Theme: Bioinformatics of Host-Pathogen Interaction

Introduction:

Host-pathogen interactions HPIs are interactions that occurs between pathogens such viruses or bacteria and hosts such as human or plants that usually cause diseases and damages to the hosts. The study of HPI is important because it seeks eventually to minimize the human diseases and the loss in crop yields and animal stocks. Through bioinformatics, the study of different HPIs is now possible. The huge amount of genomic data available, the structural information and the various computational tools for studying protein-protein interaction between the pathogen and host proteins are all foundations in drug discovery and in the development of some vaccines and antibiotics.

 

Members:

 

Aims: 

Major objective:

To use informatics techniques and computer science algorithms to study and analyze the huge amount of the Omics data (genomics, proteomics, interatomic...etc.) that is related to HPI.

Specific objectives:

1. Enhanced approaches for representation and visualization of system-biology data.
2. New algorithms to enhance classification and clustering of biological data.
3. Testing novel encoding and feature extraction approaches for biological data.

Data:

Genomic sequences, protein sequences, protein-protein interaction data, gene expression data.

Projects:

1. Study the HMM protein profile as a reference for bacterial comparison.
2. New representation paradigm of bacterial proteomes based on Gene Ontology hierarchical ordering of protein functions and essentials.
3. Using amino acids PCPs for encoding and feature extraction of protein sequences and evaluate their association in solving clustering and classification problems of different data cases.
4. Investigating the relationship between DNA repeats and various biological features of bacteria.
5. Investigating the relationship between functional patterns of protein clusters (GO or sequence based) and various features of bacteria.

What we are seeking:

1.    Students who are capable of working in a new interesting field.

2.    Ability to work in a team environment.

3.    Ability to incorporate abstraction and mathematical models to different problems.

4.    Ability to represent and apply computer science algorithms and approaches in bioinformatics.

5.    High degree of commitments to meetings, journal club, and other events.

 

Publications:

• Developing a Powerful In Silico Tool for the Discovery of Novel Caspase-3 Substrates: A Preliminary Screening of the Human Proteome. Muneef Ayyash, Hashem Tamimi and Yaqoub Ashhab. BMC Bioinformatics 2012, 13:14(highly accessed)
• Developing a New Bioinformatic Tool for Predicting Caspase3 Cleavage Motif Using Support Vector Machine". Ruba Sultan, Hashem Tamimi and Yaqoub Ashhab. 2nd Conference on Biotechnology Research and Applications in Palestine, 26-27th September, 2010.
• BACTOSOM-Viewer: a High-Throughput Bacterial Mapping Tool Based on Landmark Proteins. Bilal Tamimi, Sami Salamin, Hashem Tamimi, Yaqoub Ashhab. 2nd Conference on Biotechnology Research and Applications in Palestine, 26-27th September, 2010.

 

(Click here to Visit Journal Club Page)