A5073354692- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Plant Pathogenic Bacteria Studies
- Viral gastroenteritis research and epidemiology
- Gene expression and cancer classification
- Marine Sponges and Natural Products
- Escherichia coli research studies
- SARS-CoV-2 and COVID-19 Research
- Microbial Natural Products and Biosynthesis
- Microbial infections and disease research
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Identification and Quantification in Food
- Bacterial Genetics and Biotechnology
- Bacillus and Francisella bacterial research
- HIV Research and Treatment
- HIV/AIDS drug development and treatment
- SARS-CoV-2 detection and testing
- Yersinia bacterium, plague, ectoparasites research
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- COVID-19 diagnosis using AI
- Epigenetics and DNA Methylation
Los Alamos National Laboratory
2015-2024
United States Department of Energy
2013-2023
Joint Genome Institute
2010-2017
Bioscience (Slovakia)
2017
Los Alamos National Security (United States)
2017
United States Army Medical Research Institute of Infectious Diseases
2014
KBase
2013
We used ultra-deep sequencing to obtain tens of thousands HIV-1 sequences from regions targeted by CD8+ T lymphocytes longitudinal samples three acutely infected subjects, and modeled viral evolution during the critical first weeks infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because limited sampling; now, we have greatly increased our confidence in this observation through modeling observed earliest sample...
Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and great interest in diverse biotechnological applications, such as biofuel production bioremediation. Here we demonstrate the use a new, efficient approach recover genomes active polysaccharide degraders from natural, complex microbial assemblages, using combination fluorescently labeled substrates, fluorescence-activated cell sorting, single genomics. We employed this analyze freshwater coastal bacterioplankton...
We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with sample compartmentalization and dispersion-free transport is inherent to droplets. The allows for execution user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging sequences picoliter-volume droplets containing reagents or cells. This functionality enabled...
Next generation sequencing (NGS) technologies that parallelize the process and produce thousands to millions, or even hundreds of millions sequences in a single run, have revolutionized genomic genetic research. Because vagaries any platform’s chemistry, experimental processing, machine failure, so on, quality reads is never perfect, often declines as read extended. These errors invariably affect downstream analysis/application should therefore be identified early on mitigate unforeseen...
High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region of env in samples collected from 4 chronically HIV-infected subjects whom CCR5 antagonist (vicriviroc [VVC]) therapy failed. Between 25,000–140,000 amplified sequences were obtained per sample. Profound baseline loop sequence heterogeneity existed; predicted CXCR4-using populations identified a...
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...
In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused large outbreak bloody diarrhea in Europe which was notable for its high prevalence hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies strains associated with collection historical E. isolates using draft genome assemblies. We present complete, closed sequences isolate from 2011 (2011C-3493) two cases occurred...
Abstract There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate construction standardized and robust for disparate types projects, we have developed a complete bioinformatic workflow, with web-based component to perform phylogenetic molecular evolutionary (PhaME) analysis reads, draft assemblies completed genomes closely Furthermore, ability incorporate raw...
The assembly of high-quality genomes from mixed microbial samples is a long-standing challenge in genomics and metagenomics. Here, we describe the application ProxiMeta, Hi-C-based metagenomic deconvolution method, to deconvolve human fecal metagenome. This method uses intra-cellular proximity signal captured by Hi-C as direct indicator which sequences originated same cell, enabling culture-free de novo without any reliance on priori information. We show that ProxiMeta provides results...
Summary Human dental plaque is a complex microbial community containing an estimated 700 to 19,000 species/phylotypes. Despite numerous studies analysing species richness in healthy and diseased human subjects, the true genomic composition of microbiota remains unknown. Here we report metagenomic analysis sample using combination second‐generation sequencing platforms. A total 860 million base pairs non‐human sequences were generated. Various tools revealed presence 12 well‐characterized...
Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is fact that not all microorganisms are equally well detected, questioning universality this approach. Firmicutes known to be a dominant bacterial group. Several species endospore formers and property makes them hardy in potentially harsh conditions, thus likely present wide variety environments, even as residents functional players. While libraries can...
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability culture most microorganisms in isolation, which a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers circumvent this limitation. DNA amplified directly from single cell using the whole-genome amplification technique multiple displacement (MDA). However, MDA chromosome copy suffers bias and large loss specificity even very small amounts...
ABSTRACT In 2011, the Association of Analytical Communities (AOAC) International released a list Bacillus strains relevant to biothreat molecular detection assays. We present complete and annotated genome assemblies for 15 listed on inclusivity panel, as well 20 exclusivity panel.
Nitrification is a critical process for preventing ammonia toxicity in engineered biofilter environments. This work describes the cultivation and complete genome sequence of novel AOA representative enriched from freshwater aquarium biofilter. In addition, despite common belief industry that AOB mediate oxidation, present study suggests an situ role “ Ca . Nitrosotenuis aquarius”-like biofilters.
Robust growth of the gammaproteobacterium Methylomicrobium buryatense strain 5G on methane makes it an attractive system for CH4-based biocatalysis. Here we present a draft genome sequence that will provide valuable framework metabolic engineering core pathways production chemicals from methane.
Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced genomes that differ greatly in nucleotide compositional biases and abundance. To these we have developed post-assembly process: MetaGenomic by Merging (MeGAMerge). We compare this process the performance several assemblers, using both real, in-silico generated different composition...
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...