A5020658723- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- SARS-CoV-2 and COVID-19 Research
- Gene expression and cancer classification
- SARS-CoV-2 detection and testing
- Bacteriophages and microbial interactions
- Antibiotic Resistance in Bacteria
- Gut microbiota and health
- Plant Pathogenic Bacteria Studies
- Microbial infections and disease research
- Viral gastroenteritis research and epidemiology
- Scientific Computing and Data Management
- Biosensors and Analytical Detection
- Genetics, Bioinformatics, and Biomedical Research
- Identification and Quantification in Food
- Metal Extraction and Bioleaching
- Research Data Management Practices
- Viral Infections and Vectors
- Viral Infections and Outbreaks Research
- Hepatitis B Virus Studies
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Plant-Microbe Interactions and Immunity
- Metabolomics and Mass Spectrometry Studies
Los Alamos National Laboratory
2014-2024
Bioanalytica (Switzerland)
2024
Genomics (United Kingdom)
2024
Gilead Sciences (United States)
2022
Los Alamos National Security (United States)
2017
Joint Genome Institute
2013
A major challenge in the field of shotgun metagenomics is accurate identification organisms present within a microbial community, based on classification short sequence reads. Though existing community profiling methods have attempted to rapidly classify millions reads output from modern sequencers, combination incomplete databases, similarity among otherwise divergent genomes, errors and biases sequencing technologies, large volumes data required for metagenome has led unacceptably high...
Continued advancements in sequencing technologies have fueled the development of new applications and promise to flood current databases with raw data. A number factors prevent seamless easy use these data, including breadth project goals, wide array tools that individually perform fractions any given analysis, large associated software/hardware dependencies, detailed expertise required analyses. To address issues, we developed an intuitive web-based environment a assortment integrated...
ABSTRACT The genus Burkholderia encompasses both pathogenic (including mallei and pseudomallei , U.S. Centers for Disease Control Prevention Category B listed), nonpathogenic Gram-negative bacilli. Here we present full genome sequences a panel of 59 strains, selected to aid in detection assay development.
The National Microbiome Data Collaborative (NMDC) Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed framework aligned with the FAIR (Findable, Accessible, Interoperable Reusable) principles (1). NMDC currently hosts 10.2 terabytes of data, spanning five types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, natural organic matter characterizations), generated at two Department Energy User...
Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies pathogen genome enrichment sequencing are being used by laboratories worldwide, together with different, sometimes ad hoc, analytical procedures generating sequences. fully integrated process raw sequence to consensus determination, suited outbreaks such as the ongoing COVID-19 pandemic, is critical provide a solid genomic basis epidemiological analyses...
Early and accurate diagnosis of respiratory pathogens associated outbreaks can allow for the control spread, epidemiological modeling, targeted treatment, decision making–as is evident with current COVID-19 pandemic. Many infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, delays in getting reference laboratory tests limited availability poor sensitivity point-of-care tests, most-relied upon method clinical practice today. Here, we...
Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, reuse, applications of machine learning model biological processes. To broad accessibility workflows, the National Microbiome Data Collaborative (NMDC) has developed Empowering Development Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web...
ABSTRACT Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across projects. To facilitate the construction of robust phylogenies, we developed a method identification/characterization SNPs from reads and genome...
ABSTRACT Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome assemblies for this organism are needed to aid in detection, diagnostic, treatment technologies. Here we present the improved draft assembly of A. ATCC 19606 two scaffolds. This 3,953,621-bp contains 3,750 coding regions has a 39.1% G+C content.
Genomic sequencing of clinical samples to identify emerging variants SARS-CoV-2 has been a key public health tool for curbing the spread virus. As result, an unprecedented number genomes were sequenced during COVID-19 pandemic, which allowed rapid identification genetic variants, enabling timely design and testing therapies deployment new vaccine formulations combat variants. However, despite technological advances deep sequencing, analysis raw sequence data generated globally is neither...
ABSTRACT We report the sequences of two Klebsiella pneumoniae clinical isolates, strains JHCK1 and VA360, from a newborn with meningitis in Buenos Aires, Argentina, tertiary care medical center Cleveland, OH, respectively. Both isolates contain one chromosome at least five plasmids; isolate VA360 contains carbapenemase (KPC) gene.
The genome of strain GS3372 is the first publicly available Aeribacillus pallidus. This endospore-forming thermophilic was isolated from a deep geothermal reservoir. availability this can contribute to clarification taxonomy closely related Anoxybacillus, Geobacillus, and genera.
Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming command-line interfaces. EDGE bioinformatics was developed offer scientists with little no expertise a point-and-click platform analyzing data rapid reproducible manner. (Empowering Development Genomics Expertise) v1.0 released January 2017, is an intuitive web-based engineered...
Abstract During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and support rapid experimental examination genome-informed vaccine therapeutic designs. Given broad range methods applied generate new genomes, it is critical that consensus variant calling tools yield consistent results across disparate pipelines. Here we examine impact technologies (Illumina Oxford Nanopore) 7 different downstream...
Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based will continue detect all known viral strains. To enable continuous monitoring of assays, have developed a web-based assay validation algorithm that checks against ever-expanding genome databases using both thermodynamic edit-distance metrics. The assay-screening results displayed heatmap, showing...
We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided single clonal microcolony that was sufficient to obtain 4.9-Mbp assembly an ecologically relevant species.
We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The size draft is approximately 4.6 Mb, which smallest among all P. strains sequenced to date.
Abstract Background Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis single nucleotide polymorphism discovery. Results In this study, we present ADEPT, dynamic error detection method, based on quality scores each its neighboring nucleotides, together with their positions within read compares to...
ABSTRACT Continued advancements in sequencing technologies have fueled the development of new applications and promise to flood current databases with raw data. A number factors prevent seamless easy use these data, including breadth project goals, wide array tools that individually perform fractions any given analysis, large associated software/hardware dependencies, detailed expertise required analyses. To address issues, we developed an intuitive web-based environment a assortment...
ABSTRACT Metagenomics is emerging as an important tool in biosurveillance, public health, and clinical applications. However, ease-of-use for execution data analysis remains a barrier-of-entry to the adoption of metagenomics applied health forensics settings. In addition, these venues often have more stringent requirements reporting, accuracy, precision than traditional ecological research role technology. Here, we present PanGIA ( Pan - G enomics I nfectious A gents), novel bioinformatics...