Vladimir B Bajic

Vladimir B Bajic

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Vladimir B Bajic

Vladimir B Bajic

Publications by authors named "Vladimir B Bajic"

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Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance.

Sci Rep 2019 Dec 3;9(1):18154. Epub 2019 Dec 3.

King Abdullah University of Science and Technology (KAUST), Center for Desert Agriculture, Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1038/s41598-019-54685-yDOI Listing
December 2019

HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review.

J Clin Pharm Ther 2019 Nov 17. Epub 2019 Nov 17.

Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia.

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http://dx.doi.org/10.1111/jcpt.13073DOI Listing
November 2019

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs.

Bioinformatics 2019 Oct 4. Epub 2019 Oct 4.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btz703DOI Listing
October 2019

Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy.

Med Hypotheses 2019 Oct 3;134:109419. Epub 2019 Oct 3.

Vinca Institute of Nuclear Sciences, University of Belgrade, Laboratory of Radiobiology and Molecular Genetics, Mike Petrovica Alasa 12-14, 11000 Belgrade, Serbia.

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http://dx.doi.org/10.1016/j.mehy.2019.109419DOI Listing
October 2019

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

Bioinformatics 2019 Sep;35(17):2949-2956

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz008DOI Listing
September 2019

Mining biosynthetic gene clusters in Virgibacillus genomes.

BMC Genomics 2019 Sep 3;20(1):696. Epub 2019 Sep 3.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-019-6065-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724285PMC
September 2019

Redox control of vascular biology.

Biofactors 2019 Sep 4. Epub 2019 Sep 4.

Laboratory of Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia.

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http://dx.doi.org/10.1002/biof.1559DOI Listing
September 2019

Hybrid model for efficient prediction of poly(A) signals in human genomic DNA.

Methods 2019 Aug 13;166:31-39. Epub 2019 Apr 13.

King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.04.001DOI Listing
August 2019

Mining the deep Red-Sea brine pool microbial community for anticancer therapeutics.

BMC Complement Altern Med 2019 Jun 20;19(1):142. Epub 2019 Jun 20.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Jeddah, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s12906-019-2554-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6587256PMC
June 2019

Glutathione "Redox Homeostasis" and Its Relation to Cardiovascular Disease.

Oxid Med Cell Longev 2019 9;2019:5028181. Epub 2019 May 9.

Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica Alasa 12-14, 11000 Belgrade, Serbia.

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http://dx.doi.org/10.1155/2019/5028181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532282PMC
May 2019

Literature-Based Enrichment Insights into Redox Control of Vascular Biology.

Oxid Med Cell Longev 2019 16;2019:1769437. Epub 2019 May 16.

Vinca Institute, University of Belgrade, Laboratory for Molecular Endocrinology and Radiobiology, Belgrade, Serbia.

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http://dx.doi.org/10.1155/2019/1769437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542245PMC
May 2019

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

Bioinformatics 2019 Apr;35(7):1125-1132

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/bty752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449759PMC
April 2019

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

Nucleic Acids Res 2019 03;47(5):2699

BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkz073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412109PMC
March 2019

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

PLoS One 2018 10;13(8):e0202002. Epub 2018 Aug 10.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202002PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086437PMC
February 2019

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

BMC Genomics 2019 Feb 1;20(1):102. Epub 2019 Feb 1.

Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.

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http://dx.doi.org/10.1186/s12864-018-5387-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359853PMC
February 2019

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

Nucleic Acids Res 2019 Jan;47(D1):D128-D134

BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323930PMC
January 2019

Marine biofilms constitute a bank of hidden microbial diversity and functional potential.

Nat Commun 2019 01 31;10(1):517. Epub 2019 Jan 31.

Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.

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http://dx.doi.org/10.1038/s41467-019-08463-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355793PMC
January 2019

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

Genomics Proteomics Bioinformatics 2018 10 19;16(5):332-341. Epub 2018 Dec 19.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2018.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364045PMC
October 2018

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

Sci Rep 2018 09 6;8(1):13359. Epub 2018 Sep 6.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.

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http://www.nature.com/articles/s41598-018-31439-w
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http://dx.doi.org/10.1038/s41598-018-31439-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127254PMC
September 2018

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

Biotechnol Rep (Amst) 2018 Sep 24;19:e00278. Epub 2018 Aug 24.

Water Desalination and Reuse Center (WDRC), Saudi Arabia.

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http://dx.doi.org/10.1016/j.btre.2018.e00278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127377PMC
September 2018

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

Nucleic Acids Res 2018 07;46(12):e72

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1093/nar/gky237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037060PMC
July 2018

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

Sci Rep 2018 06 14;8(1):9110. Epub 2018 Jun 14.

Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1038/s41598-018-27495-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002400PMC
June 2018

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

BMC Genomics 2018 May 22;19(1):382. Epub 2018 May 22.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-018-4796-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964695PMC
May 2018

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

Bioinformatics 2018 04;34(7):1164-1173

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia.

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https://academic.oup.com/bioinformatics/article/34/7/1164/46
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http://dx.doi.org/10.1093/bioinformatics/btx731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998943PMC
April 2018

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

Wiley Interdiscip Rev Comput Mol Sci 2018 May-Jun;8(3):e1352. Epub 2017 Dec 4.

Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.

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http://dx.doi.org/10.1002/wcms.1352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947741PMC
December 2017

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

Front Microbiol 2017 20;8:2023. Epub 2017 Oct 20.

Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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http://dx.doi.org/10.3389/fmicb.2017.02023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664417PMC
October 2017

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

BMC Genomics 2017 Aug 15;18(1):620. Epub 2017 Aug 15.

Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-017-4033-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558757PMC
August 2017

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

RNA Biol 2017 07 7;14(7):963-971. Epub 2017 Apr 7.

a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1080/15476286.2017.1312243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546543PMC
July 2017

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

FEMS Microbiol Ecol 2017 07;93(7)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1093/femsec/fix083DOI Listing
July 2017

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.

Sci Rep 2017 07 20;7(1):5968. Epub 2017 Jul 20.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1038/s41598-017-05448-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5519719PMC
July 2017

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

Appl Microbiol Biotechnol 2017 Jun 20;101(12):4837-4851. Epub 2017 May 20.

Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.

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http://link.springer.com/10.1007/s00253-017-8310-9
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http://dx.doi.org/10.1007/s00253-017-8310-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5486811PMC
June 2017

OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models.

Sci Rep 2017 06 20;7(1):3898. Epub 2017 Jun 20.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1038/s41598-017-04281-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478657PMC
June 2017

Semantic prioritization of novel causative genomic variants.

PLoS Comput Biol 2017 04 17;13(4):e1005500. Epub 2017 Apr 17.

King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1371/journal.pcbi.1005500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411092PMC
April 2017

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

Nucleic Acids Res 2017 03;45(5):2838-2848

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1093/nar/gkw973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389649PMC
March 2017

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

Genome Announc 2017 Mar 2;5(9). Epub 2017 Mar 2.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia.

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01707-16
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http://dx.doi.org/10.1128/genomeA.01707-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334584PMC
March 2017

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

Genome Announc 2017 Mar 2;5(9). Epub 2017 Mar 2.

Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01708-16
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http://dx.doi.org/10.1128/genomeA.01708-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334585PMC
March 2017

bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli.

Bioinformatics 2017 02;33(3):334-340

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btw629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408793PMC
February 2017

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

Nucleic Acids Res 2017 02;45(4):e25

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1093/nar/gkw1015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389464PMC
February 2017

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

Genome Announc 2017 Feb 16;5(7). Epub 2017 Feb 16.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia.

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01638-16
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http://dx.doi.org/10.1128/genomeA.01638-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313623PMC
February 2017

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

Nucleic Acids Res 2017 01 26;45(D1):D145-D150. Epub 2016 Oct 26.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkw1007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210517PMC
January 2017

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

BMC Genomics 2017 01 5;18(1):33. Epub 2017 Jan 5.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-016-3389-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217662PMC
January 2017

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

Genome Announc 2017 Jan 12;5(2). Epub 2017 Jan 12.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1128/genomeA.01437-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5256217PMC
January 2017

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

Genome Announc 2017 Jan 26;5(4). Epub 2017 Jan 26.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1128/genomeA.01520-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5270703PMC
January 2017

Metagenomics as a preliminary screen for antimicrobial bioprospecting.

Gene 2016 Dec 15;594(2):248-258. Epub 2016 Sep 15.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2016.09.021DOI Listing
December 2016

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

Genome Announc 2016 Dec 22;4(6). Epub 2016 Dec 22.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1128/genomeA.01431-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180391PMC
December 2016

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

Genome Announc 2016 Nov 3;4(6). Epub 2016 Nov 3.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1128/genomeA.01214-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5095469PMC
November 2016

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

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

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia.

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http://dx.doi.org/10.1186/s13321-016-0177-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105261PMC
November 2016

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.

Mar Drugs 2016 Sep 10;14(9). Epub 2016 Sep 10.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039536PMC
http://dx.doi.org/10.3390/md14090165DOI Listing
September 2016

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

Genome Announc 2016 Jul 28;4(4). Epub 2016 Jul 28.

King Abdullah University of Science and Technology (KAUST), Center for Desert Agriculture (CDA), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1128/genomeA.00678-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966455PMC
July 2016

Mining Chemical Activity Status from High-Throughput Screening Assays.

PLoS One 2015 14;10(12):e0144426. Epub 2015 Dec 14.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144426PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682830PMC
June 2016

DENdb: database of integrated human enhancers.

Database (Oxford) 2015 5;2015. Epub 2015 Sep 5.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) and

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http://dx.doi.org/10.1093/database/bav085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560934PMC
May 2016

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge.

Sci Rep 2016 Mar 8;6:22842. Epub 2016 Mar 8.

Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.

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http://dx.doi.org/10.1038/srep22842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782131PMC
March 2016

DASPfind: new efficient method to predict drug-target interactions.

J Cheminform 2016 16;8:15. Epub 2016 Mar 16.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia.

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http://dx.doi.org/10.1186/s13321-016-0128-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793623PMC
March 2016

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

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

King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia.

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http://dx.doi.org/10.1002/wcms.1240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785608PMC
March 2016

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea.

Gene 2016 Feb 10;576(2 Pt 1):626-36. Epub 2015 Nov 10.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2015.10.032DOI Listing
February 2016

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

PLoS One 2015 26;10(2):e0117988. Epub 2015 Feb 26.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117988PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342225PMC
January 2016

DESM: portal for microbial knowledge exploration systems.

Nucleic Acids Res 2016 Jan 5;44(D1):D624-33. Epub 2015 Nov 5.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkv1147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702830PMC
January 2016

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

Nucleic Acids Res 2016 Jan 19;44(D1):D116-25. Epub 2015 Nov 19.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, GSP-1, Vavilova 32, Moscow, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia Moscow Institute of Physics and Technology, 141700, Institutskiy per. 9, Dolgoprudny, Moscow Region, Russia

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http://dx.doi.org/10.1093/nar/gkv1249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702883PMC
January 2016

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

PLoS One 2014 2;9(10):e109443. Epub 2014 Oct 2.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183604PMC
December 2015

Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool.

Environ Microbiol 2015 Oct 17;17(10):4089-104. Epub 2015 Aug 17.

KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.

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http://dx.doi.org/10.1111/1462-2920.12978DOI Listing
October 2015

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

Genomics Proteomics Bioinformatics 2015 Oct 31;13(5):304-9. Epub 2015 Oct 31.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2015.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678784PMC
October 2015

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

Genomics Proteomics Bioinformatics 2015 Oct 5;13(5):310-20. Epub 2015 Nov 5.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2015.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678792PMC
October 2015

The Value and Significance of Metagenomics of Marine Environments. Preface.

Genomics Proteomics Bioinformatics 2015 Oct 27;13(5):271-4. Epub 2015 Nov 27.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2015.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678774PMC
October 2015

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

Nucleic Acids Res 2015 Aug 27;43(14):6969-82. Epub 2015 Jun 27.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan Riken Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

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http://dx.doi.org/10.1093/nar/gkv646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538831PMC
August 2015

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

BMC Genomics 2015 Aug 18;16:616. Epub 2015 Aug 18.

Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-015-1826-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4539851PMC
August 2015

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

Sci Rep 2015 Jun 15;5:11136. Epub 2015 Jun 15.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1038/srep11136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466890PMC
June 2015

Distinct profiling of antimicrobial peptide families.

Bioinformatics 2015 Mar 10;31(6):849-56. Epub 2014 Nov 10.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btu738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380027PMC
March 2015

DEOP: a database on osmoprotectants and associated pathways.

Database (Oxford) 2014 17;2014. Epub 2014 Oct 17.

King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia

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http://dx.doi.org/10.1093/database/bau100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201361PMC
February 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).

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

Division of Life Science and Environmental Science Programs, Hong Kong University of Science and Technology , Hong Kong, China.

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http://dx.doi.org/10.1021/es5046748DOI Listing
February 2015

DEEP: a general computational framework for predicting enhancers.

Nucleic Acids Res 2015 Jan 5;43(1):e6. Epub 2014 Nov 5.

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia

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http://dx.doi.org/10.1093/nar/gku1058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288148PMC
January 2015

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

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

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

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http://dx.doi.org/10.1093/nar/gku1168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383966PMC
January 2015

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

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

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

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http://academic.oup.com/nar/article/43/D1/D187/2438893/LncRN
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http://dx.doi.org/10.1093/nar/gku1167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383965PMC
January 2015

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).

Aquat Toxicol 2014 Dec 2;157:47-56. Epub 2014 Oct 2.

Division of Life Science and Environmental Science Programs, Hong Kong University of Science and Technology, Hong Kong, China. Electronic address:

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http://dx.doi.org/10.1016/j.aquatox.2014.09.010DOI Listing
December 2014

Pyrosequencing reveals the microbial communities in the Red Sea sponge Carteriospongia foliascens and their impressive shifts in abnormal tissues.

Microb Ecol 2014 Oct 24;68(3):621-32. Epub 2014 Apr 24.

Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, People's Republic of China.

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http://link.springer.com/10.1007/s00248-014-0419-0
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October 2014

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

Front Microbiol 2014 23;5:487. Epub 2014 Sep 23.

Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt ; YJ-Science and Technology Research Center, American University in Cairo Cairo, Egypt.

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http://dx.doi.org/10.3389/fmicb.2014.00487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172156PMC
October 2014

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

Toxins (Basel) 2014 Oct 29;6(11):3058-76. Epub 2014 Oct 29.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Jeddah, Saudi Arabia.

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http://dx.doi.org/10.3390/toxins6113058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247248PMC
October 2014

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

PLoS One 2013 6;8(12):e82210. Epub 2013 Dec 6.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082210PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855842PMC
September 2014

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

FEMS Microbiol Ecol 2014 Jul 22;89(1):181-97. Epub 2014 May 22.

Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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https://academic.oup.com/femsec/article-lookup/doi/10.1111/1
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http://dx.doi.org/10.1111/1574-6941.12348DOI Listing
July 2014

Combining position weight matrices and document-term matrix for efficient extraction of associations of methylated genes and diseases from free text.

PLoS One 2013 16;8(10):e77848. Epub 2013 Oct 16.

Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077848PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797705PMC
June 2014

Effects of cytosine methylation on transcription factor binding sites.

BMC Genomics 2014 Mar 26;15:119. Epub 2014 Mar 26.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/1471-2164-15-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986887PMC
March 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Cytotoxicity and apoptosis induced by a plumbagin derivative in estrogen positive MCF-7 breast cancer cells.

Anticancer Agents Med Chem 2014 Jan;14(1):170-80

Computational Bioscience Research Center (CBRC), Building 2, Level 4, R-4336, King Abdullah University of Science and Technology (KAUST), Thuwal- 23955-6900, Kingdom of Saudi Arabia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894702PMC
http://dx.doi.org/10.2174/18715206113136660369DOI Listing
January 2014

A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea.

J Biol Chem 2014 Jan 26;289(3):1675-87. Epub 2013 Nov 26.

From the Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, AUC Avenue, P. O. Box 74, New Cairo 11835, Egypt.

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http://www.jbc.org/cgi/doi/10.1074/jbc.M113.493429
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http://dx.doi.org/10.1074/jbc.M113.493429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894346PMC
January 2014

Induction of apoptosis in cancer cell lines by the Red Sea brine pool bacterial extracts.

BMC Complement Altern Med 2013 Dec 5;13:344. Epub 2013 Dec 5.

Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/1472-6882-13-344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235048PMC
December 2013

Exploration of miRNA families for hypotheses generation.

Sci Rep 2013 Oct 15;3:2940. Epub 2013 Oct 15.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia.

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http://www.nature.com/articles/srep02940
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3796740PMC
October 2013