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Department of Applied Physics,
Faculty of Science and Technology

Universiti Kebangsaan Malaysia,
43600 UKM Bangi

Tel: +6 03 89215961
Replace (_at_) with @.

Faculty of Science & Technology
Centre for Postgraduate Studies
Universiti Kebangsaan Malaysia




Research summary
The research in my laboratory is primarily directed at investigating the molecular interactions that affect function and/or effect molecular level switching. By exploring these interactions and their associated regulatory pathways as deeply as up to the atomic level, we can elucidate the mechanisms of how many biological processes are carried out. To accomplish this, my research group studies the structure, function and evolution of biological macromolecules to compare how the atomic level differences can result in different functions by effecting regulatory or mechanistic changes. We source our data from public repositories such as GenBank and the Protein Data Bank as well as by generating internal data such as genome sequences, transcriptome sequences and methylome sequences from specific experiments. The approaches employed in exploring and investigating these datasets primarily involve bioinformatics, computational biology and genomics but also extend to structural biology (mainly X-ray crystallography), synthetic biology and systems biology. The insights revealed from these investigations can provide clues as to how molecular level regulation and responses in living systems are carried out that eventually lead to an organism’s capacity to adapt to extreme (ie. extremophiles) or diverse environments (ie. such as a bacterial pathogen or parasite adapting to a host) as well as the discovery of novel factors associated with pathogenesis (toxins and pathogenesis/virulence regulation systems). Our understanding of the atomic level interactions that define specific biological mechanisms have led to the development of applications for drug repositioning and tools for the synthetic design of nucleic acid self assembling structures.

Non-technical Research Summary
My research group studies the interactions of biological molecules to discover new mechanisms in biological processes and from there, attempt to understand how a living system is able to effect life’s many chemical reactions at the molecular level. For our investigations, we use various tools that range from high performance computing to cutting edge analytical instruments. By understanding how biological processes occur and are regulated at the atomic level, we can understand how diseases occur and in turn may lead to the discovery and design of new therapeutic agents. These efforts include the use of programmable nano-materials constructed from self assembling molecules of DNA/RNA that can be applied for diagnostics and therapy.

RNA Biology
Ribonucleic acids (RNA) have long been known as intermediary molecules between the information coded in DNA and the proteins encoded by those genes. Research has however shown that RNA molecules can also fold into complex structures which are crucial factors in determining their function just as in proteins. These RNA molecules are also involved in numerous cellular processes from regulatory roles to their long recognized roles in protein synthesis. RNA molecules such as ribozymes, riboswitches, ribosomal RNA and other families of non-coding RNA fall into this category. Studies of the occurrences and corresponding structural interactions which make up these molecules are therefore of great scientific interest. In our lab, two areas which we currently investigate are: (i) the use of computational approaches to study RNA structural interactions and 3D motifs and (ii) the discovery and annotation of non-coding RNA (novel and known) in genomic data. 

Molecular Mechanisms of Pathogenesis
The research group has also endeavoured to further understand molecular mechanisms of bacterial pathogenicity. This work involves the use of the bacterium Burkholderia pseudomallei as a model. This bacterial species is the causative agent of melioidosis and has been known to have a latent period prior to active infection which can last for decades in the host. Such an organism therefore provides an interesting avenue to further study mechanisms of host-pathogen interactions, bacterial survival and the systems which regulate the transition from latent survival to active pathogenicity. As a result, knowledge on the roles of non-coding RNAs as regulatory elements, protein-glycan interactions and the potential of products encoded by essential genes as drug targets in such a pathogen are of great value.We have also used B. pseudomallei as a platform for the study of bacterial methylomes and how methylation events regulate gene expression and various functions at the molecular level.

Structural Biology / Structural Bioinformatics
The research group is primarily interested in the the annotation and comparisons of bio-macromolecular 3D structures. We have thus developed the search tools to analyse large volumes of structural data. These annotations are used to identify novel structural arrangements/motifs, annotate function and explore applications such as drug repurposing. Using the tools developed, we have also been able to compile derive datasets into databases for use by the respective research communities.

Key specialization areas:
Computational structural biology, RNA bioinformatics, bacterial genomics

Other Research
The reearch listed here are mainly carried out in collaboration with other research groups.
-Rafflesia genomics
-G. antarctica genomics
-Phylogenomics of Galapagos iguanas
-Nucleic acid nanotechnology / self-assembling molecules
-Organic biodegradable nano-carrier platforms

Collaborators (External to faculty)
Prof. Peter Artymiuk (up to 2014)
Prof. David Rice
Prof. Peter Willett (up to 2014)
Prof. Per Bullough
Krebs Institute for Biomolecular Research
University of Sheffield

The Malaysia Genome Institute

Dr. Effirul Ikhwan Ramlan
University College Dublin
Republic of Ireland

Dr. Shandar Ahmad
Jawarharlal Nehru University
New Delhi, India

Dr. Gabriele Gentile
University of Rome Tor Vergata
Rome, Italy

See videos of some of our research:





Last updated: September 2012