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Items: 1 to 20 of 200


LncBook: a curated knowledgebase of human long non-coding RNAs.

Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z.

Nucleic Acids Res. 2019 Jan 31. doi: 10.1093/nar/gkz073. [Epub ahead of print] No abstract available.


CpG traffic lights are markers of regulatory regions in human genome.

Lioznova AV, Khamis AM, Artemov AV, Besedina E, Ramensky V, Bajic VB, Kulakovskiy IV, Medvedeva YA.

BMC Genomics. 2019 Feb 1;20(1):102. doi: 10.1186/s12864-018-5387-1.


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.


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]


Characterization and identification of long non-coding RNAs based on feature relationship.

Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z.

Bioinformatics. 2019 Jan 12. doi: 10.1093/bioinformatics/btz008. [Epub ahead of print]


TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers.

Kleftogiannis D, Ashoor H, Bajic VB.

Genomics Proteomics Bioinformatics. 2018 Oct;16(5):332-341. doi: 10.1016/j.gpb.2018.05.003. Epub 2018 Dec 19.


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.


LncBook: a curated knowledgebase of human long non-coding RNAs.

Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z.

Nucleic Acids Res. 2019 Jan 8;47(D1):D128-D134. doi: 10.1093/nar/gky960.


Genome sequence analysis of Zooshikella ganghwensis strain VG4 and its potential for the synthesis of antimicrobial metabolites.

Rehman ZU, Alam I, Kamau AA, Bajic VB, Leiknes T.

Biotechnol Rep (Amst). 2018 Aug 24;19:e00278. doi: 10.1016/j.btre.2018.e00278. eCollection 2018 Sep.


DES-Mutation: System for Exploring Links of Mutations and Diseases.

Kordopati V, Salhi A, Razali R, Radovanovic A, Tifratene F, Uludag M, Li Y, Bokhari A, AlSaieedi A, Bin Raies A, Van Neste C, Essack M, Bajic VB.

Sci Rep. 2018 Sep 6;8(1):13359. doi: 10.1038/s41598-018-31439-w.


DeepGSR: An optimized deep-learning structure for the recognition of genomic signals and regions.

Kalkatawi M, Magana-Mora A, Jankovic B, Bajic VB.

Bioinformatics. 2018 Sep 1. doi: 10.1093/bioinformatics/bty752. [Epub ahead of print]


BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria.

Motwalli O, Essack M, Salhi A, Hanks J, Mijakovic I, Bajic VB.

PLoS One. 2018 Aug 10;13(8):e0202002. doi: 10.1371/journal.pone.0202002. eCollection 2018.


DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches.

Olayan RS, Ashoor H, Bajic VB.

Bioinformatics. 2018 Nov 1;34(21):3779. doi: 10.1093/bioinformatics/bty417. No abstract available.


DPubChem: a web tool for QSAR modeling and high-throughput virtual screening.

Soufan O, Ba-Alawi W, Magana-Mora A, Essack M, Bajic VB.

Sci Rep. 2018 Jun 14;8(1):9110. doi: 10.1038/s41598-018-27495-x.


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.


In silico toxicology: comprehensive benchmarking of multi-label classification methods applied to chemical toxicity data.

Raies AB, Bajic VB.

Wiley Interdiscip Rev Comput Mol Sci. 2018 May-Jun;8(3):e1352. doi: 10.1002/wcms.1352. Epub 2017 Dec 4. Review.


Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB, Brombacher F, Suzuki H.

Sci Rep. 2018 Apr 30;8(1):6758. doi: 10.1038/s41598-018-24509-6.


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.


A novel method for improved accuracy of transcription factor binding site prediction.

Khamis AM, Motwalli O, Oliva R, Jankovic BR, Medvedeva YA, Ashoor H, Essack M, Gao X, Bajic VB.

Nucleic Acids Res. 2018 Jul 6;46(12):e72. doi: 10.1093/nar/gky237.


Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA.

PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar.

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