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, PlosOne, Scientific Reports, etc) and conferences (ISMB, RECOMB, ECCB, GECCO, etc). He is a reviewer in many reputed international journals such as Bioinformatics,  Algorithms for Molecular Biology , Biochimie, BMC Bioinformatics and Medical Science Monitor.

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 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, ISMB, BO, APBioNET, IASTED, INFORMS, ICS and NBBnet.
Academic Qualifications:
PhD. in Computer Science
Projects and Grants:
YearTitleResearch ThemeFunds (AED)Source of GrantPrincipal InvestigatorAffiliation
2014
Semantic Web for Bioinformatics
Bioinformatics, life science, semantic web
-
ICT
PI
2014
Study of Biological Networks under Differential Conditions: Applications to Cancer [Delta Networks]
Bioinformatics
392,000
NRF, UAEU
PI
2014
Privacy Protection of Biomedical Data In The Cloud
Information Security, Bio-Medical Informatics
395,000
Startup, UAEU
Co-PI
2014
Effects of Crocin "Saffron" on Human Hetaocellular Carcinoma: An in Vitro-based Metabolomic Approach
Bioinformatics, Cancer research
136,000
Terry Fox Funding
Co-PI
2013
3Moons: Modular, Multiscale, Multiomic OncOlogy Networks
Bioinformatics
291,866
NRF, UAEU
Co-PI
2012
Glycomic Screen for Novel Molecular Therapeutic Targets: Insights into Saffron's Protection against Liver Cancer
Bioinformatics, Cancer 
200,000
NRF, UAEU
Co-PI
2011
Human Cancer Protein-Protein Interaction Network: Domain Linkers Perspective
Bioinformatics
518, 540
NRF, UAEU
PI
2011
Online Service Oriented Ubiquitous Health System for Chronic Diseases Monitoring, Tracking, and Prevention in UAE
Healthcare
750,000
NRF, UAEU
Co-PI
2011
Interactive Portal and Software for Medical Database Development
Healthcare
79,500
Zayed Military Hospital
PI
2010
Arabic Semantic Analysis a novel way to predict protein interaction
Bioinformatics, data mining, machine learning
130,000
Emirates Foundation
PI
2009
Markov Chain-based Amino Acid Classification Discovery for Protein Homology Detection
Bioinformatics
18.500
UAEU
Co-PI
2008
Effect of the new mobile phone generation (3.5G) on human leukocytes
Healthcare
19,500
UAEU
PI
2007
Enhancement of Biological Databases and Software Distribution over Low-Bandwidth Networks
Bioinformatics, Networking
19,500
UAEU
PI
2006
Protein Function Prediction from Protein-Protein Interaction Data Using Machine Learning Techniques
Bioinformatics
12,500
UAEU
PI
2005
String Scoring Method for Protein Homology Detection
Bioinformatics
9,500
UAEU
PI
Research Interests:
Data Mining, Machine Learning, Bioinformatics
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:
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. Nazar Zaki and Antonio Mora (accepted) A comparative analysis of computational approaches and algorithms for protein subcomplex identification. Scientific Reports (IF 2.927), Nature.  
2. 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): 10.1371/0086456. 2014 (IF: 3.730).
3. Al Mutaz Abdalla, S. Deris and N.Zaki (2013) Extracting and Selecting Meaningful Features from Mammogram Digital Image Using Factor Analysis Technique. Inter. J. of Computer and Technology, Vol. 1, No. 5, pp 2512-2533 (IF 1.341).
4.	Zaki NM., Dmitry D. and Berengueres J. (2013), Protein Complex Detection using Interaction Reliability Assessment and Weighted Clustering Coefficient. BMC Bioinformatics, 14:163 (IF 2.75, Class A).
5.	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 (IF: 3.392, Class B).
6.	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 (IF: 3.43, Class A).
7.	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. (IF: 4.411, Class A).
8.	Zaki NM., Wassim M El-Hajj, Hesham Kamel, Fadi Sibai (2011). STRIKE: A Protein-Protein Interaction Classification Approach. Advances in Experimental Medicine and Biology. Vol. 696, pp: 263-70., Springer (IF 1.379).
9.	Ashraf A Aly, Safaai Bin Deris, NM. Zaki, (2011). A Novel Image Segmentation Enhancement Technique based on Active Contour and Topological Alignments. Advanced Computing: An International Journal (ACIJ), Vol.2, No.3, May 2011.
10.	Al Mutaz M Abdalla, Safaai Dress, NM. Zaki, (2011). Detection of Masses in Digital Mammogram Using Second Order Statistics and Artificial Neural Network. International Journal of Computer Science and Information Technology. Vol. 3, no. 3, 176 p. Jun 2011.
11.	Ashraf A Aly, Safaai Bin Deris, NM. Zaki, (2011). Research Review for Digital Image Segmentation Techniques. International Journal of Computer Science and Information Technology (IJCSIT). 3(5), 99-106, 2011.
12.	Al Mutaz .M. Abdalla, Safaai Deris, NM. Zaki, (2011). Masses Detection in Digital Mammogram by Gray Level Reduction using Texture coding Method. International Journal of Computer Applications (0975-8887) Volume 29- No.4.
13.	Ashraf A. Aly, Safaai Bin Deris, and Nazar Zaki (2011) The Effects on Cells Mobility Due to Exposure to EMF Radiation. Advanced Computing: An International Journal ( ACIJ ), Vol.2, No.4, July 2011.
14.	Ashraf A. Aly, Safaai Bin Deris and Nazar Zaki (2011) A new Algorithm for Cell Tracking Technique. Advanced Computing: An International Journal ( ACIJ ), Vol.2, No.6, November 2011.
15.	Zaki NM., Lazarova-Molnar S., El-Hajj W., Campbell P. (2009). Protein-protein interaction based on pairwise similarity. BMC Bioinformatics. 10:150. (, IF: 3.78, Class A).
16.	Zaki, NM. (2009). Prediction of Protein–Protein Interactions Using Pairwise Alignment and Inter-Domain Linker Region. Engineering Letters. Vol. 16(4).
17.	Zaki, NM., and Deris, S. (2007). Detecting Remote Protein Evolutionary Relationships via String Scoring Method. International J. of Biomedical Sciences. Vol. 2, pp: 59-66.
18.	Zaki, NM., Deris, S. and Alashwal, H. (2006). Protein-Protein Interaction Detection Based on Substring Sensitivity Measure. International J. of Biomedical Sciences, Vol. 1, pp: 148-154.
19.	Zaki, N.M., Deris, S., and Illias, R. M. (2005). Application of string kernels in protein sequence classification. Applied Bioinformatics. Vol. 4, pp: 45-52 (Class C). Selected by BioInfoBank to be among the most 13 recommended papers on proteins.
20.	Zaki, NM., and Deris, S. (2005). Representing Protein Sequence with Low Number of Dimensions. J. of Biological Sciences. Vol. 5, pp: 795-800.
21.	Zaki, N.M., Deris, S., and Illias, R. (2004). Feature Extraction for Protein Homology Detection using Hidden Markov Model combining Scores.  International J. of Computational Intelligence and Applications. Vol. 4, pp: 1-12 (Class A). (Selected as a sample for the World Scientific and Imperial College Press, 2005 catalogue).
22.	Zaki, NM., Deris, S., and Chin, KK. (2003). A comparison of quadratic programming solvers in support vector machines training. Jurnal Teknologi. Vol. 39, pp: 45-56.
23. Zaki, NM. and Deris, S. and Chin, KK. (2003). Extending the decomposition algorithm for support vector machines training. Journal of Information and Communication Technology, 1 (2). pp. 17-29. ISSN 2180-3862.
24.	Zaki, NM. Deris, S. and Illias R (2003) A Comparative Analysis of Protein Homology Detection Methods. Journal of Theoretics Volume 5-4, 2003.
25.	Zaki, NM. Deris, S. and Illias R (2003) Assignment of Protein Sequence to Functional Family Using Neural Network & Dempster Shafer Theory. Journal of Theoretics, No. 1, Volume 5, 2003.
Conferences:
Papers are downloadable from http://faculty.uaeu.ac.ae/nzaki/

1.	Eileen Marie Hanna and Nazar Zaki (2013) ProRank+: Detecting overlapping protein complexes using a protein ranking algorithm. ISMB/ECCB 2013, Berlin 22nd July, 2013. Poster.
2.	Maad Shatnawi and Nazar Zaki (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. Slides
3.	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.
4.	Maad Shatnawi 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.
5.	Maad Shatnawi, Sanja Lazarova?Molnar and Zaki, NM. (2013) Modeling and Simulation of Epidemic Spread: Recent Advances. 9th International Conference on Innovations in Information Technology (IIT), pp 118-123, 17th March 2013.
6.	Nazar Zaki “Protein ranking algorithm improves the identification of protein complexes from the protein-protein interaction network. RECOMB 2013. Beijing, April, 2013. (Poster).
7.	Jose Berengueres, Fatma Alsuwairi, Nazar Zaki and Tony Ng (2013) Emo-Bin: how to recycle more by using emoticons. 8th ACM/IEEE international conference on Human-robot interaction, pp 397-398. Best video award
8.	Fatma Al Suwairi, Jose Berengueres, Nazar Zaki and Tony Ng. (2013) Gamification of a Recycle Bin with Emoticons. 8th ACM/IEEE International Conference on Human-Robot Interaction, March 2013, Tokyo, Japan.
9.	Dmitry Efimov, Zaki, NM., Jose Berengueres (2012). Detecting Protein Complexes from Noisy Protein Interaction Data. 18th ACM SIGKDD, (BioKDD), Beijing, China, 12-16 Aug, 2012, pp: 1-7.
10.	Zaki, NM. (2012). Google PageRank Algorithm for Detecting Protein Complexes. Poster. The 11th ECCB'12. Basel Switzerland, 9-12 September, 2012. Poster.
11.	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.
12.	Zaki, NM. (2011) A combination of amino acid composition and matching for conotoxin superfamily classification. 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 10th European Conference on Computational Biology (ECCB), 17-19 July. Vienna, Austria. Poster.
13.	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.
14.	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.
15.	Zaki, NM., Piers Campbell, Stefan Wolfsheimer and Gregory Nuel (2011). "Features Extraction Using Free Score of Words for Classifying Conotoxin Superfamily", 12th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD 2011), 6-8 July 2011 in Sydney, Australia.
16.	Ashraf A. Aly; Safaai Bin Deris; Nazar Zaki (2011) Intelligent techniques for image segmentation in cell tracking and mobility analysis, 2011 International Conference on Innovations in Information Technology, IIT 2011.?2011:346-349
17.	Fadi Sibai and Nazar Zaki (2010) Parallel Protein Sequence Matching on Multicore Computers. SoCPaR 2010, 7-10 Dec 2010, Paris, France.
18.	Zaki, NM. and Wassim El-Hajj (2010) Predicting Membrane Proteins Type Using Inter-domain Linker Knowledge. The 2010 International Conference on Bioinformatics and Computational Biology (BIOCOMP'10), 12-15 July, Las Vegas, US.
19.	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).
20.	Ashraf A Aly, S Bin Deris, Nazar Zaki (2008) Research review on the biological effect of cell phone radiation on human.
21.	International Conference on Innovations in Information Technology, 140-144, UAE.
22.	El-Hajj, W.M., Aloul, F., Trabelsi Z., and Zaki, NM. (2008). Detecting Port Scanning using Fuzzy Based Intrusion Detection System. International Wireless Communications and Mobile Computing Conference (IWCMC’08). Crete Island, Greece, August 6-8, 2008.
23.	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.
24.	A Abdalla, S Deris, N Zaki (2007) Breast Cancer Detection Based on Statistical Textural Features Classification. International Conference on Innovations in Information Technology, 728-730, UAE.
25.	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.
26.	Zaki, NM., Deris, S., and Illias, R. M. (2005). Simple Representation of Protein Sequence for detecting homology. International Conference on Artificial Intelligence. Las Vegas, USA, 27-30 June 2005.
27.	Nazar Zaki; Safaai Deris (2005) Combining three scoring algorithms for representing protein sequence, Proceedings of the 2005 International Conference on Artificial Intelligence, ICAI'05.?2005;2:839-845.
28.	Yeo LC, Deris S, Illias RM, Zaki NM (2003) Advancement of Bioinformatics in Malaysia. in Advance Technology Congress. Serdang, Malaysia: Universiti Putra Malaysia.

Other Conference Papers/posters (mainly with undergraduate students):
1.	Anwaar Al Nuaimi, Nazar Zaki, Kamal Khazanehdari, Ruqaiyah A. Ail and Amr Amin (2013) Pro-apoptotic Effect of Saffron’s Bioactive Molecules: In silico Analyses. 5th International Conference on Drug Discovery and Therapy. Poster.
2.	Bothainah Al Baeie and Fatema Al Suwairi (2013) Sorting using colors. 9th International Conference on Innovations in Information Technology (IIT). Poster.
3.	Hoda Alhameidy and Nafla Al Darei (2013) Recognizing Hand-written English Letters Using Support Vector Machines. 9th International Conference on Innovations in Information Technology (IIT). Poster.
4.	Anwaar Al Nuaimi, Nazar Zaki, Kamal Khazanehdari, Ruqaiyah A. Ail and Amr Amin (2013) Pro-apoptotic Effect of Saffron’s Bioactive Molecules: In silico Analyses. 5th International Conference on Drug Discovery and Therapy. Poster.
5.	Azza AlHouqani, Hajar Alreyami, and NM. Zaki,(2012). A Web application for Protein?protein Interaction and Complex Prediction. Fourth Annual Undergraduate Research Conference on Applied Computing. Zayed University, April 18 ? 19, 2012,Dubai,UAE. Poster.
6.	Alya Al Sheraiqi and NM. Zaki,(2011). Swine Flu Detection Using Nearest Neighbor Generalization. Third Annual Undergraduate Research Conference on Applied Computing. Zayed University, May 04?05, 2011,Dubai,UAE.
7.	Azza Al Houqani and NM. Zaki,(2011). Detecting spam emails using machine learning techniques. Third Annual Undergraduate Research Conference on Applied Computing. Zayed University, May 04?05, 2011,Dubai, UAE.
8.	Hajar Alreyami and NM. Zaki,(2011).Classifying Pima Indian Diabetes Using Machine Learning Techniques. Third Annual Undergraduate Research Conference on Applied Computing. Zayed University, May 04?05, 2011,Dubai,
UAE. Engineering and Computational Science, Springer, pp 635?645. Poster.