Ramana Madupu

Summary

Affiliation: J. Craig Venter Institute
Country: USA

Publications

  1. ncbi request reprint Microbiome in human health and disease
    Ramana Madupu
    Genomic Medicine group at the J Craig Venter Institute, USA
    Sci Prog 96:153-70. 2013
  2. pmc CharProtDB: a database of experimentally characterized protein annotations
    Ramana Madupu
    J Craig Venter Institute, 9704 Medical Center Drive Rockville, MD 20850, USA
    Nucleic Acids Res 40:D237-41. 2012
  3. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
  4. 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
  5. pmc Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
    Vinita Joardar
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:6488-98. 2005
  6. pmc The comprehensive microbial resource
    Tanja Davidsen
    J Craig Venter Institute, Rockville, MD 20850, USA
    Nucleic Acids Res 38:D340-5. 2010
  7. 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
  8. pmc Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
    Herve Tettelin
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:13950-5. 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. pmc The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
    Barbara A Methe
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:10913-8. 2005

Collaborators

Detail Information

Publications19

  1. ncbi request reprint Microbiome in human health and disease
    Ramana Madupu
    Genomic Medicine group at the J Craig Venter Institute, USA
    Sci Prog 96:153-70. 2013
    ..In this chapter we present an overview of the state-of-the-art in current literature and projects pertaining to human microbiome studies...
  2. pmc CharProtDB: a database of experimentally characterized protein annotations
    Ramana Madupu
    J Craig Venter Institute, 9704 Medical Center Drive Rockville, MD 20850, USA
    Nucleic Acids Res 40:D237-41. 2012
    ..Each annotation is referenced with the source; ideally a journal reference, or, if imported and lacking one, the original database source...
  3. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
    ..We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another...
  4. 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...
  5. pmc Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
    Vinita Joardar
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:6488-98. 2005
    ..With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific...
  6. pmc The comprehensive microbial resource
    Tanja Davidsen
    J Craig Venter Institute, Rockville, MD 20850, USA
    Nucleic Acids Res 38:D340-5. 2010
    ..The code underlying the CMR website and the CMR database are freely available for download with no license restrictions...
  7. 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...
  8. pmc Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
    Herve Tettelin
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:13950-5. 2005
    ..Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes...
  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. pmc The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
    Barbara A Methe
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:10913-8. 2005
    ..Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition...
  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. 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
    ....
  13. pmc Structural flexibility in the Burkholderia mallei genome
    William C Nierman
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:14246-51. 2004
    ..Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection...
  14. 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...
  15. pmc Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades
    Rekha Seshadri
    The Institute for Genomic Research, Division of J Craig Venter Institute, Rockville, MD 20850, USA
    J Bacteriol 188:8272-82. 2006
    ..These enzymes may have bioremediative as well as industrial potential. Thus, the A. hydrophila genome sequence provides valuable insights into its ability to flourish in both aquatic and host environments...
  16. pmc Pathema: a clade-specific bioinformatics resource center for pathogen research
    Lauren M Brinkac
    J Craig Venter Institute, Rockville, MD 20850, USA
    Nucleic Acids Res 38:D408-14. 2010
    ..Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms...
  17. pmc Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus
    Jonathan H Badger
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    J Bacteriol 188:6841-50. 2006
    ..neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging...
  18. pmc The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:10181-6. 2003
    ..Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function...
  19. 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...