Publications by authors named "Vladimir B Bajic"

100Publications

PATH: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes.

Authors:
Olaa Motwalli Mahmut Uludag Ivan Mijakovic Meshari Alazmi Vladimir B Bajic Takashi Gojobori Xin Gao Magbubah Essack

ACS Synth Biol 2020 Nov 16. Epub 2020 Nov 16.

Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, 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/10.1021/acssynbio.0c00058DOI Listing
November 2020

Next-Generation Sequencing at High Sequencing Depth as a Tool to Study the Evolution of Metastasis Driven by Genetic Change Events of Lung Squamous Cell Carcinoma.

Authors:
Hicham Mansour Abdelhak Ouhajjou Vladimir B Bajic Roberto Incitti

Front Oncol 2020 5;10:1215. Epub 2020 Aug 5.

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

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http://dx.doi.org/10.3389/fonc.2020.01215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438761PMC
August 2020

Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA.

Authors:
Somayah Albaradei Arturo Magana-Mora Maha Thafar Mahmut Uludag Vladimir B Bajic Takashi Gojobori Magbubah Essack Boris R Jankovic

Gene X 2020 Dec 13;5:100035. Epub 2020 May 13.

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

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http://dx.doi.org/10.1016/j.gene.2020.100035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285987PMC
December 2020

Genome Insights of the Plant-Growth Promoting Bacterium JZ38 With Volatile-Mediated Antagonistic Activity Against .

Authors:
Abdul Aziz Eida Salim Bougouffa Floriane L'Haridon Intikhab Alam Laure Weisskopf Vladimir B Bajic Maged M Saad Heribert Hirt

Front Microbiol 2020 11;11:369. Epub 2020 Mar 11.

DARWIN21, 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.2020.00369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078163PMC
March 2020

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

Authors:
Ameerah Bokhari Magbubah Essack Feras F Lafi Cristina Andres-Barrao Rewaa Jalal Soha Alamoudi Rozaimi Razali Hanin Alzubaidy Kausar H Shah Shahid Siddique Vladimir B Bajic Heribert Hirt Maged M Saad

Sci Rep 2020 Feb 14;10(1):3001. Epub 2020 Feb 14.

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/s41598-020-58957-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7021772PMC
February 2020

The X Files: "The Mystery of X Chromosome Instability in Alzheimer's Disease".

Authors:
Vladan P Bajic Magbubah Essack Lada Zivkovic Alan Stewart Sonja Zafirovic Vladimir B Bajic Takashi Gojobori Esma Isenovic Biljana Spremo-Potparevic

Front Genet 2019 28;10:1368. Epub 2020 Jan 28.

Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia.

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http://dx.doi.org/10.3389/fgene.2019.01368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997486PMC
January 2020

Regulation of nitric oxide production in hypothyroidism.

Authors:
Zoran M Gluvic Milan M Obradovic Emina M Sudar-Milovanovic Sonja S Zafirovic Djordje J Radak Magbubah M Essack Vladimir B Bajic Gojobori Takashi Esma R Isenovic

Biomed Pharmacother 2020 Apr 24;124:109881. Epub 2020 Jan 24.

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

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http://dx.doi.org/10.1016/j.biopha.2020.109881DOI Listing
April 2020

Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities.

Authors:
Maha Thafar Arwa Bin Raies Somayah Albaradei Magbubah Essack Vladimir B Bajic

Front Chem 2019 20;7:782. Epub 2019 Nov 20.

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

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http://dx.doi.org/10.3389/fchem.2019.00782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879652PMC
November 2019

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

Authors:
Ameerah Bokhari Magbubah Essack Feras F Lafi Cristina Andres-Barrao Rewaa Jalal Soha Alamoudi Rozaimi Razali Hanin Alzubaidy Kausar H Shah Shahid Siddique Vladimir B Bajic Heribert Hirt Maged M Saad

Sci Rep 2019 12 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890672PMC
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.

Authors:
Zoran Gluvic Milan Obradovic Milena Lackovic Vladimir Samardzic Jelena Tica Jevtic Magbubah Essack Vladimir B Bajic Esma R Isenovic

J Clin Pharm Ther 2020 Apr 17;45(2):379-383. 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384187PMC
April 2020

Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy.

Authors:
Milan Obradovic Sonja Zafirovic Magbubah Essack Jelena Dimitrov Lada Zivkovic Biljana Spremo-Potparevic Djordje Radak Vladimir B Bajic Esma R Isenovic

Med Hypotheses 2020 Jan 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
January 2020

Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs.

Authors:
Tanvir Alam Meshari Alazmi Rayan Naser Franceline Huser Afaque A Momin Veronica Astro SeungBeom Hong Katarzyna W Walkiewicz Christian G Canlas Raphaël Huser Amal J Ali Jasmeen Merzaban Antonio Adamo Mariusz Jaremko Łukasz Jaremko Vladimir B Bajic Xin Gao Stefan T Arold

Bioinformatics 2020 02;36(4):1121-1128

Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btz703DOI Listing
February 2020

Redox control of vascular biology.

Authors:
Milan Obradovic Magbubah Essack Sonja Zafirovic Emina Sudar-Milovanovic Vladan P Bajic Christophe Van Neste Andreja Trpkovic Julijana Stanimirovic Vladimir B Bajic Esma R Isenovic

Biofactors 2020 Mar 4;46(2):246-262. 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187163PMC
March 2020

Mining biosynthetic gene clusters in Virgibacillus genomes.

Authors:
Ghofran Othoum Salim Bougouffa Ameerah Bokhari Feras F Lafi Takashi Gojobori Heribert Hirt Ivan Mijakovic Vladimir B Bajic Magbubah Essack

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

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

Authors:
Magbubah Essack Adil Salhi Julijana Stanimirovic Faroug Tifratene Arwa Bin Raies Arnaud Hungler Mahmut Uludag Christophe Van Neste Andreja Trpkovic Vladan P Bajic Vladimir B Bajic Esma R Isenovic

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
December 2019

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

Authors:
Luke Esau Guishan Zhang Sunil Sagar Ulrich Stingl Vladimir B Bajic Mandeep Kaur

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.

Authors:
Vladan P Bajic Christophe Van Neste Milan Obradovic Sonja Zafirovic Djordje Radak Vladimir B Bajic Magbubah Essack Esma R Isenovic

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
December 2019

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

Authors:
Fahad Albalawi Abderrazak Chahid Xingang Guo Somayah Albaradei Arturo Magana-Mora Boris R Jankovic Mahmut Uludag Christophe Van Neste Magbubah Essack Taous-Meriem Laleg-Kirati Vladimir B Bajic

Methods 2019 08 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

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

Authors:
Lina Ma Jiabao Cao Lin Liu Qiang Du Zhao Li Dong Zou Vladimir B Bajic Zhang Zhang

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

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

Authors:
Anna V Lioznova Abdullah M Khamis Artem V Artemov Elizaveta Besedina Vasily Ramensky Vladimir B Bajic Ivan V Kulakovskiy Yulia A Medvedeva

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

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

Authors:
Weipeng Zhang Wei Ding Yong-Xin Li Chunkit Tam Salim Bougouffa Ruojun Wang Bite Pei Hoyin Chiang Pokman Leung Yanhong Lu Jin Sun He Fu Vladimir B Bajic Hongbin Liu Nicole S Webster Pei-Yuan Qian

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

Uncoupled Quorum Sensing Modulates the Interplay of Virulence and Resistance in a Multidrug-Resistant Clinical Isolate Belonging to the MLST550 Clonal Complex.

Authors:
Huiluo Cao Tingying Xia Yanran Li Zeling Xu Salim Bougouffa Yat Kei Lo Vladimir B Bajic Haiwei Luo Patrick C Y Woo Aixin Yan

Antimicrob Agents Chemother 2019 04 27;63(4). Epub 2019 Mar 27.

School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China

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http://aac.asm.org/lookup/doi/10.1128/AAC.01944-18
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http://dx.doi.org/10.1128/AAC.01944-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437519PMC
April 2019

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

Authors:
Guangyu Wang Hongyan Yin Boyang Li Chunlei Yu Fan Wang Xingjian Xu Jiabao Cao Yiming Bao Liguo Wang Amir A Abbasi Vladimir B Bajic Lina Ma Zhang Zhang

Bioinformatics 2019 09;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

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

Authors:
Dimitrios Kleftogiannis Haitham Ashoor Vladimir B Bajic

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

The Genome Sequence of the Wild Tomato Provides Insights Into Salinity Tolerance.

Authors:
Rozaimi Razali Salim Bougouffa Mitchell J L Morton Damien J Lightfoot Intikhab Alam Magbubah Essack Stefan T Arold Allan A Kamau Sandra M Schmöckel Yveline Pailles Mohammed Shahid Craig T Michell Salim Al-Babili Yung Shwen Ho Mark Tester Vladimir B Bajic Sónia Negrão

Front Plant Sci 2018 4;9:1402. Epub 2018 Oct 4.

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

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https://www.frontiersin.org/article/10.3389/fpls.2018.01402/
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http://dx.doi.org/10.3389/fpls.2018.01402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186997PMC
October 2018

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

Authors:
Lina Ma Jiabao Cao Lin Liu Qiang Du Zhao Li Dong Zou Vladimir B Bajic Zhang Zhang

Nucleic Acids Res 2019 01;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

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

Authors:
Zahid Ur Rehman Intikhab Alam Allan Anthony Kamau Vladimir B Bajic TorOve Leiknes

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

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

Authors:
Vasiliki Kordopati Adil Salhi Rozaimi Razali Aleksandar Radovanovic Faroug Tifratene Mahmut Uludag Yu Li Ameerah Bokhari Ahdab AlSaieedi Arwa Bin Raies Christophe Van Neste Magbubah Essack Vladimir B Bajic

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

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

Authors:
Manal Kalkatawi Arturo Magana-Mora Boris Jankovic Vladimir B Bajic

Bioinformatics 2019 04;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

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

Authors:
Olaa Motwalli Magbubah Essack Adil Salhi John Hanks Ivan Mijakovic Vladimir B Bajic

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

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

Authors:
Rawan S Olayan Haitham Ashoor Vladimir B Bajic

Bioinformatics 2018 11;34(21):3779

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https://academic.oup.com/bioinformatics/article/34/21/3779/5
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http://dx.doi.org/10.1093/bioinformatics/bty417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198857PMC
November 2018

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

Authors:
Othman Soufan Wail Ba-Alawi Arturo Magana-Mora Magbubah Essack Vladimir B Bajic

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.

Authors:
Ghofran Othoum Salim Bougouffa Rozaimi Razali Ameerah Bokhari Soha Alamoudi André Antunes Xin Gao Robert Hoehndorf Stefan T Arold Takashi Gojobori Heribert Hirt Ivan Mijakovic Vladimir B Bajic Feras F Lafi Magbubah Essack

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

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

Authors:
Arwa B Raies Vladimir B Bajic

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

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

Authors:
Sugata Roy Sebastian Schmeier Bogumil Kaczkowski Erik Arner Tanvir Alam Mumin Ozturk Ousman Tamgue Suraj P Parihar Hideya Kawaji Masayoshi Itoh Timo Lassmann Piero Carninci Yoshihide Hayashizaki Alistair R R Forrest Reto Guler Vladimir B Bajic Frank Brombacher Harukazu Suzuki

Sci Rep 2018 04 30;8(1):6758. Epub 2018 Apr 30.

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

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http://dx.doi.org/10.1038/s41598-018-24509-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928056PMC
April 2018

Genome Reduction in Species within the Gut of an Amphipod from the Ocean's Deepest Point.

Authors:
Weipeng Zhang Ren-Mao Tian Jin Sun Salim Bougouffa Wei Ding Lin Cai Yi Lan Haoya Tong Yongxin Li Alan J Jamieson Vladimir B Bajic Jeffrey C Drazen Douglas Bartlett Pei-Yuan Qian

mSystems 2018 May-Jun;3(3). Epub 2018 Apr 10.

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

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http://dx.doi.org/10.1128/mSystems.00009-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893861PMC
April 2018

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

Authors:
Abdullah M Khamis Olaa Motwalli Romina Oliva Boris R Jankovic Yulia A Medvedeva Haitham Ashoor Magbubah Essack Xin Gao Vladimir B Bajic

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

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

Authors:
J Kenneth Baillie Andrew Bretherick Christopher S Haley Sara Clohisey Alan Gray Lucile P A Neyton Jeffrey Barrett Eli A Stahl Albert Tenesa Robin Andersson J Ben Brown Geoffrey J Faulkner Marina Lizio Ulf Schaefer Carsten Daub Masayoshi Itoh Naoto Kondo Timo Lassmann Jun Kawai Damian Mole Vladimir B Bajic Peter Heutink Michael Rehli Hideya Kawaji Albin Sandelin Harukazu Suzuki Jack Satsangi Christine A Wells Nir Hacohen Thomas C Freeman Yoshihide Hayashizaki Piero Carninci Alistair R R Forrest David A Hume

PLoS Comput Biol 2018 03 1;14(3):e1005934. Epub 2018 Mar 1.

Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1005934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849332PMC
March 2018

Draft Genome Sequences of Four subsp. Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts.

Authors:
Ran An Pengpeng Lin Salim Bougouffa Magbubah Essack David Boxrud Vladimir B Bajic Sinisa Vidovic

Genome Announc 2018 Jan 25;6(4). Epub 2018 Jan 25.

Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01550-17
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http://dx.doi.org/10.1128/genomeA.01550-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786692PMC
January 2018

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

Authors:
Rawan S Olayan Haitham Ashoor Vladimir B Bajic

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

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

Authors:
Cristina Andrés-Barrao Feras F Lafi Intikhab Alam Axel de Zélicourt Abdul A Eida Ameerah Bokhari Hanin Alzubaidy Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Ivan V Kulakovskiy Ilya E Vorontsov Ivan S Yevshin Ruslan N Sharipov Alla D Fedorova Eugene I Rumynskiy Yulia A Medvedeva Arturo Magana-Mora Vladimir B Bajic Dmitry A Papatsenko Fedor A Kolpakov Vsevolod J Makeev

Nucleic Acids Res 2018 01;46(D1):D252-D259

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, GSP-1, Vavilova 32, Moscow, Russia.

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http://dx.doi.org/10.1093/nar/gkx1106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753240PMC
January 2018

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

Authors:
Arturo Magana-Mora Manal Kalkatawi Vladimir B Bajic

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

Authors:
Adil Salhi Sónia Negrão Magbubah Essack Mitchell J L Morton Salim Bougouffa Rozaimi Razali Aleksandar Radovanovic Benoit Marchand Maxat Kulmanov Robert Hoehndorf Mark Tester Vladimir B Bajic

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

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

Authors:
Francy Jimenez-Infante David Kamanda Ngugi Manikandan Vinu Jochen Blom Intikhab Alam Vladimir B Bajic Ulrich Stingl

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

OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models.

Authors:
Arturo Magana-Mora Vladimir B Bajic

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

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

Authors:
Jens Nielsen John Archer Magbubah Essack Vladimir B Bajic Takashi Gojobori Ivan Mijakovic

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

Semantic prioritization of novel causative genomic variants.

Authors:
Imane Boudellioua Rozaimi B Mahamad Razali Maxat Kulmanov Yasmeen Hashish Vladimir B Bajic Eva Goncalves-Serra Nadia Schoenmakers Georgios V Gkoutos Paul N Schofield Robert Hoehndorf

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

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

Authors:
Adil Salhi Magbubah Essack Tanvir Alam Vladan P Bajic Lina Ma Aleksandar Radovanovic Benoit Marchand Sebastian Schmeier Zhang Zhang Vladimir B Bajic

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

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

Authors:
Feras F Lafi Intikhab Alam Ton Bisseling Rene Geurts Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Feras F Lafi Intikhab Alam Rene Geurts Ton Bisseling Vladimir B Bajic Heribert Hirt Maged M Saad

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 sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant .

Authors:
Feras F Lafi Intikhab Alam Rene Geurts Ton Bisseling Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Feras F Lafi Juan S Ramirez-Prado Intikhab Alam Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Feras F Lafi Maha L AlBladi Nida M Salem Luma Al-Banna Intikhab Alam Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Olaa Motwalli Magbubah Essack Boris R Jankovic Boyang Ji Xinyao Liu Hifzur Rahman Ansari Robert Hoehndorf Xin Gao Stefan T Arold Katsuhiko Mineta John A C Archer Takashi Gojobori Ivan Mijakovic Vladimir B Bajic

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

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

Authors:
Haitham Ashoor Caroline Louis-Brennetot Isabelle Janoueix-Lerosey Vladimir B Bajic Valentina Boeva

Nucleic Acids Res 2017 05;45(8):e58

Institut Curie, Inserm U900, Mines ParisTech, PSL Research University, F-75005 Paris, France.

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http://dx.doi.org/10.1093/nar/gkw1319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416852PMC
May 2017

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

Authors:
Feras F Lafi Intikhab Alam Rene Geurts Ton Bisseling Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Tanvir Alam Mahmut Uludag Magbubah Essack Adil Salhi Haitham Ashoor John B Hanks Craig Kapfer Katsuhiko Mineta Takashi Gojobori Vladimir B Bajic

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

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

Authors:
Othman Soufan Wail Ba-Alawi Moataz Afeef Magbubah Essack Panos Kalnis Vladimir B Bajic

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

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

Authors:
Feras F Lafi Juan S Ramirez-Prado Intikhab Alam Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Sebastian Schmeier Tanvir Alam Magbubah Essack Vladimir B Bajic

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

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

Authors:
Dimitrios Kleftogiannis Panos Kalnis Erik Arner Vladimir B Bajic

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

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

Authors:
Ilham Ayub Shahmuradov Rozaimi Mohamad Razali Salim Bougouffa Aleksandar Radovanovic Vladimir B Bajic

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

Metagenomics as a preliminary screen for antimicrobial bioprospecting.

Authors:
Soha Al-Amoudi Rozaimi Razali Magbubah Essack Mohammad Shoaib Amini Salim Bougouffa John A C Archer Feras F Lafi Vladimir B Bajic

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

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

Authors:
Soha Al-Amoudi Magbubah Essack Marta F Simões Salim Bougouffa Irina Soloviev John A C Archer Feras F Lafi Vladimir B Bajic

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.

Authors:
Feras F Lafi Ameerah Bokhari Intikhab Alam Vladimir B Bajic Heribert Hirt Maged M Saad

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

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

Authors:
Arwa B Raies Vladimir B Bajic

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

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

Authors:
Wail Ba-Alawi Othman Soufan Magbubah Essack Panos Kalnis Vladimir B Bajic

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

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

Authors:
Huiluo Cao Chunming Dong Salim Bougouffa Jiangtao Li Weipeng Zhang Zongze Shao Vladimir B Bajic Pei-Yuan Qian

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

Mining Chemical Activity Status from High-Throughput Screening Assays.

Authors:
Othman Soufan Wail Ba-alawi Moataz Afeef Magbubah Essack Valentin Rodionov Panos Kalnis Vladimir B Bajic

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

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

Authors:
Francy Jimenez-Infante David Kamanda Ngugi Manikandan Vinu Intikhab Alam Allan Anthony Kamau Jochen Blom Vladimir B Bajic Ulrich Stingl

Appl Environ Microbiol 2016 02 11;82(4):1215-1226. Epub 2015 Dec 11.

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

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http://dx.doi.org/10.1128/AEM.02852-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751848PMC
February 2016

Progress and challenges in bioinformatics approaches for enhancer identification.

Authors:
Dimitrios Kleftogiannis Panos Kalnis Vladimir B Bajic

Brief Bioinform 2016 11 3;17(6):967-979. Epub 2015 Dec 3.

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http://dx.doi.org/10.1093/bib/bbv101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142011PMC
November 2016

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

Authors:
Fangqing Zhao Vladimir B Bajic

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

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

Authors:
Ivan V Kulakovskiy Ilya E Vorontsov Ivan S Yevshin Anastasiia V Soboleva Artem S Kasianov Haitham Ashoor Wail Ba-Alawi Vladimir B Bajic Yulia A Medvedeva Fedor A Kolpakov Vsevolod J Makeev

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

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

Authors:
Marta Filipa Simões André Antunes Cristiane A Ottoni Mohammad Shoaib Amini Intikhab Alam Hanin Alzubaidy Noor-Azlin Mokhtar John A C Archer Vladimir B Bajic

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

DESM: portal for microbial knowledge exploration systems.

Authors:
Adil Salhi Magbubah Essack Aleksandar Radovanovic Benoit Marchand Salim Bougouffa Andre Antunes Marta Filipa Simoes Feras F Lafi Olaa A Motwalli Ameerah Bokhari Tariq Malas Soha Al Amoudi Ghofran Othum Intikhab Allam Katsuhiko Mineta Xin Gao Robert Hoehndorf John A C Archer Takashi Gojobori Vladimir B Bajic

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

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

Authors:
André Antunes Intikhab Alam Marta Filipa Simões Camille Daniels Ari J S Ferreira Rania Siam Hamza El-Dorry Vladimir B Bajic

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

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

Authors:
Hanin Alzubaidy Magbubah Essack Tareq B Malas Ameerah Bokhari Olaa Motwalli Frederick Kinyua Kamanu Suhaiza Ahmad Jamhor Noor Azlin Mokhtar André Antunes Marta Filipa Simões Intikhab Alam Salim Bougouffa Feras F Lafi Vladimir B Bajic John A C Archer

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

DENdb: database of integrated human enhancers.

Authors:
Haitham Ashoor Dimitrios Kleftogiannis Aleksandar Radovanovic Vladimir B Bajic

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

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

Authors:
Manal Kalkatawi Intikhab Alam Vladimir B Bajic

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

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

Authors:
Weipeng Zhang Yong Wang Salim Bougouffa Renmao Tian Huiluo Cao Yongxin Li Lin Cai Yue Him Wong Gen Zhang Guowei Zhou Xixiang Zhang Vladimir B Bajic Abdulaziz Al-Suwailem Pei-Yuan Qian

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

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

Authors:
Sugata Roy Sebastian Schmeier Erik Arner Tanvir Alam Suraj P Parihar Mumin Ozturk Ousman Tamgue Hideya Kawaji Michiel J L de Hoon Masayoshi Itoh Timo Lassmann Piero Carninci Yoshihide Hayashizaki Alistair R R Forrest Vladimir B Bajic Reto Guler Frank Brombacher Harukazu Suzuki

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

Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora.

Authors:
Zhao-Ming Gao Yong Wang Ren-Mao Tian On On Lee Yue Him Wong Zenon B Batang Abdulaziz Al-Suwailem Feras F Lafi Vladimir B Bajic Pei-Yuan Qian

PeerJ 2015 11;3:e890. Epub 2015 Jun 11.

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

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https://peerj.com/articles/890
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http://dx.doi.org/10.7717/peerj.890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465955PMC
June 2015

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

Authors:
Abdullah M Khamis Adam R Hamilton Yulia A Medvedeva Tanvir Alam Intikhab Alam Magbubah Essack Boris Umylny Boris R Jankovic Nicholas L Naeger Makoto Suzuki Matthias Harbers Gene E Robinson Vladimir B Bajic

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

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

Authors:
Othman Soufan Dimitrios Kleftogiannis Panos Kalnis Vladimir B Bajic

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

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).

Authors:
Lianguo Chen Jin Sun Huoming Zhang Doris W T Au Paul K S Lam Weipeng Zhang Vladimir B Bajic Jian-Wen Qiu Pei-Yuan Qian

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

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).

Authors:
Lianguo Chen Huoming Zhang Jin Sun Yue-Him Wong Zhuang Han Doris W T Au Vladimir B Bajic Pei-Yuan Qian

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

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

Authors:
Lina Ma Ang Li Dong Zou Xingjian Xu Lin Xia Jun Yu Vladimir B Bajic Zhang Zhang

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

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

Authors:
Arwa Bin Raies Hicham Mansour Roberto Incitti Vladimir B Bajic

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

Distinct profiling of antimicrobial peptide families.

Authors:
Abdullah M Khamis Magbubah Essack Xin Gao Vladimir B Bajic

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

DEEP: a general computational framework for predicting enhancers.

Authors:
Dimitrios Kleftogiannis Panos Kalnis Vladimir B Bajic

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

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

Authors:
Magbubah Essack Hanin S Alzubaidy Vladimir B Bajic John A C Archer

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

DEOP: a database on osmoprotectants and associated pathways.

Authors:
Salim Bougouffa Aleksandar Radovanovic Magbubah Essack Vladimir B Bajic

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

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

Authors:
Rehab Z Abdallah Mustafa Adel Amged Ouf Ahmed Sayed Mohamed A Ghazy Intikhab Alam Magbubah Essack Feras F Lafi Vladimir B Bajic Hamza El-Dorry Rania Siam

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

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

Authors:
Tanvir Alam Yulia A Medvedeva Hui Jia James B Brown Leonard Lipovich Vladimir B Bajic

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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109443PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183604PMC
December 2015

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

Authors:
Ari J S Ferreira Rania Siam João C Setubal Ahmed Moustafa Ahmed Sayed Felipe S Chambergo Adam S Dawe Mohamed A Ghazy Hazem Sharaf Amged Ouf Intikhab Alam Alyaa M Abdel-Haleem Heikki Lehvaslaiho Eman Ramadan André Antunes Ulrich Stingl John A C Archer Boris R Jankovic Mitchell Sogin Vladimir B Bajic Hamza El-Dorry

PLoS One 2014 12;9(6):e97338. Epub 2014 Jun 12.

Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097338PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055538PMC
October 2015

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

Authors:
Francy Jimenez-Infante David K Ngugi Intikhab Alam Mamoon Rashid Wail Baalawi Allan A Kamau Vladimir B Bajic Ulrich Stingl

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

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).

Authors:
Stefan W Grötzinger Intikhab Alam Wail Ba Alawi Vladimir B Bajic Ulrich Stingl Jörg Eppinger

Front Microbiol 2014 7;5:134. Epub 2014 Apr 7.

Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia.

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http://journal.frontiersin.org/article/10.3389/fmicb.2014.00
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http://dx.doi.org/10.3389/fmicb.2014.00134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985023PMC
April 2014

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

Authors:
Zhao-Ming Gao Yong Wang On On Lee Ren-Mao Tian Yue Him Wong Salim Bougouffa Zenon Batang Abdulaziz Al-Suwailem Feras F Lafi Vladimir B Bajic Pei-Yuan Qian

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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http://dx.doi.org/10.1007/s00248-014-0419-0DOI Listing
October 2014

Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus spongiarum".

Authors:
Zhao-Ming Gao Yong Wang Ren-Mao Tian Yue Him Wong Zenon B Batang Abdulaz M Al-Suwailem Vladimir B Bajic Pei-Yuan Qian

mBio 2014 Apr 1;5(2):e00079-14. Epub 2014 Apr 1.

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http://dx.doi.org/10.1128/mBio.00079-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977351PMC
April 2014