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, 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.
| Journals: |
1. 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).
2. 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).
3. 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).
4. 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).
5. 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).
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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).
13. Zaki, NM. (2009). Prediction of Protein–Protein Interactions Using Pairwise Alignment and Inter-Domain Linker Region. Engineering Letters. Vol. 16(4).
14. 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.
15. 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.
16. 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.
16. Zaki, NM., and Deris, S. (2005). Representing Protein Sequence with Low Number of Dimensions. J. of Biological Sciences. Vol. 5, pp: 795-800.
17. 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).
18. 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.
18. 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.
19. Zaki, NM. Deris, S. and Illias R (2003) A Comparative Analysis of Protein Homology Detection Methods. Journal of Theoretics Volume 5-4, 2003.
20. 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.
1. 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).
2. Zaki, NM., Kalthoom Alawar, Amna Al Dhaheri and Saad Harous (2013) Protein?protein Interaction Prediction using Arabic Semantic Analysis. Innovations 2013.
3. Maad Shatnawi and Zaki, NM. (2013) Prediction of Inter?Domain Linker Regions in Protein Sequences: A Survey. Innovations 2013.
4. Maad Shatnawi, Sanja Lazarova?Molnar and Zaki, NM. (2013) Modeling and Simulation of Epidemic Spread: Recent Advances. Innovations 2013.
5. 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
6. 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.
7. 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.
8. Zaki, NM. (2012). Google PageRank Algorithm for Detecting Protein Complexes. Poster. The 11th ECCB'12. Basel Switzerland, 9-12 September, 2012. Poster.
9. 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.
10. Nazar Zaki (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, Ausaria.
11. Nazar Zaki, Salah Bouktif and Sanja L., (2011), "A Genetic Algorithm to Enhance Transmembrane Helices Topology Prediction Using Compositional Index", 2011 Genetic and Evolutionary Computation Conference (GECCO2011), Dublin, Ireland, July 12-16. Won the Best Paper Award.
12. Nazar Zaki, Fadi Sibai and Piers Campbell (2011), "Conotoxin Protein Classification Using Pairwise Comparison and Amino Acid Composition", 2011 Genetic and Evolutionary Computation Conference (GECCO2011), Dublin, Ireland, July 12-16.
13. Nazar Zaki, 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.
14. Fadi Sibai and Nazar Zaki (2010) "Parallel Protein Sequence Matching on Multicore Computers". SoCPaR 2010, 7-10 Dec 2010, Paris, France.
15. Nazar Zaki 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.
16. Nazar Zaki (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. Published by Springer as a book chapter entitled “Advances in Electrical Engineering and Computational Science”.
(Received the Certificate of Merit).
17. Al Mutaz, M. A., Deris, S., Zaki, N. M., and Doaa, M. G. 2007. Breast Cancer Detection Based on Statistical Textural Features Classification. 4th Innovations’07 International Conference on Innovations in Information Technology. Dubai 18-20 Nov 2007.
(Won the Best Poster Award).
18. Zaki, N. M., 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.
19. Zaki, N. M. 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.
20. Zaki, N. M., 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.
21. Zaki, N. M., Deris, S., and Illias, R. 2003. Application of String Kernel in Protein Sequence Classification. International Conference on Bioinformatics. Penang, Malaysia, 8-10 Sep 2003.
22. Zaki, N. M., Deris, S., and Illias, R. 2003. Features Extraction through Hidden Markov Model Combining Scores. In International Conference on Bioinformatics. Penang, Malaysia, 8-10 Sep 2003.
23. Zaki, N. M., Deris, S., Illias, R. M., and Lee Chin, Y. 2003. Performance Analysis of String Kernel on Protein Sequence Classification. Artificial Intelligence Application in Industry. Kuala Lumpur, Malaysia, Jun 2003.
(Papers downloadable from http://faculty.uaeu.ac.ae/nzaki/)