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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 Jul 14. doi: 10.1111/1462-2920.12978. [Epub ahead of print]


Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, Guler R, Consortium F, Brombacher F, Suzuki H.

Nucleic Acids Res. 2015 Jun 27. pii: gkv646. [Epub ahead of print]


Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora.

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

PeerJ. 2015 Jun 11;3:e890. doi: 10.7717/peerj.890. eCollection 2015.


Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera.

Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB.

Sci Rep. 2015 Jun 15;5:11136. doi: 10.1038/srep11136.


DWFS: a wrapper feature selection tool based on a parallel genetic algorithm.

Soufan O, Kleftogiannis D, Kalnis P, Bajic VB.

PLoS One. 2015 Feb 26;10(2):e0117988. doi: 10.1371/journal.pone.0117988. eCollection 2015.


Hepatic proteomic responses in marine medaka (Oryzias melastigma) chronically exposed to antifouling compound butenolide [5-octylfuran-2(5H)-one] or 4,5-dichloro-2-N-octyl-4-isothiazolin-3-one (DCOIT).

Chen L, Sun J, Zhang H, Au DW, Lam PK, Zhang W, Bajic VB, Qiu JW, Qian PY.

Environ Sci Technol. 2015 Feb 3;49(3):1851-9. doi: 10.1021/es5046748. Epub 2015 Jan 16.


Proteomic changes in brain tissues of marine medaka (Oryzias melastigma) after chronic exposure to two antifouling compounds: butenolide and 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT).

Chen L, Zhang H, Sun J, Wong YH, Han Z, Au DW, Bajic VB, Qian PY.

Aquat Toxicol. 2014 Dec;157:47-56. doi: 10.1016/j.aquatox.2014.09.010. Epub 2014 Oct 2.


LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z.

Nucleic Acids Res. 2015 Jan;43(Database issue):D187-92. doi: 10.1093/nar/gku1167. Epub 2014 Nov 15.


DDMGD: the database of text-mined associations between genes methylated in diseases from different species.

Bin Raies A, Mansour H, Incitti R, Bajic VB.

Nucleic Acids Res. 2015 Jan;43(Database issue):D879-86. doi: 10.1093/nar/gku1168. Epub 2014 Nov 14.


Distinct profiling of antimicrobial peptide families.

Khamis AM, Essack M, Gao X, Bajic VB.

Bioinformatics. 2015 Mar 15;31(6):849-56. doi: 10.1093/bioinformatics/btu738. Epub 2014 Nov 10.


DEEP: a general computational framework for predicting enhancers.

Kleftogiannis D, Kalnis P, Bajic VB.

Nucleic Acids Res. 2015 Jan;43(1):e6. doi: 10.1093/nar/gku1058. Epub 2014 Nov 5.


Chemical compounds toxic to invertebrates isolated from marine cyanobacteria of potential relevance to the agricultural industry.

Essack M, Alzubaidy HS, Bajic VB, Archer JA.

Toxins (Basel). 2014 Oct 29;6(11):3058-76. doi: 10.3390/toxins6113058. Review.


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.


Aerobic methanotrophic communities at the Red Sea brine-seawater interface.

Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R.

Front Microbiol. 2014 Sep 23;5:487. doi: 10.3389/fmicb.2014.00487. eCollection 2014.


Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes.

Alam T, Medvedeva YA, Jia H, Brown JB, Lipovich L, Bajic VB.

PLoS One. 2014 Oct 2;9(10):e109443. doi: 10.1371/journal.pone.0109443. eCollection 2014.


Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

Ferreira AJ, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, Stingl U, Archer JA, Jankovic BR, Sogin M, Bajic VB, El-Dorry H.

PLoS One. 2014 Jun 12;9(6):e97338. doi: 10.1371/journal.pone.0097338. eCollection 2014.


Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats.

Jimenez-Infante F, Ngugi DK, Alam I, Rashid M, Baalawi W, Kamau AA, Bajic VB, Stingl U.

FEMS Microbiol Ecol. 2014 Jul;89(1):181-97. doi: 10.1111/1574-6941.12348. Epub 2014 May 22.


Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

Grötzinger SW, Alam I, Ba Alawi W, Bajic VB, Stingl U, Eppinger J.

Front Microbiol. 2014 Apr 7;5:134. doi: 10.3389/fmicb.2014.00134. eCollection 2014.


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.


Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus spongiarum".

Gao ZM, Wang Y, Tian RM, Wong YH, Batang ZB, Al-Suwailem AM, Bajic VB, Qian PY.

MBio. 2014 Apr 1;5(2):e00079-14. doi: 10.1128/mBio.00079-14.

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