Arnab Pain

Principal Investigator




Arnab Pain joined KAUST in June, 2010 as a member of founding faculty in the Biological and Environmental Sciences and Engineering (BESE) Division. His research career started with a Ph.D. in Molecular Microbiology obtained from the University of Cambridge (UK) in 1996, studying microbial pathogenesis in a bacterial pathogen of edible mushrooms. Upon completing PhD, he moved to the Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, to work on host-parasite interactions and cell biology of human malaria parasites. After spending five years in Oxford, he joined the Pathogen Sequencing Unit (PSU) at the Wellcome Trust Sanger Institute (WTSI) in Cambridge as a Senior Scientist. In WTSI, he was responsible for coordinating various large-scale genome projects of several apicomplexan parasites. In 2015, he was awarded a Distinguished Professorship at the Global Center for Zoonosis Control in Hokkaido university, Sapporo, Japan under the Global Institution of Collaborative Research and Education (GI-CoRE) program, funded by the Japanese government. 


To date, he has authored over 130 research publications, including book chapters and reviews, in the field of pathogen genomics and biology in several top-tier journals. Dr. Pain holds various professional memberships including Faculty of 1000 (Microbial Evolution and Genomics), British Society for Parasitology, Royal Society of Tropical Medicine and Hygiene, London and the Royal Society of Biology, London.

Research Interests

The primary focus of his current research group is to use high-throughput sequencing and other functional genomic technologies to understand biology and population diversity of key pathogens particularly relevant to the Middle-East. Genome and transcriptome analyses of these organisms is a critical first step to understand how these organisms have evolved, grow and thrive  in a susceptible host and in other environment and often cause disease. A better understanding of their biology could eventually lead to the development of new intervention strategies. His research group is using a combination of deep DNA and RNA sequencing methods coupled with functional genomics and bioinformatics tools to understand the genetic make-up and dynamics of genome variation in a number of bacteria and protists. Members of his group are also studying host-pathogen interactions in a few selected pathogen-host systems, using functional genomics and bioinformatics. His current projects particularly focus on genomics of several Apicomplexan parasites, Mycobacteria and use of bioinformatic tools for rapid pathogen discovery from deep sequencing datasets.

Selected Publications

  • Abdallah, M.A. et al., Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports, 5:15443. doi: 10.1038/srep15443, 2015.
  • Assefa, S.A. et al., Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. P.N.A.S., 112(42):13027-32. doi: 10.1073/pnas.1509534112, 2015.
  • Woo, Y.H. et al., Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites eLife, 4, art. no. E06974, pp. 1-41. doi: 10.7554/eLife.06974, 2015.
  • Weerdenburg, E.M. et al., Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. (2015), Infection and Immunity, 83 (5), pp. 1778-1788.  doi: 10.1128/IAI.03050-14, 2015
  • Coll F., et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications, 5, 4812, 2014.
  • Reid, A.J., et al. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research, 24(10):1676-85, doi: 10.1101/gr.168955.113, 2014.
  • Guttery, D., et al. Genome-wide functional analysis of Plasmodium protein phosphatases reveals pleiotropic roles during parasite development in the mosquito. Cell Host & Microbe, 16(1):128-40. doi: 10.1016/j.chom.2014.05.020., 2014.
  • Naeem, R., et al. SVAMP: Sequence Variation Analysis, Maps and Phylogeny. Bioinformatics, 30(15), 2227-2229, doi: 10.1093/bioinformatics/btu176, 2014.
  • Jackson, A.P., et al. The evolutionary dynamics of variant antigen genes in Babesia genomes reveal a history of innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11):7113-31, 2014.
  • Naeem, R. et al. READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation. Bioinformatics, 29(3):391-2, 2013. 
  • Reid, A.J., et al., Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens, 8(3) e1002567, 2012.
  • Pain, A., et al. The genome sequence of simian and human malaria parasite Plasmodium knowlesiNature, 455, 799-803, 2008.
  • Mourier, T., et al., Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparumGenome Research, 18(2): p. 281-292, 2008.
  • Pain, A., et al. Genome of the host-cell transforming parasite Theileria annulata compared with T. parvaScience, 309(5731), 131-133, 2005.​


  • Ph.D. University of Cambridge, U.K., 1996

Research Interests Keywords

Genome and transcriptome analysis Microbial genomics Apicomplexan parasites Evolution of obligate intracellular parasitism Mycobacteria Host-pathogen interactions Enteric pathogens