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Results: 1 to 20 of 128

1.

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.

PMID:
25719748
[PubMed - in process]
Free Article
2.

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.

PMID:
25555223
[PubMed - in process]
3.

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.

PMID:
25456219
[PubMed - in process]
4.

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 28;43(Database issue):D187-92. doi: 10.1093/nar/gku1167. Epub 2014 Nov 15.

PMID:
25399417
[PubMed - in process]
Free Article
5.

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

Raies AB, Mansour H, Incitti R, Bajic VB.

Nucleic Acids Res. 2015 Jan 28;43(Database issue):D879-86. doi: 10.1093/nar/gku1168. Epub 2014 Nov 14.

PMID:
25398897
[PubMed - in process]
Free Article
6.

Distinct profiling of antimicrobial peptide families.

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

Bioinformatics. 2014 Nov 10. pii: btu738. [Epub ahead of print]

PMID:
25388148
[PubMed - as supplied by publisher]
Free Article
7.

DEEP: a general computational framework for predicting enhancers.

Kleftogiannis D, Kalnis P, Bajic VB.

Nucleic Acids Res. 2015 Jan 9;43(1):e6. doi: 10.1093/nar/gku1058. Epub 2014 Nov 5.

PMID:
25378307
[PubMed - in process]
Free PMC Article
8.

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.

PMID:
25356733
[PubMed - in process]
Free PMC Article
9.

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.

PMID:
25326239
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
25295031
[PubMed]
Free PMC Article
11.

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.

PMID:
25275320
[PubMed - in process]
Free PMC Article
12.

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.

PMID:
24921648
[PubMed - in process]
Free PMC Article
13.

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.

PMID:
24785133
[PubMed - indexed for MEDLINE]
14.

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.

PMID:
24778629
[PubMed]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
24692632
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassman T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

PMID:
24670764
[PubMed - indexed for MEDLINE]
18.

Effects of cytosine methylation on transcription factor binding sites.

Medvedeva YA, Khamis AM, Kulakovskiy IV, Ba-Alawi W, Bhuyan MS, Kawaji H, Lassmann T, Harbers M, Forrest AR, Bajic VB; FANTOM consortium.

BMC Genomics. 2014 Mar 26;15:119. doi: 10.1186/1471-2164-15-119.

PMID:
24669864
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
24399144
[PubMed - indexed for MEDLINE]
20.

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

Alam I, Antunes A, Kamau AA, Ba Alawi W, Kalkatawi M, Stingl U, Bajic VB.

PLoS One. 2013 Dec 6;8(12):e82210. doi: 10.1371/journal.pone.0082210. eCollection 2013.

PMID:
24324765
[PubMed - indexed for MEDLINE]
Free PMC Article
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