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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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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 ET, Davies MR, Dougan G, Zhang F, Dahesh S, Shaw L, Gin J, Cunningham M, Merriman JA, Hütter J, Lepenies B, Rooijakkers SH, Malley R, Walker MJ, Shattil SJ, Schlievert PM, Choudhury B, Nizet V.

Cell Host Microbe. 2014 Jun 11;15(6):729-40. doi: 10.1016/j.chom.2014.05.009.


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.


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.


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.


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.


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.


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.

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