Timothy D Read

Summary

Affiliation: Naval Medical Center
Country: USA

Publications

  1. pmc Shuffling bacterial metabolomes
    Brendan Thomason
    Biological Defense Research Directorate, Naval Medical Research Center, 12300 Washington Avenue, Rockville, MD 20852, USA
    Genome Biol 7:204. 2006
  2. 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
  3. ncbi request reprint Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002
  4. pmc The complete genome sequence of Bacillus anthracis Ames "Ancestor"
    Jacques Ravel
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 191:445-6. 2009
  5. pmc Complete genome sequence of the Q-fever pathogen Coxiella burnetii
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:5455-60. 2003
  6. pmc Genetic variation and linkage disequilibrium in Bacillus anthracis
    Michael E Zwick
    Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, MD, USA
    Sci Rep 1:169. 2011
  7. pmc Genomic characterization of the Yersinia genus
    Peter E Chen
    Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, USA
    Genome Biol 11:R1. 2010
  8. pmc Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing
    Peter E Chen
    Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
    PLoS ONE 5:e12397. 2010
  9. pmc Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity
    Shanmuga Sozhamannan
    Naval Medical Research Center, Silver Spring, Maryland 20910, USA
    Appl Environ Microbiol 74:6792-6. 2008
  10. 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

Detail Information

Publications23

  1. pmc Shuffling bacterial metabolomes
    Brendan Thomason
    Biological Defense Research Directorate, Naval Medical Research Center, 12300 Washington Avenue, Rockville, MD 20852, USA
    Genome Biol 7:204. 2006
    ..This has recently been illustrated by work demonstrating the importance of HGT in the emergence of bacterial metabolic networks, with horizontally acquired genes being placed in peripheral pathways at the outer branches of the networks...
  2. 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...
  3. ncbi request reprint Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002
    ....
  4. pmc The complete genome sequence of Bacillus anthracis Ames "Ancestor"
    Jacques Ravel
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 191:445-6. 2009
    ..This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage since 1981...
  5. pmc Complete genome sequence of the Q-fever pathogen Coxiella burnetii
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:5455-60. 2003
    ..burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation...
  6. pmc Genetic variation and linkage disequilibrium in Bacillus anthracis
    Michael E Zwick
    Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, MD, USA
    Sci Rep 1:169. 2011
    ..anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains...
  7. pmc Genomic characterization of the Yersinia genus
    Peter E Chen
    Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, USA
    Genome Biol 11:R1. 2010
    ..However, there were no genomic data on the Yersinia species with more limited virulence potential, frequently found in soil and water environments...
  8. pmc Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing
    Peter E Chen
    Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
    PLoS ONE 5:e12397. 2010
    ....
  9. pmc Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity
    Shanmuga Sozhamannan
    Naval Medical Research Center, Silver Spring, Maryland 20910, USA
    Appl Environ Microbiol 74:6792-6. 2008
    ..Spontaneous AP50c-resistant B. anthracis mutants exhibit a mucoid colony phenotype...
  10. 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...
  11. pmc Identification of Bacillus anthracis spore component antigens conserved across diverse Bacillus cereus sensu lato strains
    Sanghamitra Mukhopadhyay
    Biological Defense Research Directorate, Naval Medical Research Center, Rockville, Maryland 20852, USA
    Mol Cell Proteomics 8:1174-91. 2009
    ..The results of these screens suggest the possibility of a multiepitope antigen for broad host range diagnostics or therapeutics against Bacillus spore infection...
  12. pmc Microarray-based resequencing of multiple Bacillus anthracis isolates
    Michael E Zwick
    Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
    Genome Biol 6:R10. 2005
    ..5 x 10(-6)). Population genomics studies of microbial pathogens using rapid resequencing technologies such as resequencing arrays are critical for recognizing newly emerging or genetically engineered strains...
  13. pmc Genotyping of Bacillus cereus strains by microarray-based resequencing
    Michael E Zwick
    Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, Maryland, United States of America Michael E Zwick
    PLoS ONE 3:e2513. 2008
    ..cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing...
  14. 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...
  15. pmc The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
    Ian T Paulsen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:13148-53. 2002
    ..A limited repertoire of genes homologous to known bacterial virulence factors were identified...
  16. pmc High-redundancy draft sequencing of 15 clinical and environmental Burkholderia strains
    Sanghamitra Mukhopadhyay
    Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, Maryland 20910, USA
    J Bacteriol 192:6313-4. 2010
    ..In this study, we have generated draft genome sequences of 15 strains of B. oklahomensis, B. pseudomallei, B. thailandensis, and B. ubonensis to an average sequence read coverage of 25- to 40-fold...
  17. pmc Rapid multi-locus sequence typing using microfluidic biochips
    Timothy D Read
    Biological Defense Research Directorate, Naval Medical Research Center, Rockville, Maryland, United States of America
    PLoS ONE 5:e10595. 2010
    ..The scheme involves de novo sequencing of 6-8 housekeeping loci to assign unique sequence types. In this work we adapted MLST to a rapid microfluidics platform in order to enhance speed and reduce laboratory labor time...
  18. 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...
  19. pmc Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae
    Herve Tettelin
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:12391-6. 2002
    ..agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms...
  20. pmc DIYA: a bacterial annotation pipeline for any genomics lab
    Andrew C Stewart
    Genomics Department, Biological Defense Research Directorate, Naval Medical Research Center, Rockville, MD, USA
    Bioinformatics 25:962-3. 2009
    ..The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output...
  21. pmc Microbial genome jambalaya
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 4:314. 2003
  22. pmc Arbovirus detection in insect vectors by rapid, high-throughput pyrosequencing
    Kimberly A Bishop-Lilly
    Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
    PLoS Negl Trop Dis 4:e878. 2010
    ..Therefore, these techniques may be unsuitable for situations when the causative agent of an outbreak is unknown...
  23. ncbi request reprint Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
    Science 296:2028-33. 2002
    ..These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks...