A5091639455- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Animal Genetics and Reproduction
- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- CRISPR and Genetic Engineering
- Metabolomics and Mass Spectrometry Studies
- Health, Environment, Cognitive Aging
- Evolution and Genetic Dynamics
- DNA Repair Mechanisms
- RNA and protein synthesis mechanisms
- Mycorrhizal Fungi and Plant Interactions
- Biochemical and Structural Characterization
- COVID-19 epidemiological studies
- Occupational Health and Safety Research
- Molecular Biology Techniques and Applications
- Bacterial Genetics and Biotechnology
- Environmental DNA in Biodiversity Studies
- Job Satisfaction and Organizational Behavior
- Distributed and Parallel Computing Systems
- Plant-Microbe Interactions and Immunity
- Protist diversity and phylogeny
- Organizational Leadership and Management Strategies
Lawrence Berkeley National Laboratory
2014-2021
Joint Genome Institute
2013-2021
Oak Ridge National Laboratory
2014
Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume CPU core counts, speed scalability read-processing tools becomes ever-more important. The accuracy read merging is crucial as well, errors introduced by incorrect percolate through to reduce...
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology SARS-CoV-2 Northern from late January to mid-March 2020, using samples 36 patients spanning nine counties and Grand Princess cruise ship. Phylogenetic analyses revealed cryptic introduction at least seven different lineages into California, including epidemic WA1 strains...
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger for microbial community profiling. The transition to new technologies provided more quantitative information at expense of taxonomic resolution with implications inferring metabolic traits in various ecosystems. We applied single-molecule real-time profiling, generating full-length sequences high throughput, which we propose name PhyloTags. benchmarked and...
Abstract Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary make different predictions regarding how adaptive alleles spread through populations genetic diversity is maintained. Processes predicted by competing models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural using time-series metagenomics if approach were applied over a sufficiently long time frame. Direct observations...
The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs preprocessing, error correction, assembly, structural and functional annotation, binning.
Abstract Motivation : Metagenomic sequencing allows reconstruction of microbial genomes directly from environmental samples. Omega ( o verlap-graph me ta g enome a ssembler) was developed for assembling and scaffolding Illumina data communities. Results found overlaps between reads using prefix/suffix hash table. The overlap graph simplified by removing transitive edges trimming short branches. Unitigs were generated based on minimum cost flow analysis the then merged to contigs scaffolds...
Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range HGT polymicrobial environments is limited, as we currently rely on historical events inferred from genome sequencing studies involving cultured microorganisms. We lack approaches to observe ongoing communities. To address this knowledge gap, developed DNA sequencing-based "transductomics" approach that detects characterizes transferred via...
In previous work (D. R. Harris et al., J Bacteriol 191:5240-5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated that
Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the IR-resistant Escherichia coli populations developed date. After 100 cycles selection, dose required kill 99% four replicate (IR9-100, IR10-100, IR11-100, IR12-100) has increased from 750 Gy approximately 3,000 Gy. Fitness trade-offs, specialization, clonal...
Abstract In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases significantly associated with to either Europe (odds ratio, 6.1) or New York 32.9). Viral genomes recovered from 9 12 (75%) co-clustered lineages circulating Europe.
ABSTRACT The DOE JGI Metagenome Workflow performs metagenome data processing, including assembly, structural, functional, and taxonomic annotation, binning of metagenomic datasets that are subsequently included into the Integrated Microbial Genomes Microbiomes (IMG/M) comparative analysis system (I. Chen, K. Chu, Palaniappan, M. Pillay, A. Ratner, J. Huang, Huntemann, N. Varghese, White, R. Seshadri, et al, Nucleic Acids Rsearch, 2019) provided for download via Joint Genome Institute (JGI)...
Abstract Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency and taxonomic range HGT polymicrobial environments is limited, as we currently rely on historical events inferred from genome sequencing studies involving cultured microorganisms. We lack approaches to observe ongoing communities. To address this knowledge gap, developed DNA based “transductomics” approach that detects characterizes transferred via transduction....
In this work we describe a method to automatically detect errors in de novo assembled genomes. The extends Bayesian assembly quality evaluation framework, ALE, which computes the likelihood of an given set unassembled data. Starting from ALE output, applies outlier detection algorithms identify precise locations errors. We show results microbial genome with manually curated Our detects all deletions, 82.3% insertions, and 88.8% single base substitutions. It was also able inversion error that...
Abstract We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January 21 March 2020. From 558 persons disease 2019, 101 genomes 143 available clinical samples comprised 17 lineages, including SCC1 (n = 41), WA1 9; the first reported deaths United States, postmortem diagnosis), D614G 4), ancestral Wuhan Hu-1 21), 13 others 26). Public health...