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Items: 31

1.

Marine biofilms constitute a bank of hidden microbial diversity and functional potential.

Zhang W, Ding W, Li YX, Tam C, Bougouffa S, Wang R, Pei B, Chiang H, Leung P, Lu Y, Sun J, Fu H, Bajic VB, Liu H, Webster NS, Qian PY.

Nat Commun. 2019 Jan 31;10(1):517. doi: 10.1038/s41467-019-08463-z.

2.

A multidrug resistant clinical P. aeruginosa isolate in the MLST550 clonal complex: uncoupled quorum sensing modulates the interplay of virulence and resistance.

Cao H, Xia T, Li Y, Xu Z, Bougouffa S, Lo YK, Bajic VB, Luo H, Woo PCY, Yan A.

Antimicrob Agents Chemother. 2019 Jan 22. pii: AAC.01944-18. doi: 10.1128/AAC.01944-18. [Epub ahead of print]

PMID:
30670423
3.

The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance.

Razali R, Bougouffa S, Morton MJL, Lightfoot DJ, Alam I, Essack M, Arold ST, Kamau AA, Schmöckel SM, Pailles Y, Shahid M, Michell CT, Al-Babili S, Ho YS, Tester M, Bajic VB, Negrão S.

Front Plant Sci. 2018 Oct 4;9:1402. doi: 10.3389/fpls.2018.01402. eCollection 2018.

4.

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

Othoum G, Bougouffa S, Razali R, Bokhari A, Alamoudi S, Antunes A, Gao X, Hoehndorf R, Arold ST, Gojobori T, Hirt H, Mijakovic I, Bajic VB, Lafi FF, Essack M.

BMC Genomics. 2018 May 22;19(1):382. doi: 10.1186/s12864-018-4796-5.

5.

Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean's Deepest Point.

Zhang W, Tian RM, Sun J, Bougouffa S, Ding W, Cai L, Lan Y, Tong H, Li Y, Jamieson AJ, Bajic VB, Drazen JC, Bartlett D, Qian PY.

mSystems. 2018 Apr 10;3(3). pii: e00009-18. doi: 10.1128/mSystems.00009-18. eCollection 2018 May-Jun.

6.

Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts.

An R, Lin P, Bougouffa S, Essack M, Boxrud D, Bajic VB, Vidovic S.

Genome Announc. 2018 Jan 25;6(4). pii: e01550-17. doi: 10.1128/genomeA.01550-17.

7.

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.

Salhi A, Negrão S, Essack M, Morton MJL, Bougouffa S, Razali R, Radovanovic A, Marchand B, Kulmanov M, Hoehndorf R, Tester M, Bajic VB.

Sci Rep. 2017 Jul 20;7(1):5968. doi: 10.1038/s41598-017-05448-0.

8.
9.

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.

Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, LaJeunesse TC, Voolstra CR.

Sci Rep. 2016 Dec 22;6:39734. doi: 10.1038/srep39734.

10.

bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli.

Shahmuradov IA, Mohamad Razali R, Bougouffa S, Radovanovic A, Bajic VB.

Bioinformatics. 2017 Feb 1;33(3):334-340. doi: 10.1093/bioinformatics/btw629.

11.

Metagenomics as a preliminary screen for antimicrobial bioprospecting.

Al-Amoudi S, Razali R, Essack M, Amini MS, Bougouffa S, Archer JA, Lafi FF, Bajic VB.

Gene. 2016 Dec 15;594(2):248-258. doi: 10.1016/j.gene.2016.09.021. Epub 2016 Sep 15.

12.

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.

Al-Amoudi S, Essack M, Simões MF, Bougouffa S, Soloviev I, Archer JA, Lafi FF, Bajic VB.

Mar Drugs. 2016 Sep 10;14(9). pii: E165. doi: 10.3390/md14090165.

13.

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge.

Cao H, Dong C, Bougouffa S, Li J, Zhang W, Shao Z, Bajic VB, Qian PY.

Sci Rep. 2016 Mar 8;6:22842. doi: 10.1038/srep22842.

14.

DESM: portal for microbial knowledge exploration systems.

Salhi A, Essack M, Radovanovic A, Marchand B, Bougouffa S, Antunes A, Simoes MF, Lafi FF, Motwalli OA, Bokhari A, Malas T, Amoudi SA, Othum G, Allam I, Mineta K, Gao X, Hoehndorf R, C Archer JA, Gojobori T, Bajic VB.

Nucleic Acids Res. 2016 Jan 4;44(D1):D624-33. doi: 10.1093/nar/gkv1147. Epub 2015 Nov 5.

15.

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea.

Alzubaidy H, Essack M, Malas TB, Bokhari A, Motwalli O, Kamanu FK, Jamhor SA, Mokhtar NA, Antunes A, Simões MF, Alam I, Bougouffa S, Lafi FF, Bajic VB, Archer JA.

Gene. 2016 Feb 1;576(2 Pt 1):626-36. doi: 10.1016/j.gene.2015.10.032. Epub 2015 Nov 10.

16.

Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool.

Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li Y, Cai L, Wong YH, Zhang G, Zhou G, Zhang X, Bajic VB, Al-Suwailem A, Qian PY.

Environ Microbiol. 2015 Oct;17(10):4089-104. doi: 10.1111/1462-2920.12978. Epub 2015 Aug 17.

PMID:
26171930
17.

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

Tian RM, Lee OO, Wang Y, Cai L, Bougouffa S, Chiu JM, Wu RS, Qian PY.

Front Microbiol. 2015 Jan 14;5:799. doi: 10.3389/fmicb.2014.00799. eCollection 2014.

18.

Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

Tian RM, Wang Y, Bougouffa S, Gao ZM, Cai L, Zhang WP, Bajic V, Qian PY.

MBio. 2014 Nov 4;5(6):e01980. doi: 10.1128/mBio.01980-14.

19.

DEOP: a database on osmoprotectants and associated pathways.

Bougouffa S, Radovanovic A, Essack M, Bajic VB.

Database (Oxford). 2014 Oct 17;2014. pii: bau100. doi: 10.1093/database/bau100. Print 2014.

20.

Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system.

Zhang WP, Wang Y, Tian RM, Bougouffa S, Yang B, Cao HL, Zhang G, Wong YH, Xu W, Batang Z, Al-Suwailem A, Zhang XX, Qian PY.

Sci Rep. 2014 Oct 17;4:6647. doi: 10.1038/srep06647.

21.

Transcriptome analysis elucidates key developmental components of bryozoan lophophore development.

Wong YH, Ryu T, Seridi L, Ghosheh Y, Bougouffa S, Qian PY, Ravasi T.

Sci Rep. 2014 Oct 10;4:6534. doi: 10.1038/srep06534.

22.

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge.

Tian RM, Wang Y, Bougouffa S, Gao ZM, Cai L, Bajic V, Qian PY.

Environ Microbiol. 2014 Nov;16(11):3548-61. doi: 10.1111/1462-2920.12586. Epub 2014 Aug 29.

PMID:
25088944
23.

Pyrosequencing reveals the microbial communities in the Red Sea sponge Carteriospongia foliascens and their impressive shifts in abnormal tissues.

Gao ZM, Wang Y, Lee OO, Tian RM, Wong YH, Bougouffa S, Batang Z, Al-Suwailem A, Lafi FF, Bajic VB, Qian PY.

Microb Ecol. 2014 Oct;68(3):621-32. doi: 10.1007/s00248-014-0419-0. Epub 2014 Apr 24.

PMID:
24760170
24.

Toward understanding the dynamics of microbial communities in an estuarine system.

Zhang W, Bougouffa S, Wang Y, Lee OO, Yang J, Chan C, Song X, Qian PY.

PLoS One. 2014 Apr 14;9(4):e94449. doi: 10.1371/journal.pone.0094449. eCollection 2014.

25.

Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis.

Wang Y, Tian RM, Gao ZM, Bougouffa S, Qian PY.

PLoS One. 2014 Mar 3;9(3):e90053. doi: 10.1371/journal.pone.0090053. eCollection 2014.

26.

In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system.

Lee OO, Wang Y, Tian R, Zhang W, Shek CS, Bougouffa S, Al-Suwailem A, Batang ZB, Xu W, Wang GC, Zhang X, Lafi FF, Bajic VB, Qian PY.

Sci Rep. 2014 Jan 8;4:3587. doi: 10.1038/srep03587.

27.

Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent Red Sea brine pools.

Wang Y, Cao H, Zhang G, Bougouffa S, Lee OO, Al-Suwailem A, Qian PY.

Sci Rep. 2013;3:1748. doi: 10.1038/srep01748.

28.

Distinctive microbial community structure in highly stratified deep-sea brine water columns.

Bougouffa S, Yang JK, Lee OO, Wang Y, Batang Z, Al-Suwailem A, Qian PY.

Appl Environ Microbiol. 2013 Jun;79(11):3425-37. doi: 10.1128/AEM.00254-13. Epub 2013 Mar 29.

29.

Spatial and species variations in bacterial communities associated with corals from the Red Sea as revealed by pyrosequencing.

Lee OO, Yang J, Bougouffa S, Wang Y, Batang Z, Tian R, Al-Suwailem A, Qian PY.

Appl Environ Microbiol. 2012 Oct;78(20):7173-84. Epub 2012 Aug 3.

30.

SitesIdentify: a protein functional site prediction tool.

Bray T, Chan P, Bougouffa S, Greaves R, Doig AJ, Warwicker J.

BMC Bioinformatics. 2009 Nov 18;10:379. doi: 10.1186/1471-2105-10-379.

31.

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