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Items: 1 to 50 of 74

1.

Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates.

Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM.

Front Cell Infect Microbiol. 2019 May 24;9:161. doi: 10.3389/fcimb.2019.00161. eCollection 2019.

2.

Two putative MmpL homologs contribute to antimicrobial resistance and nephropathy of enterohemorrhagic E. coli O157:H7.

Hussein SH, Samir R, Aziz RK, Toama MA.

Gut Pathog. 2019 Apr 18;11:15. doi: 10.1186/s13099-019-0296-7. eCollection 2019.

3.

Azoreductase activity of dye-decolorizing bacteria isolated from the human gut microbiota.

Zahran SA, Ali-Tammam M, Hashem AM, Aziz RK, Ali AE.

Sci Rep. 2019 Apr 2;9(1):5508. doi: 10.1038/s41598-019-41894-8.

4.

Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool.

Ziko L, Saqr AA, Ouf A, Gimpel M, Aziz RK, Neubauer P, Siam R.

Microb Cell Fact. 2019 Mar 18;18(1):56. doi: 10.1186/s12934-019-1103-3.

5.

Novel blaCTX-M variants and genotype-phenotype correlations among clinical isolates of extended spectrum beta lactamase-producing Escherichia coli.

Ramadan AA, Abdelaziz NA, Amin MA, Aziz RK.

Sci Rep. 2019 Mar 12;9(1):4224. doi: 10.1038/s41598-019-39730-0.

6.

Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt.

Attia H, Szubin R, Yassin AS, Monk JM, Aziz RK.

Microbiol Resour Announc. 2019 Feb 14;8(7). pii: e01418-18. doi: 10.1128/MRA.01418-18. eCollection 2019 Feb.

7.

Toxicomicrobiomics: Narrowing the Gap Between Environmental and Medicinal Toxicogenomics.

Aziz RK.

OMICS. 2018 Dec;22(12):788-789. doi: 10.1089/omi.2018.0183. Review. No abstract available.

PMID:
30571608
8.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

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.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

PMID:
30556814
9.

Thermal Stability of a Mercuric Reductase from the Red Sea Atlantis II Hot Brine Environment as Analyzed by Site-Directed Mutagenesis.

Maged M, El Hosseiny A, Saadeldin MK, Aziz RK, Ramadan E.

Appl Environ Microbiol. 2019 Jan 23;85(3). pii: e02387-18. doi: 10.1128/AEM.02387-18. Print 2019 Feb 1.

PMID:
30446558
10.

Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions.

Aziz RK, Hegazy SM, Yasser R, Rizkallah MR, ElRakaiby MT.

Expert Opin Drug Metab Toxicol. 2018 Oct;14(10):1043-1055. doi: 10.1080/17425255.2018.1530216. Epub 2018 Oct 9. Review.

PMID:
30269615
11.

Determination of voriconazole and co-administered drugs in plasma of pediatric cancer patients using UPLC-MS/MS: A key step towards personalized therapeutics.

Al-Ghobashy MA, Kamal SM, El-Sayed GM, Attia AK, Nagy M, ElZeiny A, Elrakaiby MT, Nooh MM, Abbassi M, Aziz RK.

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.

PMID:
30008305
12.

Interview with Prof. Ramy K. Aziz, Cairo University. The Dawn of Pharmacomicrobiomics.

Aziz RK.

OMICS. 2018 Apr;22(4):295-297. doi: 10.1089/omi.2018.0041. No abstract available.

PMID:
29652572
13.

Quercetin 3-O-glucoside recovered from the wild Egyptian Sahara plant, Euphorbia paralias L., inhibits glutamine synthetase and has antimycobacterial activity.

Safwat NA, Kashef MT, Aziz RK, Amer KF, Ramadan MA.

Tuberculosis (Edinb). 2018 Jan;108:106-113. doi: 10.1016/j.tube.2017.11.005. Epub 2017 Nov 16.

PMID:
29523309
14.

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

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.

Arch Virol. 2018 Apr;163(4):1125-1129. doi: 10.1007/s00705-018-3723-z. Epub 2018 Jan 22. No abstract available.

PMID:
29356990
15.

Kullback Leibler divergence in complete bacterial and phage genomes.

Akhter S, Aziz RK, Kashef MT, Ibrahim ES, Bailey B, Edwards RA.

PeerJ. 2017 Nov 30;5:e4026. doi: 10.7717/peerj.4026. eCollection 2017.

16.

Phage Genome Annotation Using the RAST Pipeline.

McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R.

Methods Mol Biol. 2018;1681:231-238. doi: 10.1007/978-1-4939-7343-9_17.

PMID:
29134599
17.

Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis.

Aziz RK, Ackermann HW, Petty NK, Kropinski AM.

Methods Mol Biol. 2018;1681:197-215. doi: 10.1007/978-1-4939-7343-9_15.

PMID:
29134597
18.

PATRIC as a unique resource for studying antimicrobial resistance.

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.

Brief Bioinform. 2017 Jul 31. doi: 10.1093/bib/bbx083. [Epub ahead of print]

PMID:
28968762
19.

Toward the Drug Factory Microbiome: Microbial Community Variations in Antibiotic-Producing Clean Rooms.

Hamdy AM, El-Massry M, Kashef MT, Amin MA, Aziz RK.

OMICS. 2018 Feb;22(2):133-144. doi: 10.1089/omi.2017.0091. Epub 2017 Sep 5.

PMID:
28873001
20.

Biofilm formation in enterococci: genotype-phenotype correlations and inhibition by vancomycin.

Hashem YA, Amin HM, Essam TM, Yassin AS, Aziz RK.

Sci Rep. 2017 Jul 18;7(1):5733. doi: 10.1038/s41598-017-05901-0.

21.

The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli.

Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BO, Charusanti P.

Microbiol Res. 2017 Jan;194:47-52. doi: 10.1016/j.micres.2016.10.006. Epub 2016 Nov 4.

22.

Insertion sequences enrichment in extreme Red sea brine pool vent.

Elbehery AH, Aziz RK, Siam R.

Extremophiles. 2017 Mar;21(2):271-282. doi: 10.1007/s00792-016-0900-4. Epub 2016 Dec 3.

PMID:
27915389
23.

Gut microbiome alterations in patients with stage 4 hepatitis C.

Aly AM, Adel A, El-Gendy AO, Essam TM, Aziz RK.

Gut Pathog. 2016 Sep 13;8(1):42. doi: 10.1186/s13099-016-0124-2. eCollection 2016.

24.

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments.

Adel M, Elbehery AH, Aziz SK, Aziz RK, Grossart HP, Siam R.

Sci Rep. 2016 Sep 6;6:32704. doi: 10.1038/srep32704.

25.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.

Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3801-9. doi: 10.1073/pnas.1523199113. Epub 2016 Jun 10.

26.

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics.

Elbehery AH, Aziz RK, Siam R.

OMICS. 2016 Apr;20(4):229-38. doi: 10.1089/omi.2015.0191. Epub 2016 Mar 31.

PMID:
27031878
27.

Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations.

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.

Sci Rep. 2015 Nov 4;5:16025. doi: 10.1038/srep16025.

28.

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P.

Front Microbiol. 2015 Sep 23;6:958. doi: 10.3389/fmicb.2015.00958. eCollection 2015.

29.

Contaminated water as a source of Helicobacter pylori infection: A review.

Aziz RK, Khalifa MM, Sharaf RR.

J Adv Res. 2015 Jul;6(4):539-47. doi: 10.1016/j.jare.2013.07.007. Epub 2013 Jul 21. Review.

30.

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.

Aziz RK, Dwivedi B, Akhter S, Breitbart M, Edwards RA.

Front Microbiol. 2015 May 8;6:381. doi: 10.3389/fmicb.2015.00381. eCollection 2015.

31.

Mutual exclusivity of hyaluronan and hyaluronidase in invasive group A Streptococcus.

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.

J Biol Chem. 2014 Nov 14;289(46):32303-15. doi: 10.1074/jbc.M114.602847. Epub 2014 Sep 29.

32.

A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.

Latif H, Li HJ, Charusanti P, Palsson BØ, Aziz RK.

Genome Announc. 2014 Aug 14;2(4). pii: e00821-14. doi: 10.1128/genomeA.00821-14.

33.

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.

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.

Nat Commun. 2014 Jul 24;5:4498. doi: 10.1038/ncomms5498.

34.

The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design.

van Sorge NM, Cole JN, Kuipers K, Henningham A, Aziz RK, Kasirer-Friede A, Lin L, Berends ETM, Davies MR, Dougan G, Zhang F, Dahesh S, Shaw L, Gin J, Cunningham M, Merriman JA, Hütter J, Lepenies B, Rooijakkers SHM, Malley R, Walker MJ, Shattil SJ, Schlievert PM, Choudhury B, Nizet V.

Cell Host Microbe. 2014 Jun 11;15(6):729-740. doi: 10.1016/j.chom.2014.05.009.

35.

Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

ElRakaiby M, Dutilh BE, Rizkallah MR, Boleij A, Cole JN, Aziz RK.

OMICS. 2014 Jul;18(7):402-14. doi: 10.1089/omi.2014.0018. Epub 2014 May 2. Review.

36.

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.

Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25.

37.

Applying Shannon's information theory to bacterial and phage genomes and metagenomes.

Akhter S, Bailey BA, Salamon P, Aziz RK, Edwards RA.

Sci Rep. 2013;3:1033. doi: 10.1038/srep01033. Epub 2013 Jan 8.

38.

Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes.

Saad R, Rizkallah MR, Aziz RK.

Gut Pathog. 2012 Nov 30;4(1):16. doi: 10.1186/1757-4749-4-16.

39.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

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.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

40.

A conserved UDP-glucose dehydrogenase encoded outside the hasABC operon contributes to capsule biogenesis in group A Streptococcus.

Cole JN, Aziz RK, Kuipers K, Timmer AM, Nizet V, van Sorge NM.

J Bacteriol. 2012 Nov;194(22):6154-61. doi: 10.1128/JB.01317-12. Epub 2012 Sep 7.

41.

Tracing the evolutionary history of the pandemic group A streptococcal M1T1 clone.

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.

FASEB J. 2012 Nov;26(11):4675-84. doi: 10.1096/fj.12-212142. Epub 2012 Aug 9.

42.

The important role of inflammatory biomarkers pre and post bare-metal and drug-eluting stent implantation.

Khouzam RN, Shaheen M, Aziz RK, Ibebuogu UN.

Can J Cardiol. 2012 Nov-Dec;28(6):700-5. doi: 10.1016/j.cjca.2012.05.012. Epub 2012 Jul 21. Review.

PMID:
22819358
43.

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.

Akhter S, Aziz RK, Edwards RA.

Nucleic Acids Res. 2012 Sep;40(16):e126. doi: 10.1093/nar/gks406. Epub 2012 May 14.

44.

Towards an Ecology of Collective Innovation: Human Variome Project (HVP), Rare Disease Consortium for Autosomal Loci (RaDiCAL) and Data-Enabled Life Sciences Alliance (DELSA).

Ozdemir V, Rosenblatt DS, Warnich L, Srivastava S, Tadmouri GO, Aziz RK, Reddy PJ, Manamperi A, Dove ES, Joly Y, Zawati MH, Hızel C, Yazan Y, John L, Vaast E, Ptolemy AS, Faraj SA, Kolker E, Cotton RG.

Curr Pharmacogenomics Person Med. 2011 Dec 1;9(4):243-251. No abstract available.

45.

Nutriproteomics and Proteogenomics: Cultivating Two Novel Hybrid Fields of Personalized Medicine with Added Societal Value.

Ozdemir V, Armengaud J, Dubé L, Aziz RK, Knoppers BM.

Curr Pharmacogenomics Person Med. 2010 Dec 1;8(4):240-244. No abstract available.

46.

Parameters governing invasive disease propensity of non-M1 serotype group A streptococci.

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.

J Innate Immun. 2010;2(6):596-606. doi: 10.1159/000317640. Epub 2010 Sep 2.

47.

Microevolution of group A streptococci in vivo: capturing regulatory networks engaged in sociomicrobiology, niche adaptation, and hypervirulence.

Aziz RK, Kansal R, Aronow BJ, Taylor WL, Rowe SL, Kubal M, Chhatwal GS, Walker MJ, Kotb M.

PLoS One. 2010 Apr 14;5(4):e9798. doi: 10.1371/journal.pone.0009798.

48.

Pathogen microevolution in high resolution.

Aziz RK, Nizet V.

Sci Transl Med. 2010 Jan 27;2(16):16ps4. doi: 10.1126/scitranslmed.3000713.

PMID:
20371473
49.

Helicobacter pylori: a poor man's gut pathogen?

Khalifa MM, Sharaf RR, Aziz RK.

Gut Pathog. 2010 Mar 31;2(1):2. doi: 10.1186/1757-4749-2-2.

50.

Transposases are the most abundant, most ubiquitous genes in nature.

Aziz RK, Breitbart M, Edwards RA.

Nucleic Acids Res. 2010 Jul;38(13):4207-17. doi: 10.1093/nar/gkq140. Epub 2010 Mar 9. Review.

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