Ramy Karam Aziz, PhD

last updated 1 March 2013

Education:

1999-2004: University of Tennessee Health Science Center, Memphis, TN USA: PhD in Microbiology and Immunology (Dissertation)

1990-1995: Faculty of Pharmacy, Cairo University, Cairo Egypt: BSc Pharmacy and Pharmaceutical Sciences

Current positions

• Visiting Scientist, Systems Biology Research Group, University of California San Diego, La Jolla, CA, USA (since 2011)
  
• Assistant Professor, Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University (since 2011)

Past positions

• Adjunct Faculty, College of Sciences, San Diego State University, San Diego, CA, USA (2008-2012)
• Lecturer, Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University (2006-2011)
• Research Associate (Streptococcal genome specialist), NMPDR, University of Chicago, IL, USA and San Diego State University, San Diego, CA, USA (2008-2011)
• Volunteer genome curator, NMPDR, University of Chicago, IL, USA (2006-2008)
• Part time genome curator, NMPDR, University of Chicago, IL, USA (2005-2006)
• Postdoctoral Fellow, Departments of Surgery and Ophthalmology University of Tennessee Health Science Center, Memphis, TN USA (2004-2006)

Research Interests

• Microbial systems biology
  
• Microbial pathogenesis and virulence gene discovery
• Genome annotation and interpretation
• Microbial and phage genomics
• Bioinformatics
• Immunogenetics and host-pathogen interactions
• Molecular biotechnology and genome-based medicine

Editorial Activities

• Member of the Public Library of Science (PLoS) International Advisory Group (since 2010)
• Editorial Board Member, Scientific Reports (since 2011)
  
• International Editorial Advisory Board member, Current Pharmacogenomics and Personalized Medicine (since 2011)
  
• Associate Editor, BMC Microbiology (since 2009)
• Academic Editor, PLoS ONE (since 2009)

E-courses and Workshops

Egybio Online Courses

• It's a MicrobeFul World (Formerly: "Learning Microbiology and Immunology")
  
• Bioinformatics and Systems Biology Workshops
  

Publications

• Peer-reviewed full articles:

  PubMed / Click here for a detailed analysis of the Pubmed-listed articles)
  
  Author's metrics: Total number of citations since 2001: 1429 (1323 without self citations) in 1104 articles (WoS); 1330 (1257 excluding self citations, Scopus) in 1201 articles; 1932 (Google Scholar)
  h index = 15; 16; 18 [Data from ISI Web of Science (Green); Scopus citation tracker (Red); Google Scholar (Purple)]
  

  Publication list in reverse chronological order: (citations from ISI WoS; Scopus; Google Scholar)

  
  
  Visual summary:
  
  2013:
  

  42: Akhter S, Bailey BA, Salamon P, Aziz RK, Edwards RA.
  Applying Shannon's information theory to bacterial and phage genomes and metagenomes. Sci Rep. 2013;3:1033. doi: 10.1038/srep01033. (Access metrics from the journal's website) Epub 2013 Jan 8. PMID: 23301154. (cited by 0; 0; 0)

  2012:
  

  41: Saad R, Rizkallah MR, Aziz RK.
  Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. Gut Pathog. 2012 Nov 30;4(1):16. doi: 10.1186/1757-4749-4-16.  (?) PMID: 23194438. (cited by 0; 0; 0)

  40: Aziz RK
  Rethinking pharmacogenomics in an ecosystem: drug-microbiome interactions, pharmacomicrobiomics, and personalized medicine for the human supraorganism (Editorial). Curr Pharmacogenomics Person Med.  2012 Dec 1;10(4):258-261
  View (PDF available from the publisher's site)
  (cited by -; 0; 0)

  39: Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.
  SEED Servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One. 2012; 7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.PMID: 23110173; PMCID: PMC3480482.
  (cited by 3; 2; 5)

  38: Cole JN, Aziz RK, Kuipers K, Timmer AM, Nizet V, van Sorge NM.
  A conserved UDP-glucose dehydrogenase outside the hasABC operon contributes to capsule biogenesis in group A Streptococcus J Bacteriol 2012 [Epub ahead of print]. PMID: 22961854 .
  Abstract from publisher's site. PDF file from Nizet lab website
  (cited by 0; 0; 0)

  37: Maamary PG, Ben Zakour NL, Cole JN, Hollands A, Aziz RK, Barnett TC, Cork AJ, Henningham A, Sanderson-Smith M, McArthur JD, Venturini C, Gillen CM, Kirk JK, Johnson DR, Taylor WL, Kaplan EL, Kotb M, Nizet V, Beatson SA, Walker MJ.
  Tracing the evolutionary history of the pandemic group A streptococcal M1T1 clone. FASEB J. 2012 Aug 9. [Epub ahead of print]. PMID: 22878963.
  Abstract from publisher's site. PDF file from Nizet lab website
  (cited by 1; 1; 2)

  36: Khouzam RN, Shaheen M, Aziz RK, Ibebuogu UN.
  The Important Role of Inflammatory Biomarkers Pre- and Post Bare-Metal and Drug-Eluting Stent Implantation. Can J Cardiol. 2012 Nov;28(6):700-5. doi: 10.1016/j.cjca.2012.05.012. Epub 2012 Jul 21. PubMed PMID: 22819358.
  (cited by 0; 0; 2)

  35: Rizkallah MR, Gamal-Eldin S, Saad R, Aziz RK
  The Pharmacomicrobiomics portal: a database for drug-microbiome interactions. Curr Pharmacogenomics Person Med. 2012 Sep 1;10(3):195-203.
  Abstract (from the publisher's site)
  PrePrint to be archived soon!
  (cited by -; -; 2)

  34: Akhter S, Aziz RK, Edwards RA.
  PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012 Sep 1;40(16)e126. Epub 2012 May 14. PubMed PMID: 22584627. Full text version from publisher's site (open access article)
  (cited by 4; 4; 6)

  2011:
  

  33: Ozdemir V, Rosenblatt DS, Warnich L, Srivastava S, Tadmouri GO, Aziz RK, Reddy PJ, Manamperi A, Dove ES, Joly Y, Zawati MH, Hizel C, Yazan Y, John L, Vaast E, Ptolemy AS, Faraj SA, Kolker E, Cotton RG.
  Towards an Ecology of Collective Innovation: Human Variome Project (HVP), Rare Disease Consortium for Autosomal Loci (RaDiCAL) and Data-Enabled Life Sciences Alliance (DELSA). Curr Pharmacogenomics Person Med. PMID: 22523528; PubMed Central PMCID: PMC3329442.
  (cited by -; 4; 7)

  2010:
  
  32: Ozdemir V, Armengaud J, Dubé L, Aziz RK, Knoppers BM.
  Nutriproteomics and proteogenomics: cultivating two novel hybrid fields of personalized medicine with added societal value (Editorial). Curr Pharmacogenomics Person Med. 2010 Dec 1;8(4):240-244. PMID: 21399751; PubMed Central PMCID: PMC3052357.
  (cited by -; 6; 9)

  31: Maamary PG, Sanderson-Smith ML, Aziz RK, Hollands A, Cole JN, McKay FC, McArthur JD, Kirk JK, Cork AJ, Keefe RJ, Kansal RG, Sun H, Taylor WL, Chhatwal GS, Ginsburg D, Nizet V, Kotb M, Walker MJ.
  Parameters governing invasive disease propensity of non-M1 serotype group A streptococci. J Innate Immun. 2010;2(6):596-606. Epub: 2010 Sep 2. PMID: 20814186.
  PDF file from Nizet lab website
  (cited by 4; 6; 7)

  30: Rizkallah MR, Saad R, Aziz RK
  The Human Microbiome Project, personalized medicine and the birth of pharmacomicrobiomics. Curr Pharmacogenomics Person Med. 2010 Sep 1;8(3):182-193.
  Author Pre-Print (PDF File)
  (cited by -; 6; 8)

  29: Aziz RK, Breitbart M, Edwards RA.
  Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 2010 Jul 38(13):4207-12. Epub: 2010 Mar 9. PMID: 20215432.
  Full text version from publisher's site (open access article)
  Featured as one the journal's top 5% articles in 2010 and as cover story for the July 2010 issue
  (cited by 31; 32; 52)

  28: Aziz RK, Kansal R, Aronow BJ, Taylor WL, Rowe SL, Kubal M, Chhatwal GS, Walker MJ, Kotb M.
  Microevolution of group A streptococci in vivo: capturing regulatory networks engaged in sociomicrobiology, niche adaptation, and hypervirulence. PLoS One. 2010 Apr 14;5(4):e9798.PMID: 20418946; PubMed Central PMCID: PMC2854683.Full text version from publisher's site (open access article)
  (cited by 14; 15; 21)

  27: Khalifa MM, Sharaf RR, Aziz RK.
  Helicobacter pylori: a poor man's gut pathogen? Gut Pathog. 2010 Mar 31;2(1):2. (?)PMID: 20356368; PubMed Central PMCID: PMC2861632
  Full text version from publisher's site (open access article)
  (cited by 9; -; 23)

  26: Kansal RG, Datta V, Aziz RK, Abdeltawab NF, Rowe S, Kotb M.
  Dissection of the molecular basis for hypervirulence of an in vivo-selected phenotype of the widely disseminated M1T1 strain of group A Streptococcus bacteria. J Infect Dis. Mar 15;201(6):855-65 PMID: 20151844.
  Abstract (publisher's site).
  (cited by 16; 15; 17)

  25: Milani CJ, Aziz RK^#, Locke JB, Dahesh S, Nizet V, Buchanan JT.
  The novel polysaccharide deacetylase homolog Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae. Microbiology. 2010 Feb;156(Pt 2):543-54. Epub 2009 Sep 17.PMID: 19762441.
  Accepted version (PDF file from Nizet lab website)
  # Joint first author
  (cited by 7; 8; 12)

  24: Aziz RK, Nizet V.
  Pathogen microevolution in high resolution. Sci Transl Med. 2010; 2:16ps4
  Publisher's site (abstract), PDF file (from Nizet lab website)
  (cited by 3; 8; 11)

  
  2009:
  

  23: Aziz RK.
  A hundred-year-old insight into the gut microbiome! Gut Pathog. 2009 Dec 7;1(1):21. (?)PMID: 19653908
  publisher's site (open access article)
  (cited by 3; -; 7)

  22: Khouzam RN, Aziz RK.
  A case report: can altitude change blood pressure that much? J Clin Hypertens (Greenwich). 2009 Sep;11(9):498-9.PMID: 19751462.
  (cited by 0; 0; 0)

  21: McNeil LK, Aziz RK.
  In silico reconstruction of the metabolic and pathogenic potential of bacterial genomes using subsystems. Genome Dyn. 2009;6:21-34. Epub 2009 Aug 19. PMID: 19696491
  publisher's site (abstract only)
  (cited by -; 2; 3)

  20: Aziz RK.
  The case for biocentric microbiology. Gut Pathog. 2009 Aug 4;1(1):16. (?)PMID: 19653908
  publisher's site (open access article)
  (cited by 4; -; 6)
  Article rated by Faculty of 1000 'Recommended' F1000 Factor 3.0

  19: Cox KH, Ruiz-Bustos E, Courtney HS, Dale JB, Pence MA, Nizet V, Aziz RK, Gerling I, Price SM, Hasty DL.
  Inactivation of DltA modulates virulence factor expression in Streptococcus pyogenes. PLoS One. 2009;4(4):e5366. Epub 2009 Apr 29. PMID: 19401780; PMCID: PMC2671602.
  publisher's site (open access article)
  (cited by 8; 9; 10)

  
  2008:
  

  18: Hollands A, Aziz RK, Kansal R, Kotb M, Nizet V, Walker MJ.
  A naturally occurring mutation in ropB suppresses SpeB expression and reduces M1T1 group A streptococcal systemic virulence. PLoS ONE. 2008;3(12):e4102. Epub 2008 Dec 31.PMID: 19116661
  publisher's site (open access article)
  (cited by 15; 18; 20)

  17: Kotb M, Fathey N, Aziz R, Rowe S, Williams RW, Lu L.
  Unbiased forward genetics and systems biology approaches to understanding how gene-environment interactions work to predict susceptibility and outcomes of infections. Novartis Found Symp. 2008;293:156-65.PMID: 18972751
  (cited by -; 2; 4)

  16: Aziz RK, Kotb M.
  Rise and persistence of global M1T1 clone of Streptococcus pyogenes. Emerg Infect Dis. 2008 Oct;14(10):1511-7.publisher's site (full text freely available)
  (cited by 46; 48; 55)

  15: Locke JB, Aziz RK, Vicknair MR, Nizet V, Buchanan JT.
  Streptococcus iniae M-like protein contributes to virulence in fish and is a target for live attenuated vaccine development. PLoS ONE. 2008 Jul 30;3(7):e2824. PMID: 18665241publisher's site (open access article)
  (cited by 13; 17; 28)

  14: Abdeltawab NF, Aziz RK, Kansal R, Rowe SL, Su Y, Gardner L, Brannen C, Nooh MM, Attia RR, Abdelsamed H, Taylor WL, Lu L, Williams RW, Kotb M.
  An unbiased systems genetics approach to mapping genetic loci modulating susceptibility to severe streptococcal sepsis. PLoS Pathog. 2008 4(4): e1000042. doi:10.1371/journal.ppat.1000042 publisher's site (open access article)
  (cited by 15; 16; 25)

  13: Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.
  The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008 Feb 8;9:75. (?) PMID: 18261238publisher's site (open access article)
  (cited by 625; 650; 791)
  Article rated by Faculty of 1000 'Must Read' F1000 Factor 6.0

  
  2007:
  

  12: Arthur JC, Lich JD, Aziz RK, Kotb M, Ting JP.
  Heat shock protein 90 associates with Monarch-1 and regulates its ability to promote degradation of NF-{kappa}B-inducing kinase. J Immunol. 2007 Nov 1;179(9):6291-6. PMID: 17947705 [PubMed - indexed for MEDLINE]publisher's site (free abstract)
  (cited by 21; 20; 22)

  11: Walker MJ, Hollands A, Sanderson-Smith ML, Cole JN, Kirk JK, Henningham A,McArthur JD, Dinkla K, Aziz RK, Kansal RG, Simpson AJ, Buchanan JT, Chhatwal GS, Kotb M, Nizet V.
  DNase Sda1 provides selection pressure for a switch to invasive group A streptococcal infection. Nat Med. 2007 Aug;13(8):981-5. Epub 2007 Jul 15. PMID: 17632528 [PubMed - indexed for MEDLINE]publisher's site (free abstract)
  (cited by 102; 110; 129)
  Article rated by Faculty of 1000 'Recommended' F1000 Factor 3.0

  10: Aziz RK, Kansal R, Abdeltawab NF, Rowe SL, Su Y, Carrigan D, Nooh MM, Attia RR, Brannen C, Gardner LA, Lu L, Williams RW, Kotb M.
  Susceptibility to severe streptococcal sepsis: use of a large set of isogenic mouse lines to study genetic and environmental factors. Genes Immun. 2007 Jul;8(5):404-415. Epub 2007 May 24. PMID: 17525705 [PubMed - indexed for MEDLINE]publisher's site
  (cited by 13; 15; 18)

  9: McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R.
  The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. Epub 2006 Dec 1. PMID: 17145713
  (cited by 53; 59; 75)

  8: Kwinn LA, Khosravi A, Aziz RK, Timmer AM, Doran KS, Kotb M, Nizet V.
  Genetic characterization and virulence role of the RALP3/LSAP locus upstream of the streptolysin S operon in invasive M1T1 group A Streptococcus. J Bacteriol. 2007 Feb;189(4):1322-9. Epub 2006 Nov 17. PMID: 17114267
  (cited by 18; 19; 20)

  
  2006:
  

  7: Nooh MM, Aziz RK^#, Kotb M, Eroshkin A, Chuang WJ, Proft T, Kansal R.
  Streptococcal mitogenic exotoxin, SmeZ, is the most susceptible M1T1 streptococcal superantigen to Degradation by the Streptococcal Cysteine Protease, SpeB. J Biol Chem. 2006 Nov 17;281(46):35281-8. Epub 2006 Sep 15.PMID: 16980693
  # Joint first author
  (cited by 13; 14; 17)

  6: Buchanan JT, Simpson AJ, Aziz RK, Liu GY, Kristian SA, Kotb M, Feramisco J, Nizet V.
  DNase expression allows the pathogen group A Streptococcus to escape killing in neutrophil extracellular traps. Curr Biol. 2006 Feb 21;16(4):396-400.PMID: 16488874
  (cited by 183; 180; 232)
  Article rated by Faculty of 1000 'Must Read' F1000 Factor 4.8

  
  2005:
  

  5: Kansal RG, Aziz RK, Kotb M.
  Modulation of expression of superantigens by human transferrin and lactoferrin: a novel mechanism in host-Streptococcus interactions. J Infect Dis. 2005 Jun 15;191(12):2121-9. Epub 2005 May 11. PMID: 15897999
  (cited by 7; 8; 12)

  4: Aziz RK, Edwards RA, Taylor WW, Low DE, McGeer A, Kotb M.
  Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes. J Bacteriol. 2005 May;187(10):3311-8. PMID: 15866915
  (cited by 61; 64; 74)

  
  2001-2004:
  

  3: Aziz RK, Ismail SA, Park HW, Kotb M.
  Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes. Mol Microbiol. 2004 Oct;54(1):184-97.PMID: 15458415
  (cited by 30; 32; 43)

  2: Aziz RK, Pabst MJ, Jeng A, Kansal R, Low DE, Nizet V, Kotb M.
  Invasive M1T1 group A Streptococcus undergoes a phase-shift in vivo to prevent proteolytic degradation of multiple virulence factors by SpeB. Mol Microbiol. 2004 Jan;51(1):123-34. PMID: 14651616
  (cited by 60; 68; 81)

  1: Kazmi SU, Kansal R, Aziz RK, Hooshdaran M, Norrby-Teglund A, Low DE, Halim AB, Kotb M.
  Reciprocal, temporal expression of SpeA and SpeB by invasive M1T1 group A streptococcal isolates in vivo. Infect Immun. 2001 Aug;69(8):4988-95. PMID: 11447177
  (cited by 47; 50; 63)

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• Books:

  Ramy Karam Aziz (2009) Molecular Dissection of the Clonal M1T1 Group A Streptococci, 164. Publisher: VDM Verlag. ISBN-13: 978-3639196597
  Amazon's record

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• Book Chapters:

  2: Kotb M, Fathey N, Aziz R, Rowe S, Williams RW, Lu L.
  Unbiased forward genetics and systems biology approaches to understanding how gene-environment interactions work to predict susceptibility and outcomes of infections. Aug 4 2008. In Genetic Effects on Environmental Vulnerability to Disease (Novartis Foundation Symposia)ISBN-13: 978-0470777800

  1: Kotb M, Williams RW, Fathey N, Nooh M, Rowe S, Kansal R, and Aziz R.
  Biotools for determining the genetics of susceptibility to infectious diseases and expediting research translation into effective countermeasures. Jul 2008. In National Institute of Allergy and Infectious Diseases, NIH: Volume 1: Frontiers in Research (Infectious Disease) ISBN-13: 978-1934115770

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• Published Conference Proceedings:

  3: Amin HM, Hashem A, Aziz RK.
  Bioinformatics determination of ETEC signature genes as potential targets for molecular diagnosis and reverse vaccinology. BMC Bioinformatics 2009; 10 (Suppl7): A8
  doi: 10.1186/1471-2105-10-S7-A8
  (cited by -; -; 2)

  2: Aziz RK, McNeil LK.
  Reconstructing the virulome of the human pathogen Streptococcus pyogenes using NMPDR subsystems-based annotation BMC Bioinformatics 2009; 10 (Suppl7): A7
  doi: 10.1186/1471-2105-10-S7-A7

  1: Aziz RK, Kotb, M.
  Integrating proteomics, genomics, and bioinformatics tools to define unique features of the clonal M1T1 substrain of S. pyogenes. International Congress Series 1289 (2006) 175-179. (Abstract)