Derrick E Fouts

Summary

Affiliation: J. Craig Venter Institute
Country: USA

Publications

  1. pmc Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD, USA
    Virol J 10:165. 2013
  2. pmc PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
    Derrick E Fouts
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 40:e172. 2012
  3. pmc Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen
    Derrick E Fouts
    The J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS ONE 7:e48289. 2012
  4. pmc Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD 20850, USA
    J Transl Med 10:174. 2012
  5. pmc Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
    Derrick E Fouts
    J Craig Venter Institute, Rockville, Maryland, USA
    PLoS Genet 4:e1000141. 2008
  6. pmc Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 189:52-64. 2007
  7. pmc Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
  8. pmc Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
    Derrick E Fouts
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 3:e15. 2005
  9. pmc Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain
    Steven R Gill
    Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:2426-38. 2005
  10. ncbi request reprint Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004

Detail Information

Publications25

  1. pmc Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD, USA
    Virol J 10:165. 2013
    ..We aimed at a complete molecular characterization of both phages and elucidation of their genetic and structural differences and assessment of their genetic relatedness to the N4-like phage group...
  2. pmc PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
    Derrick E Fouts
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 40:e172. 2012
    ..The clusters that did not agree were inspected for evidence of correctness resulting in 85 high-confidence manually curated clusters that were used to compare all four methods...
  3. pmc Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen
    Derrick E Fouts
    The J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS ONE 7:e48289. 2012
    ....
  4. pmc Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD 20850, USA
    J Transl Med 10:174. 2012
    ....
  5. pmc Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
    Derrick E Fouts
    J Craig Venter Institute, Rockville, Maryland, USA
    PLoS Genet 4:e1000141. 2008
    ....
  6. pmc Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 189:52-64. 2007
    ..This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species...
  7. pmc Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
    ..Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs...
  8. pmc Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
    Derrick E Fouts
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 3:e15. 2005
    ....
  9. pmc Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain
    Steven R Gill
    Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:2426-38. 2005
    ..Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis...
  10. ncbi request reprint Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  11. pmc Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:5646-51. 2004
    ....
  12. pmc Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus
    Robert T Deboy
    J Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 190:5455-63. 2008
    ..Approximately 50% of the predicted C. japonicus plant-degradative apparatus appears to be shared with S. degradans, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms...
  13. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
    ..gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease...
  14. pmc Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences
    Derrick E Fouts
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 34:5839-51. 2006
    ..This method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes...
  15. doi request reprint Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche
    Janaki Purushe
    Department of Human Genomic Medicine, The J Craig Venter Institute JCVI, Rockville, MD 20850, USA
    Microb Ecol 60:721-9. 2010
    ..Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species...
  16. ncbi request reprint Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
    Rekha Seshadri
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:105-8. 2005
    ..Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph...
  17. ncbi request reprint The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
    ..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis...
  18. pmc Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry
    Derrick E Fouts
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 188:3402-8. 2006
    ..The genomes of these two phages were identical except at three variable loci, which showed heterogeneity within individual lysates and among Cherry, Wbeta, Fah, and four Gamma bacteriophage sequences...
  19. pmc The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:977-88. 2004
    ..The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk...
  20. pmc Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence
    Yuansha Chen
    The J Craig Venter Institute, Rockville, MD, USA
    BMC Genomics 12:294. 2011
    ..The sixth pandemic strain sequenced in this study was serotype O4:K68...
  21. pmc Sequencing viral genomes from a single isolated plaque
    Jessica Depew
    Department of Genomic Medicine, The J Craig Venter Institute JCVI, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Virol J 10:181. 2013
    ..This method can be used for de novo whole genome next-generation sequencing of any cultivable virus without the need for large-scale production of viral stocks or viral purification using centrifugal techniques...
  22. pmc Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD, USA
    J Hepatol 56:1283-92. 2012
    ..The aims of our study were to investigate dynamics of bacterial translocation and changes in the enteric microbiome in early stages of liver disease...
  23. ncbi request reprint A pseudomonas syringae pv. tomato DC3000 Hrp (Type III secretion) deletion mutant expressing the Hrp system of bean pathogen P. syringae pv. syringae 61 retains normal host specificity for tomato
    Derrick E Fouts
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Mol Plant Microbe Interact 16:43-52. 2003
    ..These observations support the concept that the P. syringae effector proteins, rather than secretion system components, are the primary determinants of host range at both the species and cultivar levels of host specificity...
  24. pmc Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor
    Derrick E Fouts
    Department of Plant Pathology, Cornell University, Ithaca, NY 14853 4203, USA
    Proc Natl Acad Sci U S A 99:2275-80. 2002
    ..Additional candidate effector genes, hopPtoA2, hopPtoB2, and an avrRps4 homolog, were preceded by Hrp promoter-like sequences, but these had HMM expectation values of relatively low significance and were not detectably activated by HrpL...
  25. pmc The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages
    Shanmuga Sozhamannan
    Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
    BMC Microbiol 6:34. 2006
    ..The B. anthracis genome sequence contains four putative lambdoid prophages. We undertook this study in order to understand whether the four prophages are unique to B. anthracis and whether they produce active phages...