Current Research

Apicomplexans are obligate intracellular parasites that evolved from a common ancestor hundreds of millions of years ago that also gave rise to ciliates, dinoflagellates, and the relatively recently discovered group of alga commonly referred to as 'chromerids'. Arguably, apicomplexans represent the world’s most successful and diverse parasitic lineage with a global impact on human health, food security and economics. Malaria-causing Plasmodium species, Toxoplasma and Cryptosporidium are amongst the worst known parasites of mankind. Parasites such as Neospora, Theileria, Babesia and Eimeria are important threat to global food security. To understand how a parasitic life style has originated and diversified in apicomplexans, we are engaged in sequencing and comparative genome analysis of a large number of apicomplexans and photosynthetic chromerids, the closest known photosynthetic relatives of apicomplexans. We are also engaged in studying host-parasite interactions in apicomplexan parasites using functional genomics approaches.
Hajj is the largest, most diverse mass gathering of people in the world. It attracts more than 2·5 million pilgrims from more than 160 countries all over the world who visit Mecca in Saudi Arabia every year. The pilgrims perform the same activities at the same time in a limited area of land. The population density that can reach up to seven people per square meter and the nature of the performed activities amplify potential health risks. In collaboration with the Saudi MoH, we are conducting a pilot study to identify and characterize the enteric pathogens that predominate during Hajj. The objectives of the study are: (1) To identify the etiology of diarrheal infections during Hajj, (2) To investigate the variations in the distribution of enteric pathogens, clonal types and antimicrobial resistance, (3) To detect the emergence of new variants and (4) To develop an optimized protocol for the usage of WGS in the diagnosis of enteric infections during mass gatherings.
In the hierarchy of microbial evolution, Mycobacteria represent a distinct group. The genus Mycobacterium contains more than 150 species and 11 sub-species, which are separated in three major groups, that is, M. tuberculosis complex (MTBC) which can cause tuberculosis in humans and animals, M. leprae, the causative agent of Hansen's disease or leprosy, and mycobacteria other than MTBC and M. leprae, collectively referred to as non-tuberculous mycobacteria (NTM), also known as environmental mycobacteria, residing in soil and in water and can cause pulmonary disease resembling tuberculosis, lymphadenitis, skin disease, or disseminated disease.  M. tuberculosis, the most prominent member of the MTBC, is an obligate human pathogen and the causative agent of tuberculosis (TB), which remains one of the leading global public health problems. To decipher the biology and the evolution of present day mycobacterial species, we are building complete genetic maps of these species using comparative and functional genomics approaches.
We are involved with the development of software tools for visualising genome-scale datasets on pathogen discovery and genome variation. SVAMP - Sequence variation analysis, maps and phylogeny software was developed to visualise single nucleotide polymorphisms (SNPs) and Insertions/Deletions (INDELs) in genomes of sequenced strains/isolates. READSCAN is a highly scalable pathogen discovery tool that was developed to screen for sequences of pathogen origin and also to identify contamination in deep-sequencing datasets. For more details on the tools developed in our lab see the software section. Members of our group are also involved in routine bioinformatics-driven genome-scale analysis using software pipelines implemented on our compute cluster.