Selected Key Projects

This project develops methods to efficiently extract associations between entities in domain of life science. It combines various resources with different types of information and attempts to provide efficient way for finding information of interest with all of its associated concepts. The technical solutions are generic and applicable to many domains beyond life science.

The current volume of the data generated through high-throughput experiments and the volume of data publicly available makes it imperative to have bioinformatics applications that are time-efficient. This requires development of the solutions that will utilize efficiently highly parallelized architecture of HPC systems. In this project we are focusing on developing such methodologies and solutions for ab initio motif detection, for transcription regulation modeling, for various DNA signal recognitions and for efficient indexing of information in bioinformatics resources for use on HPC systems.

This project focuses on the studies of the metagenomic samples from water columns and brine pools in Red Sea. CBRC develops methods and tools for efficient functional annotation for data obtained from such samples and systems for targeted search for industrially and pharmacologically interesting enzymes. The research is performed in collaboration with American University in Cairo and KAUST Red Sea Research Center.

The project focuses on development of new methods for modeling interactions between transcription factors (TFs) and DNA, new TF binding sites (TFBSs) prediction models, annotation of promoters and other gene regulatory regions. It aims at determining the most complete set of associations between transcription co-factors, TFs, promoters and TFBSs, and associated transcripts. The project also encompasses microRNA, their regulation and their regulatory effects.

The primary focus of this research program is to use deep sequencing and other functional genomic technologies to understand biology and population diversity of several important pathogens and pathogen vectors of significant impact on human and animal health within the Kingdom of Saudi Arabia. In this program, a combination of high-throughput nucleic acid sequencing platforms coupled with functional genomics and bioinformatics tools will be used to understand genetic make-up and dynamics of genome variation in a selected number of viral, bacterial and protozoan pathogens. A comprehensive genomic resource for visualization of natural sequence variation data in geographically distinct populations of pathogens will be developed using the large-scale pathogen genome variation datasets currently being generated within this program. A number of these projects are being undertaken in collaboration with several partners within the Kingdom and outside.

Microbial biotechnology offers a range of innovative solutions for new and/or improved processes within the Saudi Arabian petrochemical and environmental sectors. In our group, we are concentrating on renewable chemical syntheses using synthetically engineered cyanobacterial cell factories and genetic and dynamic modelling of oil field microbial communities.

Engineering photosynthetic microbial cell factories for renewable chemical syntheses

We are developing an engineering pipeline to generate photosynthetic microbial cell factories that can convert CO2 to a variety of industrial feed stock chemicals. Sunlight, available land, access to water and a vast supply of CO2 from the petrochemical industry place Saudi Arabia in a leading position from which to exploit photosynthetic cell factories as a clean, sustainable manufacturing technology.

Our research combines microbiology, genomics, metabolic reconstruction and synthetic biology. We are:

• isolating, screening and identifying new microalgal and cyanobacterial strains from the Red Sea, Arabian Gulf and across KSA.
• applying genomics-led metabolic reconstruction to develop genome and cell models.
• mining new and existing genome sequences to build a library of standardised genetic parts for cyanobacterial engineering.
• designing robust genetic control systems, introducing novel approaches to culture-induction, -monitoring, -maintenance and self-regulation.
 
• constructing bespoke metabolic pathways for the production of high-value chemicals using clean, sustainable, scalable technology

Chassis strain isolation

Our programme capitalises on the diversity of the Red Sea and Arabian Gulf. We have developed a microbiological isolation and screening pipeline that has generated a library of axenic, physiologically robust microalgae and cyanobacteria that exhibit appropriate physiological, genetic and metabolic features. High insolation, thermo- and halo-tolerance, genetic tractability and high biomass accumulation make these select lead organisms attractive candidates for engineering a photosynthetic, cell-based manufacturing platform capable of synthesising a range of chemical products.

Genome-scale modelling

We generate genome-scale genetic and metabolic models that are validated by high throughput experiment to refine an overall cell model which supports subsequent engineering. We are using computational tools to screen for genetic control sequences, regulatory circuits and novel actuators which will form the basis of a registry of standardised modular parts for cyanobacterial synthetic biology.

Cyanobacterial synthetic biology

Synthetic biology approaches are catalysing a paradigm shift in genetic manipulation and the engineering of biological systems. Established design principles, facile assembly from standardised modular parts with predictable performance define modern engineering and represent the core goals of Synthetic Biology. We are developing a new suite of standardised measurement and characterisation tools to automate the inference of parameters associated with genetic devices, which informs system design and provide variables for computational models. We are engineering cells with innovative genetic control systems for culture-induction, -monitoring, -maintenance and self-regulation that are combined with bespoke metabolic pathways for the production of high-value chemicals using clean, sustainable, scalable technology.

Scale-up

Working with industrial partners, we are developing medium and large-scale photobioreactor pilot schemes. These will be used translate research into the development of this new technology field.

Metagenomic analysis and modelling of oil field microbial communities

Oil reservoirs are ancient, complex, carbon rich, biologically diverse microbial habitats. Oil extraction both perturbs and is in turn perturbed by the dynamic microbial populations resident in these reservoirs. However, despite its economic and scientific importance, little is known of the microbiology of the vast Saudi Arabian oil field system. To address this, we are combining geochemical survey data with longitudinal whole-genome metagenomic studies, to build dynamic genetic and metabolic models of oil field microbial populations. Using KAUST\\\''\''s Blue Gene supercomputer, we analyse millions of metagenomic reads to build taxonomic and metabolic time-based models of microbial populations within the oil field seeking to understand the physicochemical factors that shape microbial population structure and metabolic capabilities and what their potential mass effect may be on the quality and quantity of recoverable oil.