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Items: 1 to 20 of 143


Mining Chemical Activity Status from High-Throughput Screening Assays.

Soufan O, Ba-Alawi W, Afeef M, Essack M, Rodionov V, Kalnis P, Bajic VB.

PLoS One. 2015 Dec 14;10(12):e0144426. doi: 10.1371/journal.pone.0144426. eCollection 2015.


Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs.

Jimenez-Infante F, Ngugi DK, Vinu M, Alam I, Kamau AA, Blom J, Bajic VB, Stingl U.

Appl Environ Microbiol. 2015 Dec 11;82(4):1215-26. doi: 10.1128/AEM.02852-15.


Progress and challenges in bioinformatics approaches for enhancer identification.

Kleftogiannis D, Kalnis P, Bajic VB.

Brief Bioinform. 2015 Dec 3. pii: bbv101. [Epub ahead of print]


The Value and Significance of Metagenomics of Marine Environments.

Zhao F, Bajic VB.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):271-4. doi: 10.1016/j.gpb.2015.10.002. Epub 2015 Nov 27. No abstract available.


HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D116-25. doi: 10.1093/nar/gkv1249. Epub 2015 Nov 19.


Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea - A Metagenomic Approach.

Simões MF, Antunes A, Ottoni CA, Amini MS, Alam I, Alzubaidy H, Mokhtar NA, Archer JA, Bajic VB.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):310-20. doi: 10.1016/j.gpb.2015.07.002. Epub 2015 Nov 5.


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.


First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea.

Antunes A, Alam I, Simões MF, Daniels C, Ferreira AJ, Siam R, El-Dorry H, Bajic VB.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):304-9. doi: 10.1016/j.gpb.2015.06.004. Epub 2015 Oct 31.


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.


DENdb: database of integrated human enhancers.

Ashoor H, Kleftogiannis D, Radovanovic A, Bajic VB.

Database (Oxford). 2015 Sep 5;2015. pii: bav085. doi: 10.1093/database/bav085. Print 2015.


BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

Kalkatawi M, Alam I, Bajic VB.

BMC Genomics. 2015 Aug 18;16:616. doi: 10.1186/s12864-015-1826-4.


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.


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; Fantom Consortium, Brombacher F, Suzuki H.

Nucleic Acids Res. 2015 Aug 18;43(14):6969-82. doi: 10.1093/nar/gkv646. Epub 2015 Jun 27.


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.

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