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Selected Publications
Journal Papers:
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HM Ismail, B Belkhouche, N Zaki (2018)
Semantic Twitter sentiment analysis based on a fuzzy thesaurus.
Soft Computing, Springer Nature, 1:14. (ISI IF 2.472) |
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AA Moustafa, M Hassan, DH Hewedi, I Hewedi, J. Garami, H. Al
Ashwal, N. Zaki, et al. (2018)
Genetic underpinnings in Alzheimer’s disease–a review.
Reviews in the Neurosciences, Vol. 29(1), 21-38. |
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Nazar Zaki, Chandana Tennakoon (2017)
BioCarian: search engine for exploratory searches in
heterogeneous biological databases. BMC Bioinformatics,
Vol. 18, No. 1, Page 435 (ISI IF 2.448) |
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Ahmed A Moustafa, Mubashir Hassan, Doaa H Hewedi, Iman Hewedi,
Julia K Garami, Hany Al Ashwal, Nazar Zaki, et.al. (2017)
Genetic underpinnings in Alzheimer’s disease–a review.
Reviews in the Neurosciences, 2017 (ISI IF 2.546) |
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1 |
AM Ismail, MS Mohamad, HA Majid, KH Abas, S Deris (2017)
An Improved Hybrid of Particle Swarm Optimization and the
Gravitational Search Algorithm to Produce a Kinetic Parameter
Estimation of Aspartate Biochemical Pathways. Biosystems,
2017. |
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2 |
WH Chan, MS Mohamad, S Deris, N Zaki, S Kasim (2016)
Identification of informative genes and pathways using an
improved penalized support vector machine with a weighting
scheme. Computers in biology and medicine, 2016 |
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3. |
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) |
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4. |
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 (2016)
Saffron-Based Crocin Prevents Early Lesions of Liver Cancer: In
Vivo, In Vitro and In Silico Insights. Recent Patents on
Anti-Cancer Drug Discovery, Vol. 11 , Issue 1 , 2016 (ISI IF 4.3). |
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5. |
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). |
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6. |
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. |
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7. |
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). |
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8. |
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. |
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9. |
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. |
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10. |
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. |
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11. |
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. |
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12. |
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. |
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13. |
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). |
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14. |
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. |
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15. |
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. |
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16. |
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). |
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17. |
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. |
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18. |
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). |
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19. |
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. |
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20. |
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. |
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21. |
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. |
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22. |
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).
Supplementary Materials.
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23. |
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).
Slides. |
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24. |
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). |
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Book Chapters:
1. Nazar Zaki,
(2016) PageRank Algorithm to Improve the Peer-Led Team Learning
Pedagogical Approach, Smart Education and e-Learning, Volume 59 of the
series Smart Innovation, Systems and Technologies pp 225-234, Springer.
2. F. Alnajjar,
F. Harib, S. AlAmeri, A. Almarzoqi, M. Itkonen, H. Yamasaki, N. Zaki and
S. Shimoda (2016) The Role of Inputs Combination to Enhance the Internal
Model and Body Control Ability. Converging Clinical and Engineering
Research on Neurorehabilitation II, Volume 15 of the series Biosystems &
Biorobotics, Publisher: Elsevier, pp 901-905.
3. N. Zaki and
Elfadil mohammed (2015) A Combination of Protein-Protein Interaction
Network Topological and Biological Process Features For Multiprotein
Complex Detection, Emerging Trends in Applications and Infrastructures
for Computational Biology, Bioinformatics, and Systems Biology Systems
and Applications, Publisher: Elsevier, pp.305-315.
4. Zaki,
NM.
(2009)
Protein‐Protein Interaction Prediction Using
Homology and Inter‐domain Linker Region Information.
Advances in Electrical Engineering and Computational
Science, Springer, pp 635‐645.
Conference Papers:
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Nazar Zaki, Chandana Tennakoon, Hany Al Ashwal,
Knowledge graph construction and search for biological
databases, Research and Innovation in Information
Systems (ICRIIS), 2017 International Conference on, pp
1-6, July 2017.
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Nazar Zaki and Chandana Tennakoon (2017) BioCarian: A Search
Engine for Performing Exploratory Searches of Biological
Databases,
International Conference on Big Data Analytics, Data Mining and
Computational Intelligence 2017 (BigDaCI 2017), Portugal, July
20-23, 2017 |
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Nazar Zaki and Chandana Tennakoon (2016) Efficient Exploration
of Biological Data using Semantic Web Compatible Databases. The
2016 3rd Intl. Conference on Soft Computing & Machine
Intelligence (ISCMI 2016), Dubai, Nov. 23-25, 2016. |
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Heba Ismail, Nazar Zaki and Boumediene Belkhouche (2016)
Using Custom Fuzzy Thesaurus to Incorporate Semantic and
Reduce Data Sparsity for Twitter Sentiment Analysis. The
2016 3rd Intl. Conference on Soft Computing & Machine
Intelligence (ISCMI 2016), Dubai, Nov. 23-25, 2016. |
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Alramzana Navaz, Elfadil Mohammed, Mohamed Adel Serhani
and Nazar Zaki (2016) The Use of Data Mining Techniques
to Predict Mortality and Length of Stay in an ICU. The
12th International Conference on Innovations in
Information Technology (IIT’16), Dubai, Nov. 28-29, 2016 |
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1. |
Nayla Alkhatri, Nazar Zaki, Elfadil Mohammed and Musa
Shallal (2016) The Use of Data Mining Techniques to
Predict the Ranking of E-Government Services. The 12th
International Conference on Innovations in Information
Technology (IIT’16), Dubai, Nov. 28-29, 2016. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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). |
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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. |
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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. |
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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 |
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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. |
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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. |
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