Ramy Karam Aziz, PhD

- updated 15 October 2021 -

Education:

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

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

Current position

• Head, Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357 (since Feb 2021)
• Professor of Microbiology and Immunology, Faculty of Pharmacy, Cairo University (since Oct 2016)

Past positions

• Chair (Department Head), Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University (Oct 2017-Feb 2021)
• Acting Chair, Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University (Aug 2016- Sep 2017)
• Adjunct Faculty, Biology Department The American University in Cairo (2015-2016)
• Assistant Professor, Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University (2011-2016)
• Visiting Scientist, Systems Biology Research Group, University of California San Diego, La Jolla, CA, USA (2011-2016)
  
• 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, PeerJ (since 2014)
  
• 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 (old site, temporary site)

Educational Blogs

• 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)
  

  Visual summary: (2010 & 2016)
  
  

  Publication list in reverse chronological order: (citations from ISI WoS; Scopus; Google Scholar - Citations are still not up-to-date)
  * = corresponding author

  
  2001-2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 | 2019 | 2020 | 2021 | in press
  
  List from PubReminer (updated 15 Oct 2021)
  
  
  In Press:
  

  95: Abdelsattar AS, Dawoud A, Makky S, Nofal R, Aziz RK, El-Shibiny A.
  Bacteriophages: from isolation to application. Curr Pharm Biotechnol. 2021 Apr 25. doi: 10.2174/1389201022666210426092002. Epub ahead of print. PMID: 33902418. (cited by 1; 2; 3)

  2021:
  

  94: Zahran SA, Ali-Tammam M, Ali AE, Aziz RK*.
  Compositional variation of the human fecal microbiome in relation to azo-reducing activity: a pilot study. Gut Pathog. 2021 Oct 8;13(1):58. doi: 10.1186/s13099-021-00454-0. PMID: 34625106; PMCID: PMC8499468. (cited by -; -; -)

  93: Krupovic M, Turner D, Morozova V, Dyall-Smith M, Oksanen HM, Edwards R, Dutilh BE, Lehman SM, Reyes A, Baquero DP, Sullivan MB, Uchiyama J, Nakavuma J, Barylski J, Young MJ, Du S, Alfenas-Zerbini P, Kushkina A, Kropinski AM, Kurtböke I, Brister JR, Lood C, Sarkar BL, Yigang T, Liu Y, Huang L, Wittmann J, Chanishvili N, van Zyl LJ, Rumnieks J, Mochizuki T, Jalasvuori M, Aziz RK, Łobocka M, Stedman KM, Shkoporov AN, Gillis A, Peng X, Enault F, Knezevic P, Lavigne R, Rhee SK, Cvirkaite-Krupovic V, Moraru C, Moreno Switt AI, Poranen MM, Millard A, Prangishvili D, Adriaenssens EM. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Arch Virol. 2021 Nov;166(11):3239-3244. doi: 10.1007/s00705-021-05205-9. PMID:34417873. (cited by -; -; -)

  92: Maina AN, Mwaura FB, Jumba M, Kiefts K, Nour El-Din HT, Aziz RK*.
  Novel PhoH-encoding vibriophages with lytic activity against environmental Vibrio strains.Arch Microbiol. 2021 Nov;203(9):5321-5331. doi: 10.1007/s00203-021-02511-3. Epub 2021 Aug 11. PMID: 34379161. (cited by -; -; -)

  91: Moustafa A*, Khalel RS, Aziz RK*.
  Traces of SARS-CoV-2 RNA in peripheral blood cells of patients with COVID-19. OMICS. 2021 Aug;25(8):475-483. doi: 10.1089/omi.2021.0068. Epub 2021 Jul 19. PMID: 34280038; PMCID: PMC8377512. (cited by -; -; 4)

  90: ElBanna SA, Moneib NA, Aziz RK*, Samir R*.
  Genomics-guided identification of a conserved CptBA-like toxin-antitoxin system in Acinetobacter baumannii. J Adv Res. 2020 Nov 23;30:159-170. doi: 10.1016/j.jare.2020.11.007. PMID: 34026293; PMCID: PMC8132199. (cited by -; -; 2)

  89: Hashem YA, Abdelrahman KA, Aziz RK*.
  Phenotype-genotype correlations and distribution of key virulence factors in Enterococcus faecalis isolated from patients with urinary tract infections. Infect Drug Resist. 2021 May 10;14:1713-1723. doi: 10.2147/IDR.S305167. PMID: 34007190; PMCID: PMC8123086. (cited by -; -; 1)

  88: Sallam IE, Abdelwareth A, Attia H, Aziz RK, Homsi MN, von Bergen M, Farag MA.
  Effect of gut microbiota biotransformation on dietary tannins and human health implications. Microorganisms. 2021 Apr 29;9(5):965. doi: 10.3390/microorganisms9050965. PMID: 33947064; PMCID: PMC8145700. (cited by -; -; -)

  87: Hemeda AA, Ahmad Mohamed A, Aziz RK, Abdel-Hakeem MS, Ali-Tammam M.
  Impact of IL10, MTP, SOD2, and APOE gene polymorphisms on the severity of liver fibrosis induced by HCV genotype 4. Viruses. 2021 Apr 20;13(4):714. doi: 10.3390/v13040714. PMID: 33924242; PMCID: PMC8074775. (cited by -; -; -)

  86: Soliman MS, AbdelFattah M, Aman SMN, Ibrahim LM, Aziz RK.
  A Gapless, unambiguous RNA metagenome-assembled genome sequence of a unique SARS-CoV-2 variant encoding spike S813I and ORF1a A859V substitutions. OMICS. 2021 Feb;25(2):123-128. doi: 10.1089/omi.2020.0194. Epub 2020 Nov 30. PMID: 33253058. (cited by -; -; -)

  2020:
  

  85: Soliman MS, Soliman NS, El-Manakhly AR, ElBanna SA, Aziz RK, El-Kholy AA.
  Genomic Characterization of methicillin-resistant Staphylococcus aureus (MRSA) by high-throughput sequencing in a tertiary care hospital. Genes (Basel). 2020 Oct 17;11(10):1219. doi: 10.3390/genes11101219. PMID: 33080885; PMCID: PMC7603108. (cited by -; -; -)

  84: Nelson J, El-Gendy AO, Mansy MS, Ramadan MA, Aziz RK*
  The biosurfactants iturin, lichenysin and surfactin, from vaginally isolated lactobacilli, prevent biofilm formation by pathogenic Candida. FEMS Microbiol Lett. 2020 Aug 1;367(15):fnaa126. doi: 10.1093/femsle/fnaa126. PMID: 32710776. (cited by -; -; -)

  83: Adriaenssens EM, Sullivan MB, Knezevic P, van Zyl LJ, Sarkar BL, Dutilh BE, Alfenas-Zerbini P, Łobocka M, Tong Y, Brister JR, Moreno Switt AI, Klumpp J, Aziz RK, Barylski J, Uchiyama J, Edwards RA, Kropinski AM, Petty NK, Clokie MRJ, Kushkina AI, Morozova VV, Duffy S, Gillis A, Rumnieks J, Kurtböke İ, Chanishvili N, Goodridge L, Wittmann J, Lavigne R, Jang HB, Prangishvili D, Enault F, Turner D, Poranen MM, Oksanen HM, Krupovic M.
  Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol. 2020 May;165(5):1253-1260. doi: 10.1007/s00705-020-04577-8. PMID:32162068. (cited by -; -; -)

  82: Abdelsalam NA, Ramadan AT, ElRakaiby MT, Aziz RK*
  *. Toxicomicrobiomics: The human microbiome vs. pharmaceutical, dietary, and environmental xenobiotics. Front Pharmacol. 2020Apr 16;11:390. doi: 10.3389/fphar.2020.00390. eCollection 2020. PMID: 32372951. (cited by -; -; -)

  81: Özdemir V, Arga KY, Aziz RK, Bayram M, Conley SN, Dandara C, Endrenyi L, Fisher E, Garvey CK, Hekim N, Kunej T, Şardaş S, Von Schomberg R, Yassin AS, Yılmaz G, Wang W.
  Digging deeper into precision/personalized medicine: cracking the sugar code, the third alphabet of life, and sociomateriality of the Cell. OMICS. 2020 Feb;24(2):62-80. doi: 10.1089/omi.2019.0220. Epub 2020 Jan 28. PMID: 32027574. (cited by -; -; -)

  80: Aziz RK*, Rizkallah MR, Saad R, ElRakaiby MT
  Translating pharmacomicrobiomics: three actionable challenges/prospects in 2020. OMICS. 2020 Feb;24(2):60-61. doi: 10.1089/omi.2019.0205. Epub 2020 Jan 9. PMID: 31916888 (cited by -; -; -)

  79: Kashef MT, Aziz RK*
  Drug factory microbiome: top three actionable challenges and prospects. OMICS. 2020 Jan;24(1):55-56. doi: 10.1089/omi.2019.0202. PMID: 31935167 (Letter to the editor). (cited by -; -; -)

  78: Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, Chlenski P, Conrad N, Dickerman A, Dietrich EM, Gabbard JL, Gerdes S, Guard A, Kenyon RW, Machi D, Mao C, Murphy-Olson D, Nguyen M, Nordberg EK, Olsen GJ, Olson RD, Overbeek JC, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomas C, VanOeffelen M, Vonstein V, Warren AS, Xia F, Xie D, Yoo H, Stevens R.
  The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 2020 Jan 8;48(D1):D606-D612. doi: 10.1093/nar/gkz943. PubMed PMID: 31667520. (cited by -; -; -)

  2019:
  

  77: Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE.
  Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol. 2019 Oct;4(10):1727-1736. doi: 10.1038/s41564-019-0494-6. Epub 2019 Jul 8. PMID: 31285584 (cited by -; -; -)

  76: ElRakaiby MT, Gamal-Eldin S, Amin MA, Aziz RK*
  Hospital microbiome variations as analyzed by high-throughput sequencing. OMICS. 2019 Sep;23(9):426-438. doi: 10.1089/omi.2019.0111. Epub 2019 Aug 8. PMID: 31393213. (cited by -; -; -)

  75: Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.
  PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform. 2019 Jul 19;20(4):1094-1102. doi: 10.1093/bib/bbx083. PMID: 28968762 (cited by -; -; -)

  74: Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ Aziz RK, Monk JM.
  Comparative genome-scale Metabolic modeling of metallo-beta-lactamase-producing multidrug-resistant Klebsiella pneumoniae clinical isolates. Front Cell Infect Microbiol. 2019 May 24;9:161. doi: 10.3389/fcimb.2019.00161. eCollection 2019. PMID: 31179245 (cited by -; -; -)

  73: Hussein SH, Samir R, Aziz RK*, Toama MA.
  Two putative MmpL homologs contribute to antimicrobial resistance and nephropathy of enterohemorrhagic E. coli O157:H7. Gut Pathog. 2019 Apr 18;11:15. doi: 10.1186/s13099-019-0296-7. eCollection 2019. PMID: 31019555 (cited by -; -; -)

  72: Zahran SA, Ali-Tammam M, Hashem AM, Aziz RK*, Ali AE.
  Azoreductase activity of dye-decolorizing bacteria isolated from the human gut microbiota. Sci Rep. 2019 Apr 2;9(1):5508. doi: 10.1038/s41598-019-41894-8. PMID: 30940826 (cited by -; -; -)

  71: Ziko L, Saqr AA, Ouf A, Gimpel M, Aziz RK, Neubauer P, Siam R.
  Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool. Microb Cell Fact. 2019 Mar 18;18(1):56. doi: 10.1186/s12934-019-1103-3. PubMed PMID: 30885206 (cited by -; -; -)

  70: Ramadan AA, Abdelaziz NA, Amin MA, Aziz RK*
  Novel blaCTX-M variants and genotype-phenotype correlations among clinical isolates of extended spectrum beta lactamase-producing Escherichia coli. Sci Rep. 2019Mar 12;9(1):4224. doi: 10.1038/s41598-019-39730-0. PMID: 30862858. (cited by -; -; -)

  69: Maged M, El Hosseiny A, Saadeldin MK, Aziz RK, Ramadan E.
  Thermal stability of a mercuric reductase from the Red Sea Atlantis II hot brine environment as analyzed by site-directed mutagenesis. Appl Environ Microbiol. 2019 Jan 23;85(3). pii: e02387-18. doi: 10.1128/AEM.02387-18. Print 2019 Feb 1. PMID: 30446558 (cited by -; -; -)

  68: Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.
  Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17. PMID: 30556814 (cited by -; -; -)

  2018:
  

  67: Aziz RK*
  Toxicomicrobiomics: Narrowing the gap between environmental and medicinal toxicogenomics. OMICS. 2018 Dec;22(12):788-789. doi: 10.1089/omi.2018.0183. PubMed PMID: 30571608 (Letter to the editor) (cited by -; -; -)

  66: Aziz RK*, Hegazy SM, Yasser R, Rizkallah MR, ElRakaiby MT
  Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions. Expert Opin Drug Metab Toxicol. 2018Oct;14(10):1043-1055. doi: 10.1080/17425255.2018.1530216. Epub 2018 Oct 9. Review. PubMed PMID: 30269615 (cited by -; -; -)

  65: Aziz RK*
  Interview with Prof. Ramy K. Aziz, Cairo University. The Dawn of pharmacomicrobiomics. OMICS. 2018 Apr;22(4):295-297. doi: 10.1089/omi.2018.0041. PubMed PMID: 29652572. (cited by -; -; -)

  64: Al-Ghobashy MA, Kamal SM, El-Sayed GM, Attia AK, Nagy M, ElZeiny A, Elrakaiby MT, Nooh MM, Abbassi M, Aziz RK*
  Determination of voriconazole andco-administered drugs in plasma of pediatric cancer patients using UPLC-MS/MS: A key step towards personalized therapeutics. J Chromatogr B Analyt Technol Biomed Life Sci. 2018 Aug 15;1092:489-498. doi: 10.1016/j.jchromb.2018.06.043. Epub 2018 Jun 27. PubMed PMID: 30008305 (cited by -; -; -)

  63: Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J.
  Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol. 2018 Apr;163(4):1125-1129. doi:10.1007/s00705-018-3723-z. Epub 2018 Jan 22. PubMed PMID: 29356990 (cited by -; -; -)

  62: Safwat NA, Kashef MT, Aziz RK, Amer KF, Ramadan MA.
  Quercetin 3-O-glucoside recovered from the wild Egyptian Sahara plant, Euphorbia paralias L., inhibits glutamine synthetase and has antimycobacterial activity. Tuberculosis (Edinb). 2018Jan;108:106-113. doi: 10.1016/j.tube.2017.11.005. Epub 2017 Nov 16. PubMed PMID: 29523309 (cited by -; -; -)

  2017:
  

  61: Akhter S, Aziz RK*, Kashef MT, Ibrahim ES, Bailey B, Edwards RA*.
  Kullback Leibler divergence in complete bacterial and phage genomes. PeerJ. 2017 Nov 30;5:e4026. doi: 10.7717/peerj.4026. eCollection 2017. PubMed PMID: 29204318 (cited by 1; 1; 1)

  60: Hamdy AM, El-Massry M, Kashef MT, Amin MA, Aziz RK*.
  Toward the drug factory microbiome: microbial community variations in antibiotic-producing clean rooms. OMICS. 2017 Sep 5. doi: 10.1089/omi.2017.0091. [Epub ahead of print] PubMed PMID: 28873001 (cited by -; -; -)

  59: Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.
  PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform. 2017 Jul 31. doi: 10.1093/bib/bbx083. [Epub ahead of print] PubMed PMID: 28968762 (cited by 0; 1; 1)

  58: Hashem YA, Amin HM, Essam TM, Yassin AS, Aziz RK*.
  Biofilm formation in enterococci: genotype-phenotype correlations and inhibition by vancomycin. Sci Rep. 2017 Jul 18;7(1):5733. doi: 10.1038/s41598-017-05901-0. PubMed PMID: 28720810 (cited by 0; 0; 1)

  57: Elbehery AH, Aziz RK, Siam R.
  Insertion sequences enrichment in extreme Red Sea brine pool vent. Extremophiles. 2017 Mar;21(2):271-282. doi: 10.1007/s00792-016-0900-4. Epub 2016 Dec 3. PubMed PMID: 27915389

  56: Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BØ, Charusanti P.
  The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microb Res. 2017. Jan;194:47-52. doi: 10.1016/j.micres.2016.10.006. PubMed PMID: 27938862 (cited by 0; 0; 0)

  2016:
  

  55: Aly AM, Adel A, El-Gendy AO, Essam TM, Aziz RK*.
  Gut microbiome alterations in patients with stage 4 hepatitis C. Gut Pathog. 2016 Sep 13;8(1):42. doi:10.1186/s13099-016-0124-2. PubMed PMID: 27625705 (cited by 2; 3; 6)

  54: Adel M, Elbehery AH, Aziz SK, Aziz RK, Grossart HP, Siam R.
  Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments. Sci Rep. 2016 Sep 6;6:32704. doi: 10.1038/srep32704. PubMed PMID: 27596223 (cited by 2; 2; 3)

  53: Bosi E, Monk JM, Aziz RK Fondi M, Nizet V, Palsson BO.
  Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proc Natl Acad Sci USA. 2016 Jun 10. pii: 201523199. [Epub ahead of print] PubMed PMID: 27286824. (cited by 6; 7; 10)

  52:Elbehery AH, Aziz RK, Siam R.
  Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics. OMICS. 2016 Apr;20(4):229-38. doi: 10.1089/omi.2015.0191. Epub 2016 Mar 31. PubMed PMID:27031878. (cited by 4; 6;8)

  2015:
  

  51: Aziz RK Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO, Charusanti P.
  Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Sci Rep. 2015 Nov 4;5:16025. doi: 10.1038/srep16025. PubMed PMID: 26531810; PubMed Central PMCID: PMC4631998.

  (cited by 3; 3;4)

  50: Aziz RK, Khaw V, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BO, Charusanti P.
  Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpCFront Microbiol. 2015 . Aug 28;6. doi:10.3389/fmicb.2015.00958. (Article from the journal's site) (cited by 1; 2;2)

  49: Aziz RK*, Khalifa MM, Sharaf RR.
  Contaminated water as a source of Helicobacter pylori infection: A review. J Adv Res. 2015 Jul;6(4):539-47. doi: 10.1016/j.jare.2013.07.007. Epub 2013 Jul 21. PubMed PMID: 26199743 (cited by -; 13; 24)

  48: Aziz RK*, Dwivedi B, Akhter S, Breitbart M, Edwards RA*.
  Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. Front Microbiol. 2015 May 8;6:381. doi: 10.3389/fmicb.2015.00381. eCollection 2015. PubMed PMID: 26005436 (cited by -; 0; 1)

  2014:
  

  47: Henningham A, Yamaguchi M, Aziz RK, Kuipers K, Buffalo CZ, Dahesh S, Choudhury B, Van Vleet J, Yamaguchi Y, Seymour LM, Ben Zakour NL, He L, Smith HV, Grimwood K, Beatson SA, Ghosh P, Walker MJ, Nizet V, Cole JN.
  Mutual exclusivity of hyaluronan and hyaluronidase in invasive group A Streptococcus. J Biol Chem. 2014 Nov 14;289(46):32303-15. doi: 10.1074/jbc.M114.602847. Epub 2014 Sep 29. PubMed PMID: 25266727. (cited by 5; 5; 8)

  46: Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA.
  A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014 Jul 24;5:4498. doi: 10.1038/ncomms5498. PubMed PMID: 25058116; PubMed Central PMCID: PMC4111155. (cited by 47; 53; 73)

  45: van Sorge NM, Cole JN, Kuipers K, Henningham A, Aziz RK, Kasirer-Friede A, Lin L, Berends ET, Davies MR, Dougan G, Zhang F, Dahesh S, Shaw L, Gin J, Cunningham M, Merriman JA, H端tter J, Lepenies B, Rooijakkers SH, Malley R, Walker MJ, Shattil SJ, Schlievert PM, Choudhury B, Nizet V.
  The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design. Cell Host Microbe. 2014 Jun 11;15(6):729-40. doi:10.1016/j.chom.2014.05.009. PubMed PMID: 24922575; PubMed Central PMCID: PMC4078075. (cited by 1; 0; 4)

  44: ElRakaiby M, Dutilh BE, Rizkallah MR, Boleij A, Cole JN, Aziz RK*.
  Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. OMICS. 2014 Jul;18(7):402-14. doi: 10.1089/omi.2014.0018. Epub 2014 May 2. PubMed PMID: 24785449; PubMed Central PMCID: PMC4086029. (cited by 1; 1; 109)

  2013:
  

  43:Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BO.
  Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci USA. 2013 Nov 25. [Epub ahead of print] PubMed PMID: 24277855. (cited by 45; 46; 75)

  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 2; 3; 5)

  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 11; 10; 14)

  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 -; 2; 3)

  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 16; 16; 28)

  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 10; 13; 15)

  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 7; 9; 10)

  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 -; 5; 5)

  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 19; 19; 32)

  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 -; 14; 16)

  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 -; 10; 12)

  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 14; 14; 16)

  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 -; 13; 15)

  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 62; 63; 108)

  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 16; 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 67; 68; 84)

  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 1227; 1226; 2322)
  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 158; 158; 196)
  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 254; 268; 369)
  Article rated by Faculty of 1000 'Must Read' F1000 Factor 4.8

  
  2001-2005:
  

  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)

  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)

  ---

• Genome Reports/Announcements: (3)

  3: Elkenawy NM, Youssef NH, Aziz RK, Amin MA, Yassin AS.
  Draft genome sequence of a prodigiosin-hyperproducing Serratia marcescens strain isolated from Cairo, Egypt. G3 (Bethesda). 2021 Sep 27;11(10):jkab284. doi: 10.1093/g3journal/jkab284. (cited by -; -; -)

  2: Attia H, Szubin R, Yassin AS, Monk JM, Aziz RK*.
  Draft Genome sequences of four metallo-beta-lactamase-producing multidrug-resistant Klebsiella pneumoniae clinical isolates, including two colistin-resistant strains, from Cairo, Egypt. Microbiol Resour Announc. 2019 Feb 14;8(7). pii: e01418-18. doi: 10.1128/MRA.01418-18. eCollection 2019 Feb. PubMed PMID: 30801061. (cited by -; -; 5)

  1: Latif H, Li HJ, Charusanti P, Palsson BO, Aziz RK*.
  A gapless, unambiguous genome sequence of the enterohemorrhagic Escherichia coli O157:H7 strain EDL933.Genome Announc. 2014 Aug 14;2(4). pii: e00821-14. doi: 10.1128/genomeA.00821-14. PubMed PMID: 25125650; PubMed Central PMCID: PMC4132626. (cited by -; -; 53)

  ---

• Book:

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

  ---

• Book Chapters: (8)

  (including conference talks published as full articles in books or journals' special issues)

  8: Speicher DJ, Aziz RK.
  Profiling the Human Oral Mycobiome in Tissue and Saliva Using ITS2 DNA Metabarcoding Compared to a Fungal-Specific Database. PMID: 34410650. doi: 10.1007/978-1-0716-1518-8_15.
  In: The Oral Microbiome. Methods Mol Biol. 2021;2327:253-269. doi: 10.1007/978-1-0716-1518-8_15. Edited by: Adami GR. (ISBN: 978-1-0716-1517-1) Humana Press- Springer.

  7: McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R
  Phage Genome Annotation using the RAST Pipeline In: Bacteriophages: Methods and Protocols, Volume 3. Edited by: Clokie MRJ, Kropinski A, Lavigne R. (ISBN: 978-1-4939-7341-5) - Springer

  6: Aziz RK*, Ackermann H-W, Petty NK, Kropinski A.
  Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis In: Bacteriophages: Methods and Protocols, Volume 3. Edited by: Clokie MRJ, Kropinski A, Lavigne R. (ISBN: 978-1-4939-7341-5) - Springer

  5: Dutilh BE and Aziz RK*.
  Genomes, Metagenomes, and Microbiomes: A New Biology for a New Millennium. In New Life Sciences: Linking Science to Society. 2013. In: TWAS/ Biovision Alexandria.NXT 2012, Alexandria, Egypt. Edited by: Serageldin I and Yahia M. (ISBN: 978-977-452-226-8)

  4: Aziz RK* and Binfield P.
  Open Access: The Next Revolution in Scholarly Publishing. In Publishing Scientific Papers in the Developing World. 2012. TWAS/ Biovision Alexandria.NXT 2010, Alexandria, Egypt. Edited by: Serageldin I and Massoud E. (ISBN: 978-977-452-209-3).

  3: 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

  2: 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

  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)

  ---

• Publications in Local Journals: (3)

  3: Mohamed, A.A., Hemeda, A.A., Aziz, R.K, Abdel-Hakeem MS, Ali-Tammam M.
  Body mass index (BMI) and alpha-fetoprotein (AFP) level correlate with the severity of HCV-induced fibrosis in a cohort of Egyptian patients with chronic HCV. Futur J Pharm Sci. 2020 Oct; 6(1), 71. https://doi.org/10.1186/s43094-020-00085-3 . (cited by 2)

  2: Hamed DM, Yassin AS, Aziz RK, Amin MA.
  Detection of beta-lactamase genes in Bacillus cereus isolated from food samples in Egypt. N Egypt J Microbiol. 2012 33:11-22.

  1: Aziz RK*.
  Bioinformatic analysis of streptococcal peptidoglycan deacetylases family that confers resistance to lysozyme. Bulletin Fac Pharm Cairo Univ. 2008.

  ---

• Published Conference Proceedings: (17)

  17: Attia H, Sallam IE, Abdelwareth A, Mira A, Khattab RA, Yassin AS, Farag MA, Aziz RK.
  Investigating potential chemoprotective role of pomegranate juice through analyzing its reciprocal interactions with the gut microbiota. Journal of Clinical Gastroenterology. 2020. 54, S22-S22 Supplement: 1

  16: Ghattas MZ, Elrakaiby MT, Aziz RK, Zedan HH.
  Investigation of competition between staphylococcal members of the human nasal microbiota and multi-resistant S. Aureus. Journal of Clinical Gastroenterology. 2018. 52, S90-S91

  15: Saif NA, Amin HM, Aziz RK.
  Variable distribution patterns of fucose utilization genes and pathways in Enterobacteria and their potential role in gut microbiome communication with passenger bacteria. Journal of Clinical Gastroenterology. 2018. 52, S109-S109

  14: Ghattas MZ, ElRakaiby M, Aziz RK, Zedan HH.
  Pilot investigation of the competition between commensal and pathogenic staphylococci within the human nasal microbiome. In: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proceedings. 2017. 11 (9), 9. P3

  13: Elmassry M, ElRakaiby, M, Aziz RK.
  Human vs. Nature: Islands and bridges within the microbiome continuum.In: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proceedings. 2017. 11 (9), 9. P4

  12: Lotfy M, Elmassry M, Marcel J, Khattab RA, Abdelfattah MM, Gilbert JA, Aziz RK.
  Role of the human eye microbiome in development of conjunctivitis.In: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proceedings. 2017. 11 (9), 9. P5

  11: Lotfy M, Elmassry M, Marcel J, Khattab RA, Abdelfattah MM, Gilbert JA, Aziz RK.
  An inside job: the role of human eye microbiome in development of conjunctivitis. F1000Research. 2016. Posters 5: 788

  10: Henningham A, Yamaguchi M, Aziz RK, Kuipers K, Dahesh S, Yamaguchi Y, Seymour L, Ben Zakour N, He L, Smith H, Grimwood K, Beatson S, Walker M, Nizet V,Cole JN.
  Nonencapsulated group A Streptococcus associated with human invasive disease. FASEB J. 2014. 28 (1) Supplement 790.1

  9: Cole JN, van Sorge N, Kuipers K, Henningham A, Aziz RK, Kasirer-Friede A, Lin L, Berends E, Davies M, Dougan G, Zhang F, Dahesh S, Shaw L, Gin J, Cunningham M, Merriman J, Rooijakkers S, Malley R, Walker M, Shattil S, Schlievert P, Choudhury B, Nizet V.
  Genetics and virulence role of the classical group A Streptococcus Lancefield antigen. FASEB J. 2014. 28 (1) Supplement 790.2

  8: Aziz RK, Dwivedi B, Breitbart M, Edwards RA.
  Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets. BMC Bioinformatics. 2011; 12(Suppl 7): A9. Published online 2011 August 5. doi: 10.1186/1471-2105-12-S7-A9 PMCID: PMC3194218

  7: Aziz RK, Saad R, Rizkallah MR.
  PharmacoMicrobiomics or how bugs modulate drugs: an educational initiative to explore the effects of human microbiome on drugs BMC Bioinformatics. 2011; 12(Suppl 7): A10. Published online 2011 August 5. doi: 10.1186/1471-2105-12-S7-A10 PMCID: PMC3194200

  6: Aziz RK
  In silico analysis of a family of extracellular polysaccharide deacetylases involved in virulence of pathogenic gram-positive cocci BMC Bioinformatics. 2010; 11(Suppl 4): P8. Published online 2010 July 23. doi: 10.1186/1471-2105-11-S4-P8 PMCID: PMC3290091

  5: Mahmoud AA, Aziz RK
  Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives? BMC Bioinformatics. 2010; 11(Suppl 4): P28. Published online 2010 July 23. doi: 10.1186/1471-2105-11-S4-P28 PMCID: PMC3290082

  4: Aziz RK, Aronow BJ, Taylor WL, Rowe SL, Kansal R, Walker MJ, Kotb M.
  Integrating neighbor clustering, coexpression clustering and subsystems analysis to define dynamic changes in regulatory networks associated with group A streptococcal sociomicrobiology and niche adaptation BMC Bioinformatics. 2010; 11(Suppl 4): P12. Published online 2010 July 23. doi: 10.1186/1471-2105-11-S4-P12 PMCID: PMC3290066

  3: Aziz RK
  Subsystems-based servers for rapid annotation of genomes and metagenomes BMC Bioinformatics. 2010; 11(Suppl 4): O2. Published online 2010 July 23. doi: 10.1186/1471-2105-11-S4-O2 PMCID: PMC3290056

  2: 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
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  1: 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