Personal information

Comparative genomics, metagenome

Biography


Expertise

Comparative genomics studies of human pathogens
Eukaryotic genome annotation and analysis
Experimental design and next generation sequence (NGS) analysis of for metagenomics study
Bioinformatic applications development for single genome/metagenome study

Activities

Employment (1)

Los Alamos National Laboratory: Los Alamos, NM, US

1998-03-08 to present | Scientist II (B-10: Biosecurity and Public Health)
Employment
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Los Alamos National Laboratory

Works (50 of 51)

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Page 1 of 2

Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes

BMC Research Notes
2021-12 | Journal article
Contributors: Gary Xie; Jeanne M. Fair
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Crossref

Shortest Unique Representative Hidden Markov Model (SurHMM) for Detecting Protein Toxins, Virulence Factors and Antibiotic Resistance Genes

2021-02-05 | Preprint
Contributors: Gary Xie; Jeanne M Fair
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Crossref

Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya

PLOS Neglected Tropical Diseases
2021-02-01 | Journal article
Contributors: Jessica Z. Kubicek-Sutherland; Elsio Wunder; Gary Xie; Migun Shakya; Priya K. Dighe; Lindsey L. Jacobs; Hajnalka Daligault; Karen Davenport; Loreen R. Stromberg; Zachary R. Stromberg et al.
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Crossref

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia

BMC GENOMICS
2016 | Journal article
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Los Alamos National Laboratory

Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak Differences within the High Heterogeneity Zones

GENOME BIOLOGY AND EVOLUTION
2016 | Journal article
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Los Alamos National Laboratory

Genetic diversity within the botulinum neurotoxin-producing bacteria and their neurotoxins

TOXICON
2015 | Journal article
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Los Alamos National Laboratory

Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes

INFECTION GENETICS AND EVOLUTION
2015 | Journal article
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Los Alamos National Laboratory

Contrasting elevational diversity patterns between eukaryotic soil microbes and plants

ECOLOGY
2014 | Journal article
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Los Alamos National Laboratory

Deficiency of BrpB causes major defects in cell division, stress responses and biofilm formation by Streptococcus mutans

MICROBIOLOGY-SGM
2014 | Journal article
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Los Alamos National Laboratory

From Genus to Phylum Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2014 | Journal article
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Los Alamos National Laboratory

Molecular Characterization of a Novel Botulinum Neurotoxin Type H Gene

JOURNAL OF INFECTIOUS DISEASES
2014 | Journal article
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Los Alamos National Laboratory

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

PLOS ONE
2014 | Journal article
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Los Alamos National Laboratory

Clostridium botulinum Strain Af84 Contains Three Neurotoxin Gene Clusters Bont/A2, bont/F4 and bont/F5

PLOS ONE
2013 | Journal article
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Los Alamos National Laboratory

Complete genome sequence of Arthrobacter sp strain FB24

STANDARDS IN GENOMIC SCIENCES
2013 | Journal article
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Los Alamos National Laboratory

Genetic diversity between and within botulinum neurotoxin serotypes

TOXICON
2013 | Journal article
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Los Alamos National Laboratory

Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three Aquificales lineages

FRONTIERS IN MICROBIOLOGY
2013 | Journal article
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Los Alamos National Laboratory

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2012 | Journal article
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Los Alamos National Laboratory

Capturing Single Cell Genomes of Active Polysaccharide Degraders An Unexpected Contribution of Verrucomicrobia

PLOS ONE
2012 | Journal article
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Los Alamos National Laboratory

Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide

ENVIRONMENTAL MICROBIOLOGY
2012 | Journal article
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Los Alamos National Laboratory

Genome Sequence of Kingella kingae Septic Arthritis Isolate PYKK081

JOURNAL OF BACTERIOLOGY
2012 | Journal article
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Los Alamos National Laboratory

Genomic Comparison of Escherichia coli O104 H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

PLOS ONE
2012 | Journal article
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Los Alamos National Laboratory

Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates a zone of high heterogeneity (HHZ) as a tool for epidemiological studies

CLINICAL MICROBIOLOGY AND INFECTION
2012 | Journal article
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Los Alamos National Laboratory

Saliva microbiomes distinguish caries-active from healthy human populations

ISME JOURNAL
2012 | Journal article
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Los Alamos National Laboratory

The Alternative Translational Profile That Underlies the Immune-Evasive State of Persistence in Chlamydiaceae Exploits Differential Tryptophan Contents of the Protein Repertoire

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
2012 | Journal article
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Los Alamos National Laboratory

The Redox-Sensing Regulator Rex Modulates Central Carbon Metabolism, Stress Tolerance Response and Biofilm Formation by Streptococcus mutans

PLOS ONE
2012 | Journal article
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Los Alamos National Laboratory

An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics

BMC GENOMICS
2011 | Journal article
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Los Alamos National Laboratory

Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

PLOS ONE
2011 | Journal article
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Los Alamos National Laboratory

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

STANDARDS IN GENOMIC SCIENCES
2011 | Journal article
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Los Alamos National Laboratory

GENOMICS FOR KEY PLAYERS IN THE N CYCLE FROM GUINEA PIGS TO THE NEXT FRONTIER

Methods in Enzymology
2011 | Journal article
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Los Alamos National Laboratory

Pathogen comparative genomics in the next-generation sequencing era genome alignments, pangenomics and metagenomics

BRIEFINGS IN FUNCTIONAL GENOMICS
2011 | Journal article
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Los Alamos National Laboratory

Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing

MOLECULAR ORAL MICROBIOLOGY
2010 | Journal article
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Los Alamos National Laboratory

Comparative genomics of clinical and environmental Vibrio mimicus

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2010 | Journal article
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Los Alamos National Laboratory

Dynamics of Streptococcus mutans Transcriptome in Response to Starch and Sucrose during Biofilm Development

PLOS ONE
2010 | Journal article
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Los Alamos National Laboratory

Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp tularensis A1 and Schu S4

PLOS ONE
2010 | Journal article
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Los Alamos National Laboratory

Whole Genome Sequences of Two Xylella fastidiosa Strains (M12 and M23) Causing Almond Leaf Scorch Disease in California

JOURNAL OF BACTERIOLOGY
2010 | Journal article
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Los Alamos National Laboratory

Cohesion Group Approach for Evolutionary Analysis of Aspartokinase, an Enzyme That Feeds a Branched Network of Many Biochemical Pathways

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
2009 | Journal article
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Los Alamos National Laboratory

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

GENOME RESEARCH
2009 | Journal article
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Los Alamos National Laboratory

Complete Genome Sequence of Francisella tularensis Subspecies holarctica FTNF002-00

PLoS One
2009 | Journal article
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Los Alamos National Laboratory

Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1

APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2009 | Journal article
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Los Alamos National Laboratory

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009 | Journal article
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Los Alamos National Laboratory

Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis

APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2009 | Journal article
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Los Alamos National Laboratory

Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains

BMC BIOLOGY
2009 | Journal article
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Los Alamos National Laboratory

Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2009 | Journal article
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Los Alamos National Laboratory

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

NATURE BIOTECHNOLOGY
2008 | Journal article
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Los Alamos National Laboratory

The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)

ENVIRONMENTAL MICROBIOLOGY
2008 | Journal article
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Los Alamos National Laboratory

Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains BoNT/A3, BoNT/Ba4 and BoNT/B1 Clusters Are Located within Plasmids

PLoS One
2007 | Journal article
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Los Alamos National Laboratory

Complete genome sequence of Haemophilus somnus (Histophilus somni) strain 129Pt and comparison to Haemophilus ducreyi 35000HP and Haemophilus influenzae Rd

JOURNAL OF BACTERIOLOGY
2007 | Journal article
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Los Alamos National Laboratory

Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii

APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2007 | Journal article
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Los Alamos National Laboratory

The complete genome sequence of Bacillus thuringiensis Al Hakam

JOURNAL OF BACTERIOLOGY
2007 | Journal article
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Los Alamos National Laboratory

A 360-kb interchromosomal duplication of the human HYDIN locus

GENOMICS
2006 | Journal article
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Los Alamos National Laboratory
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