A5068732878- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- Scientific Computing and Data Management
- Gut microbiota and health
- Genetic Mapping and Diversity in Plants and Animals
- Machine Learning in Bioinformatics
- Respiratory viral infections research
- Distributed and Parallel Computing Systems
- Plant Virus Research Studies
- Genetics, Bioinformatics, and Biomedical Research
- Bacterial Identification and Susceptibility Testing
- Research Data Management Practices
- Computational Physics and Python Applications
- Environmental DNA in Biodiversity Studies
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Chromosomal and Genetic Variations
- Biomedical Text Mining and Ontologies
- Plant and Fungal Interactions Research
- Plant Disease Resistance and Genetics
- Genomics and Rare Diseases
- Wound Healing and Treatments
- Protist diversity and phylogeny
- Diabetic Foot Ulcer Assessment and Management
University of Arizona
2016-2025
University of Chicago
2017
Helmholtz Centre for Infection Research
2017
Cold Spring Harbor Laboratory
2006-2010
Zero to Three
2010
Cornell University
2007
Royal College of General Practitioners
1995
Viruses of microbes impact all ecosystems where drive key energy and substrate transformations including the oceans, humans industrial fermenters. However, despite this recognized importance, our understanding viral diversity impacts remains limited by too few model systems reference genomes. One way to fill these gaps in knowledge is through detection signal microbial genomic data. While multiple approaches have been developed applied for prophages (viral genomes integrated a genome), new...
Maize is an important crop species of high genetic diversity. We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines discovered that the genome was characterized by highly divergent haplotypes showed 10- to 30-fold variation in recombination rates. Most chromosomes have pericentromeric regions with suppressed appear influenced effectiveness selection during development may be a major component heterosis. found hundreds selective sweeps...
This paper presents standards and best practices for reporting genome sequences of uncultivated viruses. We present an extension the Minimum Information about any (x) Sequence (MIxS) standard virus genomes. Uncultivated Virus Genome (MIUViG) were developed within Genomic Standards Consortium framework include origin, quality, annotation, taxonomic classification, biogeographic distribution in silico host prediction. Community-wide adoption MIUViG standards, which complement a Single...
Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry horizontal gene transfer. While databases resources for studying function in uncultured bacterial communities relatively advanced, fewer exist viral counterparts. The issue is largely technical that the majority (often 90%) sequences functionally 'unknown' making a virtually untapped resource functional physiological information. Here, we provide community organizes this...
Rapid warming in the highly productive western Antarctic Peninsula (WAP) region of Southern Ocean has affected multiple trophic levels, yet viral influences on microbial processes and ecosystem function remain understudied Ocean. Here we use cultivation-independent quantitative ecological metagenomic assays, combined with new comparative bioinformatic techniques, to investigate double-stranded DNA viruses during WAP spring-summer transition. This study demonstrates that (i) temperate...
Abstract Background Marine ecosystem function is largely determined by matter and energy transformations mediated microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer metabolic reprogramming. Results Here we explore the nature extent of viral reprogramming throughout Pacific Ocean depth continuum. We describe 35 marine families with potential to reprogram flux central pathways recovered from waters. Four these have been...
Abstract A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks recent advances in field genomics, extensive sequencing has been performed for a deep genomic analysis this huge samples. strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics metatranscriptomics, chosen size-fractionated...
Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating mapping agriculturally important phenotypes. The first step in optimizing design studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment population structure pattern linkage disequilibrium (LD) species interest. In present study, we provide such an grapevine (genus Vitis), world's most economically fruit crop....
Summary Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration purification methods across four combinations as follows: (i) tangential flow filtration (TFF) DNase + CsCl, (ii) FeCl 3 precipitation DNase, (iii) CsCl (iv) sucrose. Taxonomic data (30% of reads) suggested that were statistically...
Gramene ( www.gramene.org ) is a curated resource for genetic, genomic and comparative genomics data the major crop species, including rice, maize, wheat many other plant (mainly grass) species. an open-source project. All software are freely downloadable through ftp site ftp.gramene.org/pub/gramene available use without restriction. Gramene's core types include genome assembly annotations, DNA/mRNA sequences, genetic physical maps/markers, genes, quantitative trait loci (QTLs), proteins,...
Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, metagenome (virome) sequencing is transforming our ability to quantify diversity impacts. Although some bottlenecks, for example, few reference genomes nonquantitative viromics, have been overcome, void of centralized data sets specialized tools now prevents viromics from being broadly applied answer fundamental ecological questions. Here we...
Significance Microorganisms and their viruses are increasingly recognized as drivers of myriad ecosystem processes. However, our knowledge roles is limited by the inability culture-dependent culture-independent (e.g., metagenomics) methods to be fully implemented at scales relevant diversity found in nature. Here we combine advances bioinformatics (shared k-mer analyses) social networking (regression modeling) develop an annotation- assembly-free visualization analytical strategy for...
Efficient response to the pandemic through mobilization of larger scientific community is challenged by limited reusability available primary genomic data. Here, Genomic Standards Consortium board highlights essential need for contextual data FAIRness, empowering key data-driven biological questions.
Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and estimation species trees. Our test data are a collection genes cultivated rice (genus Oryza) most closely related wild species, generated using high-throughput sequencing protocol bioinformatics pipeline. Trees inferred independent display levels that far...
The detailed know-how to implement research protocols frequently remains restricted the group that developed method or technology. This knowledge often exists at a level is too for inclusion in methods section of scientific articles. Consequently, are not easily reproduced, leading loss time and effort by other researchers. challenge develop method-centered collaborative platform connect with fellow researchers discover state-of-the-art knowledge. Protocols.io an open-access detailing,...
Microbiome samples are inherently defined by the environment in which they found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, critical.
As new computational tools for detecting phage in metagenomes are being rapidly developed, a critical need has emerged to develop systematic benchmarks.
We describe the establishment and analysis of a genus-wide comparative framework composed 12 bacterial artificial chromosome fingerprint end-sequenced physical maps representing 10 genome types Oryza aligned to O. sativa ssp. japonica reference sequence. Over 932 Mb end sequence was analyzed for repeats, simple miRNA single nucleotide variations, providing most extensive date.
Aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist Buchnera plus several bacteria not required for survival. Among latter, 'Candidatus Regiella insecticola' and Hamiltonella defensa' found in pea aphids other hosts have been shown to protect from natural enemies. We sequenced almost entire genome R. insecticola (2.07 Mbp) compared it with recently published H. defensa (2.11 Mbp). Despite being sister species two genomes...
Test the choice of 16S rRNA gene amplicon and data analysis method on accuracy identification clinically important bacteria utilizing a benchtop sequencer. Nine amplicons were tested an Ion Torrent PGM to identify 41 strains clinical importance. The V1–V2 region identified 40 isolates species level. Three methods tested, finding that Ribosomal Database Project's SequenceMatch outperformed BLAST Reporter Metagenomics pipeline. Lastly, sequencing mixtures four through six log range dilution...