Faculty Profile

Nazar Zaki
Associate Professor
Intelligent Systems
E-mail: nzaki [At] uaeu.ac.ae
Office Phone: +971 3 713 5571
Homepage: http://faculty.uaeu.ac.ae/nzaki

Biography:
Dr. Nazar Zaki is an Associate Professor and coordinator of two tracks namely Intelligent Systems and Software Development. His research interest is in the field of bioinformatics, data mining and machine learning. He mainly focuses on developing an intelligent data mining algorithms to solve specific biological problems, such as protein function/structure prediction, protein interaction network analysis and protein complex detection.  He has published many scientific results in world class journals (BMC Bioinformatics, Proteins: Structure, Function, and Bioinformatics, PloS one, Scientific Reports, IEEE/Trans. CBB etc.) and conferences (ISMB, RECOMB, ECCB, GECCO, etc). He reviews papers in many reputed international journals such as Bioinformatics,  Algorithms for Molecular Biology , Biochimie, BMC Bioinformatics and IEEE/Transactions on Computational Biology and Bioinformatics.

?Dr. Zaki received many scholarship awards such as the Faculty Recognition Award for Excellence in Scholarship in 2007 and 2012, respectively, certificate of merit in the World Congress on Engineering, Imperial College in 2008, and best paper award in ACM Genetic and Evolutionary Computation Conference GECCO in 2011.

Dr Zaki has several valuable research collaborators in prestigious institutions such as MAP5, University Paris-Descartes, Paris, France;  Center for Computational Science (CCS), University of Miami, USA; Institute of Clinical Physiology, Experimental Oncology Unit, CNR, Siena, Italy; Laboratory of Integrative Systems Medicine (LISM), CNR, Pisa, Italy; NYU Bioinformatics group, NYU, USA.

Dr. Zaki was one of the executive members who established the Middle East Association of Healthcare Informatics (MEAHI)? in UAE in 2005. He is currently a member of many other professional societies such as ACM, IEEE, ISCB, APBioNET, IASTED and NBBnet.
Academic Qualifications:
PhD. in Computer Science
Research Interests:
Data Mining, Machine Learning, Bioinformatics, social network mining
Tools:
Perl, C/C++, classification software (SVM, NN, decision tree, etc), Bioinformatics software and databases (CLC, BLAST, FASTA, Cytoscape, Gephi, etc), Matlab, Linux, Windows, image and video editing software.
Teaching Interests:
Data Mining, Machine Learning, Bioinformatics
Awards:
2013 Received the best video award at the 8th ACM/IEEE International Conf. on Human-Robot Interaction, Japan.
2012 Received the FIT Recognition Award for Excellence in Scholarship.
2012 Won the top academic prize, the Software Development Trade Show (SDTS 2012)
2012 Received the FIT Recognition Award for Excellence in Scholarship.
2011 Best paper award at GECCO 2011, Dublin, Ireland.
2008 Best Paper Award (The 2008 International Conference of Systems Biology and Bioengineering, Imperial College, London, UK)
2007 Received the College Recognition Award for Excellence in Scholarship.
2007 Best Student Paper Award
2006 Best Student Senior Project Award
2006 Listed by Marquis Who's Who in Science and Engineering
2005 Selected paper (The World Scientific and Imperial College Press for the 2005 catalogue)
2004 Best PhD student, Univeriti Teknologi Malaysia
2004 Completed S* Bioinformatics course with distinction (National University of Singapore)
2001 Fellowship, Universiti Teknologi Malaysia
1996 Best MSc student.
Books:
1. Zaki, NM. and Mohamed E.A. (2016) A combination of protein-protein interaction network topological and biological process features for multi-protein complex detection. Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology (Springer- 978-0-12-804203-8).

2. Nazar Zaki (2009), Protein-Protein Interaction Prediction Using Homology and Inter-domain Linker Region Information", Advances in Electrical Engineering and Computational Science, Springer, pp 635-645.
Journals:
Papers are downloadable from http://faculty.uaeu.ac.ae/nzaki/

1. EM. Hanna, Nazar Zaki and Amr Amin (2015) Detecting Protein Complexes in Protein Interaction Networks Modeled as Gene Expression Biclusters. PLoS ONE 10(12): e0144163/journal.pone.0144163. (ISI IF 3.234)

2. Amr Amin, Alaaeldin A. Hamza, Sayel Daoud, Nazar Zaki, Kourosh Salehi-Ashtiani, Ala’a Al-Hrout1, Amphun Chaiboonchoe, Badriya Baig1, Kamal Khazanehdari, Thomas E. Adrian (Accepted) Saffron-Based Crocin Prevents Early Lesions of Liver Cancer: In Vivo, In Vitro and In Silico Insights. Recent Patents on Anti-Cancer Drug Discovery (ISI IF 4.3).	
 
3. Federico Malusa, Monia Taranta, Nazar Zaki, Caterina Cinti and Enrico Capobianco (2015) Time-course Gene Profiling and Networks in Demethylated Retinoblastoma cell line. Oncotarget,  (ISI IF 6.63).
 
4. Antonio Mora, Monia Taranta, Nazar Zaki, Caterina Cinti, and Enrico Capobianco (2015) Epigenetically-driven Network Cooperativity: Meta-analysis in Multi-drug Resistant Osteosarcoma, Journal of Complex Networks. doi: 10.1093/comnet/cnv017.	 

5. Amr Amin, Asma Bashir, Nazar Zaki, Diane McCarthy, Sanjida Ahmed, Mohamed Lofty (2015) Insights into glycan biosynthesis of chemically-induced hepatocellular carcinoma in rats: A glycomic analysis. World J. Gastroenterol. 2015 May 28; 21(20):6167-79. doi: 10.3748/wjg.v21.i20.6167. (ISI IF 2.369).	
 
6. M. Shatnawi, NM. Zaki (2015) Inter-domain Linker Prediction Using Amino Acid Compositional Index. Computational Biology and Chemistry (ISI IF 1.595), Vol. 55, April 2015, Pages 23–30.	 
NM. Zaki , AM. Elfadil and Mora A. (2015) Characterization of Protein Complexes and Sub-complexes in Protein-protein Interaction Databases. Biochemistry Research International. Vol. 2015, 245075.	
 
7. O. Y. Al-Jarrah, P. D. Yoo, K. Taha, S. Muhaidat, A. Shami and NM. Zaki (2014) Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 99: pp 1545-5963, (ISI IF 1.536), 2014.	 

8. Shatnawi M., Zaki, NM. and Yoo P. (2014) Protein Inter-Domain Linker Prediction Using Random Forest and Amino Acid Physiochemical Properties. BMC Bioinformatics Volume 15: 12, S20, (ISI IF 2.670)2014.	 

9. EM. Hanna and N. Zaki(2014) Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. BMC Bioinformatics, 15:204. (ISI IF 3.024), 2014.	
 
10. E. Capobianco, A. Mora, D. La Sala, A. Roberti, N. Zaki, E. Badidi, M. Taranta and C. Cinti  (2014) Separate and Combined Effects of DNMT and HDAC Inhibitors in treating Human Multi-Drug Resistant Osteosarcoma HosDXR150 cell line. PloS ONE, 10.1371/journal.pone.0095596 (ISI IF: 3.730).	 

11. A. Mora, M. Taranta, N. Zaki, E. Badidi , C. Cinti, E. Capobianco (2014) Ensemble Inference by Integrative Cancer Networks. Frontiers Genetics, Front. Genet. 5:59. doi: 10.3389/fgene.2014.00059, Nature Group.	 

12. Nazar Zaki and Antonio Mora (2014) A comparative analysis of computational approaches and algorithms for protein subcomplex identification. Scientific Reports,  4: 4262, (ISI IF 5.078), Nature Group.  Supp. materials.
 
13. Bouktif S., Hanna EM., Zaki NM and Abu Khousa E. (2014) Ant Colony Optimization Algorithm for Interpretable Bayesian Classifiers Combination: Application to Medical Predictions. PLoS ONE 9(2): 10. 2014 (ISI IF: 3.534).	 

14. Zaki NM., Dmitry D. and Berengueres J. (2013), Protein Complex Detection using Interaction Reliability Assessment and Weighted Clustering Coefficient. BMC Bioinformatics, 14:163 ( , ISI IF 3.02).Supp. Materials.

15. Zaki NM., Berengueres J., Efimov D. (2012). Detection of protein complexes using a protein ranking algorithm.Proteins: Structure, Function, and Bioinformatics.  80(10): pp 2459-2468, 2012. Wiley (ISI IF: 3.392).	
 
16. Zaki NM., Wolfsheimer S., Nuel G. and Khuri S. (2011). Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines. BMC Bioinformatics. 2011, 12:217 (ISI IF: 3.43). Supp. Materials.

17. Zaki NM., Bouktif S. and Lazarova-Molnar S. (2011) A Combination of Compositional Index and Genetic Algorithm for Predicting Transmembrane Helical Segments. PLoS One 6(7): 2011. (ISI IF: 4.411). Supp. Materials.

18. Zaki NM., W. El-Hajj, H. Kamel, F. Sibai (2011). STRIKE: A Protein-Protein Interaction Classification Approach. Advances in Exp. Medicine and Biology. Vol. 696, pp: 263-70., Springer (ISI IF 1.379). Supp.  Materials.
 
19. Zaki NM., Lazarova-Molnar S., El-Hajj W., Campbell P. (2009). Protein-protein interaction based on pairwise similarity. BMC Bioinformatics. 10:150. (, ISI IF: 3.78).	
Conferences:
Papers are downloadable from http://faculty.uaeu.ac.ae/nzaki/

1. Zaki, NM.  (Accepted) PageRank Algorithm to Improve the Peer-Led Team Learning Pedagogical Approach.	
 
2. Eiman Al Nuaimi, Samira Al Marzooqi and Zaki, NM. (2016) Predicting the Decision for the Provision of Municipal Services Using Data Mining Approaches. ICBDSC 2016, 3rd International Conference on Big Data and Smart City, Oman, Muscat, 15-16 March 2016.

 3. Noura AlDarmaki,Noura AlMansouri, Elfadil A. Mohamed and Zaki, NM. (2016) Prediction of the Closing Price in the Dubai Financial Market: A Data Mining Approach. ICBDSC 2016, 3rd International Conference on Big Data and Smart City, Oman, Muscat, 15-16 March 2016.

 4. Eileen Marie Hanna and Zaki, NM.  (2015) Detecting Protein Complexes using Gene Expression Biclusters. 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 1-7, Niagara Falls, ON, 12-15 Aug 2-15.

 5. Maad Shatnawi and Zaki, NM.  (2015) Novel Domain Identification Approach for Protein-Protein Interaction Prediction. 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 1-8, Niagara Falls, ON, 12-15 Aug 2-15.

6. N. Zaki and A. Mora (2014) Characterization of Nested Complexes in Protein Interaction Networks. 2014 International Conference on Mathematics and Computers in Sciences and in Industry (MCSI). 48-54,  Varna, Bulgaria, 13-15 Sept. 2014.

7. N. Zaki (2014) Multi-protein complex detection by integrating network topological features and biological process information. ICBES'14, Prague, Czech Republic, Aug 12th, 2014.

8. Eileen M. Hanna and Nazar Zaki (2014) Dynamic Protein-Protein Interaction Networks and the Detection of Protein Complexes: An Overview. The 14th International Conference on Bioinformatics & Computational Biology (BIOCOMP'14), 21-24 July, US.

9. Hanna EM. and Zaki, NM. (2014) ProRank+: A Method for Detecting Protein Complexes in Protein Interaction Networks. BIOINFORMATICS, 5th Int. Conference. March, 2014. Loire Valley, France.

10. Shatnawi M. and Zaki, NM. (2013) Prediction of Protein Inter-Domain Linkers Using Compositional Index and Simulated Annealing, in BIO13, Genetic and Evolutionary Computation Conference (GECCO '13). pp 1603-1608, Amsterdam, 6th July, 2013.

 11. Zaki, NM., Kalthoom Alawar, Amna Al Dhaheri and Saad Harous (2013) Protein?protein Interaction Prediction using Arabic Semantic Analysis. 9th International Conference on Innovations in Information Technology (IIT), pp 243-247, 17th March 2013.

12. Shatnawi M. and Zaki, NM. (2013) Prediction of Inter?Domain Linker Regions in Protein Sequences: A Survey. 9th International Conference on Innovations in Information Technology (IIT), pp 237-242, 17th March 2013.

13. Efimov D., Zaki, NM., Berengueres J. (2012). Detecting Protein Complexes from Noisy Protein Interaction Data. 18th ACM SIGKDD, (BioKDD), Beijing, China, 12-16 Aug, 2012, pp: 1-7.

14. Zaki, NM., Jose P. Dmitry D. (2012). ProRank: A Method for Detecting Protein Complexes. The 14th international conference on Genetic and evolutionary computation conference (GECCO '12), pp: 209-216, July 7–11, 2012, Philadelphia, Pennsylvania, USA.

 15. Zaki, NM., Salah Bouktif and Sanja L., (2011), "A Genetic Algorithm to Enhance Transmembrane Helices Topology Prediction Using Compositional Index", 2011 ACM GECCO2011, Dublin, Ireland, July 12-16. Won the Best Paper Award.

16. Zaki, NM., Fadi Sibai and Piers Campbell (2011), "Conotoxin Protein Classification Using Pairwise Comparison and Amino Acid Composition", 2011 ACM Genetic and Evolutionary Computation Conference (GECCO2011), Dublin, Ireland, July 12-16.

 17. Zaki, NM. (2009). Protein-Protein Interaction Prediction using Homology and Inter-domain Linker Region Information. The 2008 International Conference of Systems Biology and Bioengineering, Imperial College, London, U.K., 2nd July 2008. (Received the Certificate of Merit, published by Springer).

 18. Ashraf A Aly, S Bin Deris, NM. Zaki (2008) Research review on the biological effect of cell phone radiation on human. International Conference on Innovations in Information Technology, 140-144, UAE.

 19. Zaki, NM., Deris, S., and Alwahaishi, S. (2007). SubSS: A Protein-Protein Interaction Detection Tool. 6th ACIS International Conference on Computer and Information Science. pp. 999-1004. Melbourne, Australia, 11-13 July 2007.

 20. Al Mutaz Abdalla, Safaai Deris, Nazar Zaki and Doaa Ghoneim (2007) Breast Cancer Detection Based on Statistical Textural Features Classification. 4th International Conference on Innovations in Information Technology (IIT '07). pp: 728 - 730, 18 Nov. 2007, Dubai, UAE. Download

21. Zaki, NM. (2006). Detecting Remote Protein Evolutionary and Structural Relationships via String Scoring Method. International Conference on Machine Learning and Cybernetics (ICMLC'06). Dalian, China, 13-16 Aug 2006.

 22. S. Deris, H. Alashwal, MS. Mohamad, Y. Lee Chin, MR. Othman, Y. Zakaria, S. Zainudin, NM. Zaki, S. Othman, SN. Arjunan (2005). Bioinformatics: A Tool for Bio-Knowledge Generation (Keynote Speech). The International Conference on Information Technology & Multimedia (ICIMU’05). November 22-24, 2005. Cyberjaya, Malaysia.