylococcus
- Algorithms and Data Compression
- Clostridium difficile and Clostridium perfringens research
- Advanced biosensing and bioanalysis techniques
- Cell Image Analysis Techniques
- Diet and metabolism studies
- Bacillus and Francisella bacterial research
- Traumatic Brain Injury Research
- Genomics and Rare Diseases
- Biosensors and Analytical Detection
Rice University
2018-2025
University of Maryland, College Park
2011-2024
University of California System
2024
University of Houston
2020
Johns Hopkins University
2011-2014
Johns Hopkins Medicine
2011-2014
Battelle
2013
J. Craig Venter Institute
2011
Centre National de la Recherche Scientifique
2009-2011
Institut Pasteur
2008-2011
Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling efficient clustering search of massive sequence collections. reduces large sequences sets small, representative sketches, from which global distances can be rapidly estimated. We demonstrate several use cases, including all 54,118 NCBI RefSeq genomes in 33 CPU h; real-time database using assembled or unassembled Illumina, Pacific Biosciences, Oxford...
Abstract Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods limited in their ability to perform sequence comparisons of multiple simultaneously. Here we present the Harvest suite core-genome visualization tools rapid simultaneous analysis thousands intraspecific strains. includes Parsnp, a fast multi-aligner, Gingr, dynamic visual platform. Together they provide interactive alignments, variant calls, recombination...
New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects decode genomes previously unsequenced organisms. The lowest-cost can generate deep coverage most species, including mammals, in just a few days. sequence data generated by one these consist millions or billions short DNA sequences (reads) that range from 50 150 nt length. These must then be assembled de novo before genome analyses begin....
Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as main source adaptive functional novelty in eukaryotes. While there ample evidence gene prokaryotes, it not clear whether outweighs contribution horizontal transfer expansion families. We analyzed closely related prokaryote strains species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized (Bacillus, Enterobacteriaceae), large...
The oral microbiome, the complex ecosystem of microbes inhabiting human mouth, harbors several thousands bacterial types. proliferation pathogenic bacteria within mouth gives rise to periodontitis, an inflammatory disease known also constitute a risk factor for cardiovascular disease. While much is about individual species associated with pathogenesis, system-level mechanisms underlying transition from health are still poorly understood. Through sequencing 16S rRNA gene and whole community...
Abstract We describe MetAMOS, an open source and modular metagenomic assembly analysis pipeline. MetAMOS represents important step towards fully automated analysis, starting with next-generation sequencing reads producing genomic scaffolds, open-reading frames taxonomic or functional annotations. can aid in reducing errors, commonly encountered when assembling samples, improves assignment accuracy while also computational cost. be downloaded from: https://github.com/treangen/MetAMOS .
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology implicates airborne transmission; aerosol infectiousness and impacts of masks variants on shedding are not well understood.
Abstract A Modular Open‐Source Assembler (AMOS) was designed to offer a modular approach genome assembly. AMOS includes wide range of tools for assembly, including the lightweight de novo assemblers Minimus and Minimo, Bambus 2, robust scaffolder able handle metagenomic polymorphic data. This protocol describes how configure use assembly Next Generation sequence Additionally, we provide three tutorial examples that include bacterial, viral, datasets with specific tips improving quality....
Abstract Background A major goal of metagenomics is to characterize the microbial composition an environment. The most popular approach relies on 16S rRNA sequencing, however this can generate biased estimates due differences in copy number gene between even closely related organisms, and PCR artifacts. taxonomic also be determined from metagenomic shotgun sequencing data by matching individual reads against a database reference sequences. One limitation prior computational methods used for...
The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another assembly, CR_1.0, also available but substantially more fragmented than rheMac2 with smaller contigs scaffolds. Annotations these two assemblies are limited in completeness accuracy. High quality files required wide...
Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds known and unknown species, contain multiple strain variants vary greatly within across environments. Many microbes found in microbial communities not easily grown culture making their DNA sequence our only clue into evolutionary history biological function. assembly is a computational process aimed reconstructing genes genomes from metagenomic mixtures. Current methods have made significant strides...
The secondary injury cascade that is activated following traumatic brain (TBI) induces responses from multiple physiological systems, including the immune system. These are not limited to area of injury; they can also alter peripheral organs such as intestinal tract. Gut microbiota play a role in regulation cell populations and microglia activation, microbiome dysbiosis implicated dysregulation behavioral abnormalities. However, changes gut induced after acute TBI remains largely unexplored....
Abstract Motivation: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data clonal organisms are, however, unable adequately process derived Results: We present a new scaffolder, Bambus 2, address some challenges encountered when metagenomes. Our approach relies on combination novel method...
ABSTRACT Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P -value significance test, enabling efficient clustering search of massive sequence collections. reduces large sequences sets small, representative sketches, from which global distances can be rapidly estimated. We demonstrate several use cases, including all 54,118 NCBI RefSeq genomes in 33 CPU hours; real-time database using assembled or unassembled Illumina, Pacific...
Highlights•In silico predictions of miR-2392 as a miRNA involved with SARS-CoV-2•Overexpression produces similar biological response COVID-19 infection•miR-2392 is confirmed to circulate in serum and urine patients COVID-19•Development initiated potential antiviral therapeutic against COVID-19SummaryMicroRNAs (miRNAs) are small non-coding RNAs post-transcriptional gene regulation that have major impact on many diseases provide an exciting avenue toward therapeutics. From patient...
Most genome editing analyses to date are based on quantifying small insertions and deletions. Here, we show that CRISPR-Cas9 can induce large gene modifications, such as deletions, insertions, complex local rearrangements in different primary cells cell lines. We analyzed deletion events hematopoietic stem progenitor (HSPCs) using methods, including clonal genotyping, droplet digital polymerase chain reaction, single-molecule real-time sequencing with unique molecular identifier,...