Ramy K Aziz

Summary

Publications

  1. doi request reprint The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli
    Ramy K Aziz
    Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Electronic address
    Microbiol Res 194:47-52. 2017
  2. pmc SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
    Ramy K Aziz
    Computation Institute, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e48053. 2012
  3. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
  4. pmc The novel polysaccharide deacetylase homologue Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae
    Carlo J E Milani
    Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093 0687, USA
    Microbiology 156:543-54. 2010
  5. pmc A conserved UDP-glucose dehydrogenase encoded outside the hasABC operon contributes to capsule biogenesis in group A Streptococcus
    Jason N Cole
    Department of Pediatrics, University of California San Diego, La Jolla, California, USA
    J Bacteriol 194:6154-61. 2012
  6. doi request reprint Pathogen microevolution in high resolution
    Ramy K Aziz
    Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
    Sci Transl Med 2:16ps4. 2010
  7. pmc Transposases are the most abundant, most ubiquitous genes in nature
    Ramy K Aziz
    Computation Institute, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 38:4207-17. 2010
  8. pmc Streptococcus iniae M-like protein contributes to virulence in fish and is a target for live attenuated vaccine development
    Jeffrey B Locke
    Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 3:e2824. 2008
  9. pmc Rise and persistence of global M1T1 clone of Streptococcus pyogenes
    Ramy K Aziz
    Department of Microbiologyand Immunology, Cairo University, Cairo, Egypt
    Emerg Infect Dis 14:1511-7. 2008
  10. pmc Applying Shannon's information theory to bacterial and phage genomes and metagenomes
    Sajia Akhter
    Computational Science Research Center, San Diego State University, San Diego, CA, USA
    Sci Rep 3:1033. 2013

Collaborators

Detail Information

Publications15

  1. doi request reprint The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli
    Ramy K Aziz
    Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Electronic address
    Microbiol Res 194:47-52. 2017
    ..coli robustness, demonstrated by the bacterial deployment of a generalist enzyme (here AldA) in multiple pathways to survive carbon starvation and to grow on a non-native substrate when no native carbon source is available...
  2. pmc SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
    Ramy K Aziz
    Computation Institute, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e48053. 2012
    ..Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users...
  3. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
    ..The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them...
  4. pmc The novel polysaccharide deacetylase homologue Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae
    Carlo J E Milani
    Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0687, La Jolla, CA 92093 0687, USA
    Microbiology 156:543-54. 2010
    ..iniae. Identification of Pdi and other S. iniae virulence proteins is a necessary initial step towards the development of appropriate preventive and therapeutic measures against diseases and economic losses caused by this pathogen...
  5. pmc A conserved UDP-glucose dehydrogenase encoded outside the hasABC operon contributes to capsule biogenesis in group A Streptococcus
    Jason N Cole
    Department of Pediatrics, University of California San Diego, La Jolla, California, USA
    J Bacteriol 194:6154-61. 2012
    ..The identification of redundant UDP-glucose 6-dehydrogenases underscores the importance of HA capsule expression for M1T1 GAS pathogenicity and survival in the human host...
  6. doi request reprint Pathogen microevolution in high resolution
    Ramy K Aziz
    Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
    Sci Transl Med 2:16ps4. 2010
    ..aureus strain, can provide new clues about the geographical origin and intrahospital spread of important microbial pathogens...
  7. pmc Transposases are the most abundant, most ubiquitous genes in nature
    Ramy K Aziz
    Computation Institute, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 38:4207-17. 2010
    ..By securing their own replication and dissemination, transposases guarantee to thrive so long as nucleic acid-based life forms exist...
  8. pmc Streptococcus iniae M-like protein contributes to virulence in fish and is a target for live attenuated vaccine development
    Jeffrey B Locke
    Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 3:e2824. 2008
    ..Through pyrosequencing of the S. iniae genome we have identified two gene homologues to classical surface-anchored streptococcal virulence factors: M-like protein (simA) and C5a peptidase (scpI)...
  9. pmc Rise and persistence of global M1T1 clone of Streptococcus pyogenes
    Ramy K Aziz
    Department of Microbiologyand Immunology, Cairo University, Cairo, Egypt
    Emerg Infect Dis 14:1511-7. 2008
    ....
  10. pmc Applying Shannon's information theory to bacterial and phage genomes and metagenomes
    Sajia Akhter
    Computational Science Research Center, San Diego State University, San Diego, CA, USA
    Sci Rep 3:1033. 2013
    ....
  11. pmc Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics
    Marwa Elrakaiby
    1 Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
    OMICS 18:402-14. 2014
    ..Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed...
  12. pmc Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations
    Ramy K Aziz
    Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
    Sci Rep 5:16025. 2015
    ..These findings pinpoint specific ways in which to improve the predictive ability of metabolic models, and highlight one potential application of systems biology to drug discovery and translational medicine. ..
  13. pmc The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
    Leslie Klis McNeil
    National Center for Supercomputing Applications, Urbana, IL 61801, USA
    Nucleic Acids Res 35:D347-53. 2007
    ..Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development...
  14. ncbi request reprint Streptococcal mitogenic exotoxin, SmeZ, is the most susceptible M1T1 streptococcal superantigen to degradation by the streptococcal cysteine protease, SpeB
    Mohammed M Nooh
    Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
    J Biol Chem 281:35281-8. 2006
    ..The study provides evidence for the effect of subtle structural differences between highly similar SAgs on their biological activity...
  15. pmc Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes
    Ramy K Aziz
    Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis 38163, USA
    J Bacteriol 187:3311-8. 2005
    ..Y, replacing it with a different module identical to that found on a related M3 phage. Taken together, the data demonstrate that mosaicism of the GAS prophages has contributed to the emergence and diversification of the M1T1 subclone...