Nazar Zaki
Associate Professor and Coordinator

 

 

TEACHING

RESEARCH

PUBLICATIONS

EVENTS

 

 

Research

 

Positions: Research Assistant (or Postdoc) - 2 years contract

Semantic Web for Bioinformatics

We are searching for outstanding Research Assistant, Postdoc to join a project aims to utilize semantic web to develop a search engine for life science. The objective of the project is to advance the state of the Semantic Web with application to Healthcare and Life Sciences domains. This project will deliver a solution for practicing biologists to find relevant information and increase their understanding of a disease, an essential step towards finding a cure, while at the same time contributing to the Semantic Web technology and web mining.  The expectation is to bring information from several scientific data sources, and provide Semantic Web integration for these knowledge and information repositories. This information will then be made available through a very rich and interactive portal application. The successful candidate is expected to have knowledge and experience of Semantic Web integration, web mining and web design/development. Experience/ knowledge of life science databases and biology is desirable.

 

To apply please send your CV to Dr. Nazar Zaki (nzaki@uaeu.ac.ae). We regret that only shortlisted candidates will be contacted.

 

 

 

Positions: Research Assistant (or Postdoc)

Project Title: Privacy Protection of Biomedical Data In The Cloud

We are currently seeking a Research Assistant (or Postdoc)  in Bioinformatics to work on developing innovative algorithms to be applied on genomic sequences. The successful candidate is expected to work on campus with the project PI and Co-PIs. The qualified candidates should be highly motivated in research and preferably have a Ph.D. in bioinformatics, computational biology, computer Science or related field upon the job start date. The successful candidate should have some experience in analyzing high-throughput genomic data and proven skills in at least one programming language (Perl, Java, or C/C++). Good understanding of molecular biology and familiarity with biostatistics are plus.

Applicants should send a CV, brief statement of research interests, and references to:
Dr. Nazar Zaki or Dr. Ahmed AL Faresi, College of Information Technology, United Arab Emirates University.
 

 

 

 

Software, data and supplementary materials:
 

DyCluster: Supplementary Materials
Detecting protein complexes in protein interaction networks modeled as gene expression biclusters

Data and codes
 

SVM-Net: Supplementary Materials
Multi-protein complex detection by integrating network topological features and biological process information

Data
 

TRIBAL: Supplementary Materials
Nazar Zaki and Antonio Mora (2014) A comparative analysis of computational approaches and algorithms for protein subcomplex identification. Scientific Reports, 4: 4262. Nature Group.

Supplementary File, Code1, Code2

 

CISA: Supplementary Materials
Maad Shatnawi & Nazar Zaki (submitted) "Inter-domain linker prediction using simulated annealing".

Data and Codes
 

Nested Complexes: Supplementary Materials
Nazar Zaki & Antonio Mora (Submitted) "Characterization of Nested Complexes in Protein Interaction Networks".

Code, Data

 

ProRank+: Supplementary Materials
Eileen Hana & Nazar Zaki (
Submitted) "Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure".

Data, Codes

 

PEWCC: Supplementary Materials
Nazar Zaki, Dmitry Efimov & Jose Berengueres (2013) "Protein Complex Detection using Interaction Reliability Assessment and Weighted Clustering Coefficient". BMC Bioinformatics, 14:163.

Code , Data

 

ProRank: Supplementary Materials
Nazar Zaki, Jose Berengueres, Dmitry Efimov (2012). "Detection of protein complexes using a protein ranking algorithm". Proteins, 80(10): 2459-68, 2012. Wiley

ProRank-0.1SimMat Data  Results  ReadMe 

 

TMHindex: Supplementary Materials
Nazar Zaki, Salah Bouktif, Sanja L., (2011) "A Combination of Compositional Index and Genetic Algorithm for Predicting Transmembrane Helical Segments". PLoS ONE 6(7): e21821. doi:10.1371/journal.pone.0021821.

DATASET-1 (test_seq), DATASET-2 (test_seq)
Compositional Index and GA
Predictions on DATASET-1, Predictions on DATASET-2, Comparisons

 

SVM-Freescore: Supplementary Materials
Nazar Zaki, Stefan Wolfsheimer, Gregory Nuel, Sawsan Khuri (2011) "Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines", BMC Bioinformatics 2011, 12:217

Freescore, LIBSVM

DATASET1DATASET2

 

STRIKE: Supplementary Materials
Nazar Zaki, 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.

The tool runs under windows platform (cygwin).

STRIKE , Data

 

PPI-PS: Supplementary Materials
Nazar Zaki, Sanja L Lazarova-Molnar, Wassim M El-Hajj, Piers Campbell (2009), "Protein-protein interaction based on pairwise similarity". BMC Bioinformatics. 10:150.

Data and source codes (Exp. no. 1, 3 and 4),  Data and source codes (Exp. no. 2)

 

                  

Grants:

 

Year

Title

Research Theme

Funds (AED)

Source of Grant

Principal Investigator

 

 

 

 

 

 

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, Bioinformatics

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, ML

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 PPI Data Using Machine Learning Techniques

Bioinformatics

12,500

UAEU

PI

2005

String Scoring Method for Protein Homology Detection

Bioinformatics

9,500

UAEU

PI

 

 

 

 

 

 

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