Robert D Fleischmann

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains
    R D Fleischmann
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:5479-90. 2002
  2. pmc In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism
    Srilatha Kuntumalla
    Pathogen Functional Genomics Resource Center, J, Craig Venter Institute, Rockville, MD 20850, USA
    BMC Microbiol 11:147. 2011
  3. pmc The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins
    Rembert Pieper
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Proteomics 9:5029-45. 2009
  4. doi request reprint Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis
    Rembert Pieper
    J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Microbiology 155:498-512. 2009
  5. pmc Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
    Rembert Pieper
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Microbiol 10:30. 2010
  6. pmc Using chemical derivatization and mass spectrometric analysis to characterize the post-translationally modified Staphylococcus aureus surface protein G
    Moo Jin Suh
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    Biochim Biophys Acta 1804:1394-404. 2010
  7. pmc Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence
    Leka Papazisi
    Pathogen Functional Genomics Resource Center PFGRC, The J Craig Venter Institute JCVI, Rockville, MD 20850, USA
    Genomics 98:26-39. 2011
  8. pmc Recombinant expression and functional analysis of proteases from Streptococcus pneumoniae, Bacillus anthracis, and Yersinia pestis
    Keehwan Kwon
    Pathogen Functional Genomics Resource Center, J, Craig Venter Institute, Rockville, Maryland 20850, USA
    BMC Biochem 12:17. 2011
  9. pmc Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay
    Gagan A Pandya
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Microbiol 9:213. 2009
  10. pmc Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes
    Rembert Pieper
    Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, USA
    Proteome Sci 7:5. 2009

Research Grants

Collaborators

Detail Information

Publications28

  1. pmc Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains
    R D Fleischmann
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:5479-90. 2002
    ..Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity...
  2. pmc In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism
    Srilatha Kuntumalla
    Pathogen Functional Genomics Resource Center, J, Craig Venter Institute, Rockville, MD 20850, USA
    BMC Microbiol 11:147. 2011
    ....
  3. pmc The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins
    Rembert Pieper
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Proteomics 9:5029-45. 2009
    ..The outer membrane protein OmpA, the heat shock protein HtpG and OspC2 represent novel SD1 subunit vaccine candidates and drug targets...
  4. doi request reprint Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis
    Rembert Pieper
    J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Microbiology 155:498-512. 2009
    ..pestis cells with trypsin. Proteases and other stress-response-inducing factors may constitute environmental cues resulting in the activation of the T6SS in Y. pestis...
  5. pmc Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
    Rembert Pieper
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Microbiol 10:30. 2010
    ..pestis strain KIM6+ at two physiologically relevant temperatures (26 degrees C and 37 degrees C)...
  6. pmc Using chemical derivatization and mass spectrometric analysis to characterize the post-translationally modified Staphylococcus aureus surface protein G
    Moo Jin Suh
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    Biochim Biophys Acta 1804:1394-404. 2010
    ....
  7. pmc Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence
    Leka Papazisi
    Pathogen Functional Genomics Resource Center PFGRC, The J Craig Venter Institute JCVI, Rockville, MD 20850, USA
    Genomics 98:26-39. 2011
    ..anthracis, the evolution of this species and its close relatives was associated with an overall shift in the fraction of genes devoted to energy metabolism, cellular processes, transport, as well as virulence...
  8. pmc Recombinant expression and functional analysis of proteases from Streptococcus pneumoniae, Bacillus anthracis, and Yersinia pestis
    Keehwan Kwon
    Pathogen Functional Genomics Resource Center, J, Craig Venter Institute, Rockville, Maryland 20850, USA
    BMC Biochem 12:17. 2011
    ..It has been observed that cloning, expression and purification of proteases often fail due to their catalytic functions which, in turn, cause toxicity in the E. coli heterologous host...
  9. pmc Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay
    Gagan A Pandya
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Microbiol 9:213. 2009
    ..However, lower cost typing schemes are necessary in order to enable typing of hundreds or even thousands of isolates...
  10. pmc Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes
    Rembert Pieper
    Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, USA
    Proteome Sci 7:5. 2009
    ..The total number of proteins associated with Y. pestis membranes increased to 456 and included representatives of all six beta-barrel OM protein families and 25 distinct IM transporter families...
  11. doi request reprint Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change
    Rembert Pieper
    J Craig Venter Institute, Rockville, MD 20850, USA
    Proteomics 8:1442-58. 2008
    ..pestis life cycle were strongly altered in abundance. This included a putative nitrate/sulfonate/bicarbonate-specific SBP (Y1004), encoded by the virulence-associated plasmid pMT1 and increased in abundance at 37 degrees C...
  12. pmc Tracing phylogenomic events leading to diversity of Haemophilus influenzae and the emergence of Brazilian Purpuric Fever (BPF)-associated clones
    Leka Papazisi
    Pathogen Functional Genomics Resource Center PFGRC, The J Craig Venter Institute JCVI, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genomics 96:290-302. 2010
    ....
  13. pmc High quality protein microarray using in situ protein purification
    Keehwan Kwon
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Biotechnol 9:72. 2009
    ..Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays...
  14. pmc Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome
    Srilatha Kuntumalla
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Proteome Sci 7:22. 2009
    ..A high correlation was observed for subunits of soluble cellular protein complexes in several cases, demonstrating versatile applications of the APEX method in quantitative proteomics...
  15. pmc The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results
    John C Braisted
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Bioinformatics 9:529. 2008
    ..This predicted spectral count is compared to the protein's observed MS total spectral count during APEX computation of protein abundances...
  16. pmc Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome
    Moo Jin Suh
    The J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
    Proteome Sci 10:30. 2012
    ..abstract:..
  17. pmc A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform
    Gagan A Pandya
    Pathogen Functional Genomics Resource Center, The Institute for Genomic Research at the J Craig Venter Institute, Rockville, MD 20850, USA
    Nucleic Acids Res 35:e148. 2007
    ..Our approach eliminated 91% of the false-positive single-nucleotide polymorphism calls identified in the SCHU S4 query sample, at the cost of 10.7% of the true positives, yielding a total base-calling accuracy of 99.992%...
  18. 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...
  19. ncbi request reprint Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin
    Rembert Pieper
    The Institute for Genomic Research, Rockville, MD, USA
    Proteomics 6:4246-58. 2006
    ....
  20. ncbi request reprint Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays
    Scott N Peterson
    The Pathogen Functional Genomics Resource Center, The Institute for Genomic Research, Rockville, MD 20850, USA
    Mol Microbiol 51:1051-70. 2004
    ..Many of the induced loci were subjected to gene disruption mutagenesis, allowing us to establish that among 124 CSP-inducible genes, 67 were individually dispensable for transformation, whereas 23 were required for transformation...
  21. ncbi request reprint Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus
    Christine L Gatlin
    The Institute for Genomic Research, Rockville, MD, USA
    Proteomics 6:1530-49. 2006
    ....
  22. pmc Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative sigma factor, SigH
    Deepak Kaushal
    Department of Medicine, Center for Tuberculosis Research, Johns Hopkins School of Medicine, 424 North Bond Street, Baltimore, MD 21231, USA
    Proc Natl Acad Sci U S A 99:8330-5. 2002
    ..This phenotype demonstrates that beyond an ability to grow and persist within the host, M. tuberculosis has distinct virulence mechanisms that elicit deleterious host responses and progressive pulmonary disease...
  23. pmc Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis
    David Alland
    Department of Medicine, Center for Emerging Pathogens, New Jersey Medical School, Newark, New Jersey 07103, USA
    J Bacteriol 185:3392-9. 2003
    ..Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure...
  24. pmc Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis
    Tsute Chen
    Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA
    J Bacteriol 186:5473-9. 2004
    ....
  25. pmc Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis
    David Alland
    Division of Infectious Disease, Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
    J Clin Microbiol 45:39-46. 2007
    ..tuberculosis. Group B and C LSPs may represent polymorphisms that occur due to selective pressure and affect the phenotype of the organism, while group A LSPs are preferable phylogenetic markers...
  26. pmc Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis
    Roberto Colangeli
    Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
    PLoS Pathog 3:e87. 2007
    ..An improved understanding of the role of lsr2 may provide important insights into the mechanisms of action of antibiotics and the way that mycobacteria adapt to stresses such as antibiotic treatment...
  27. pmc Attenuation of late-stage disease in mice infected by the Mycobacterium tuberculosis mutant lacking the SigF alternate sigma factor and identification of SigF-dependent genes by microarray analysis
    Deborah E Geiman
    Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Infect Immun 72:1733-45. 2004
    ..Microarray analysis has identified SigF-dependent genes and a putative SigF consensus recognition site...
  28. ncbi request reprint Improved quantitation and reproducibility in Mycobacterium tuberculosis DNA microarrays
    Benjamin G Schroeder
    The Institute for Genomic Research, Rockville, MD 20850, USA
    J Mol Microbiol Biotechnol 4:123-6. 2002
    ..We show that optimizing the labeling protocol is a critical element in conducting microarray experiments and obtaining reproducible and interpretable data...

Research Grants1

  1. THE COMPLETE GENOME SEQUENCE AND ANALYSIS OF M SMEGMATIS
    Robert Fleischmann; Fiscal Year: 2002
    ..The data will be made available to the research community through the TIGR Microbial Database on the World Wide Web (www.tigr.org). ..