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Items: 1 to 50 of 195

1.

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.

PMID:
30715521
2.

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.

3.

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.

4.

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
5.

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]

PMID:
30649200
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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]

PMID:
30184052
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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

Olayan RS, Ashoor H, Bajic VB.

Bioinformatics. 2018 Apr 1;34(7):1164-1173. doi: 10.1093/bioinformatics/btx731.

23.

Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium.

Andrés-Barrao C, Lafi FF, Alam I, de Zélicourt A, Eida AA, Bokhari A, Alzubaidy H, Bajic VB, Hirt H, Saad MM.

Front Microbiol. 2017 Oct 20;8:2023. doi: 10.3389/fmicb.2017.02023. eCollection 2017.

24.

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ.

Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259. doi: 10.1093/nar/gkx1106.

25.

Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA.

Magana-Mora A, Kalkatawi M, Bajic VB.

BMC Genomics. 2017 Aug 15;18(1):620. doi: 10.1186/s12864-017-4033-7.

26.

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.

27.

Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade.

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

FEMS Microbiol Ecol. 2017 Jul 1;93(7). doi: 10.1093/femsec/fix083.

PMID:
28645159
28.

OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models.

Magana-Mora A, Bajic VB.

Sci Rep. 2017 Jun 20;7(1):3898. doi: 10.1038/s41598-017-04281-9.

29.

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity.

Nielsen J, Archer J, Essack M, Bajic VB, Gojobori T, Mijakovic I.

Appl Microbiol Biotechnol. 2017 Jun;101(12):4837-4851. doi: 10.1007/s00253-017-8310-9. Epub 2017 May 20. Review.

30.

Semantic prioritization of novel causative genomic variants.

Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R.

PLoS Comput Biol. 2017 Apr 17;13(4):e1005500. doi: 10.1371/journal.pcbi.1005500. eCollection 2017 Apr.

31.

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.

Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB.

RNA Biol. 2017 Jul 3;14(7):963-971. doi: 10.1080/15476286.2017.1312243. Epub 2017 Apr 7.

32.

Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea.

Lafi FF, Alam I, Bisseling T, Geurts R, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2017 Mar 2;5(9). pii: e01708-16. doi: 10.1128/genomeA.01708-16.

33.

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium.

Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2017 Mar 2;5(9). pii: e01707-16. doi: 10.1128/genomeA.01707-16.

34.

Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea.

Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2017 Feb 16;5(7). pii: e01638-16. doi: 10.1128/genomeA.01638-16.

35.

Draft Genome Sequence of Plant Growth-Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia.

Lafi FF, Ramirez-Prado JS, Alam I, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2017 Jan 26;5(4). pii: e01520-16. doi: 10.1128/genomeA.01520-16.

36.

Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan.

Lafi FF, AlBladi ML, Salem NM, Al-Banna L, Alam I, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2017 Jan 12;5(2). pii: e01437-16. doi: 10.1128/genomeA.01437-16.

37.

In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.

Motwalli O, Essack M, Jankovic BR, Ji B, Liu X, Ansari HR, Hoehndorf R, Gao X, Arold ST, Mineta K, Archer JA, Gojobori T, Mijakovic I, Bajic VB.

BMC Genomics. 2017 Jan 5;18(1):33. doi: 10.1186/s12864-016-3389-4.

38.

HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics.

Ashoor H, Louis-Brennetot C, Janoueix-Lerosey I, Bajic VB, Boeva V.

Nucleic Acids Res. 2017 May 5;45(8):e58. doi: 10.1093/nar/gkw1319.

39.

Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea.

Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2016 Dec 22;4(6). pii: e01431-16. doi: 10.1128/genomeA.01431-16.

40.

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.

41.

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts.

Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks JB, Kapfer C, Mineta K, Gojobori T, Bajic VB.

Nucleic Acids Res. 2017 Mar 17;45(5):2838-2848. doi: 10.1093/nar/gkw973.

42.

DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning.

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

J Cheminform. 2016 Nov 10;8:64. eCollection 2016.

43.

Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta.

Lafi FF, Ramirez-Prado JS, Alam I, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2016 Nov 3;4(6). pii: e01214-16. doi: 10.1128/genomeA.01214-16.

44.

TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions.

Schmeier S, Alam T, Essack M, Bajic VB.

Nucleic Acids Res. 2017 Jan 4;45(D1):D145-D150. doi: 10.1093/nar/gkw1007. Epub 2016 Oct 26.

45.

Discriminative identification of transcriptional responses of promoters and enhancers after stimulus.

Kleftogiannis D, Kalnis P, Arner E, Bajic VB.

Nucleic Acids Res. 2017 Feb 28;45(4):e25. doi: 10.1093/nar/gkw1015.

46.

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.

47.

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.

48.

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.

49.

Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris.

Lafi FF, Bokhari A, Alam I, Bajic VB, Hirt H, Saad MM.

Genome Announc. 2016 Jul 28;4(4). pii: e00678-16. doi: 10.1128/genomeA.00678-16.

50.

In silico toxicology: computational methods for the prediction of chemical toxicity.

Raies AB, Bajic VB.

Wiley Interdiscip Rev Comput Mol Sci. 2016 Mar;6(2):147-172. Epub 2016 Jan 6. Review.

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