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 200 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

  • AK Subudhi, JL Green, R Satyam, RP Salunke, T Lenz, M Shuaib, et al., DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages, Nature Microbiology, 1-16, 2023, 10.1038/s41564-023-01497-6
  • M Shuaib, S Adroub, T Mourier, S Mfarrej, H Zhang, L Esau, A Alsomali, et al., Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations on the inflammatory immune response in COVID-19 severity, Genome Medicine, 15 (1), 54, 2023, 10.1186/s13073-023-01208-0
  • AK Subudhi, AL Bienvenu, G Bonnot, R Abu-Shamma, F Khamis, et al., The first case of artemisinin treatment failure of Plasmodium falciparum imported to Oman from Tanzania, Journal of Travel Medicine, 30 (3), taac092, 2023, 10.1093/jtm/taac092
  • M Haidar, S Tajeri, L Momeux, T Mourier, F Ben-Rached, S Mfarrej, et al., miR-34c-3p Regulates Protein Kinase A Activity Independent of cAMP by Dicing prkar2b Transcripts in Theileria annulata-Infected Leukocytes, Msphere, 8 (2), e00526-22, 2023, 10.1128/msphere.00526-22
  • A Zuccolo, S Mfarrej, M Celii, S Mussurova, LF Rivera, V Llaca, et al., The gyrfalcon (Falco rusticolus) genome, G, G3: Genes, Genomes, Genetics 13 (3), jkad001, 2023, 10.1093/g3journal/jkad001
  • AN Alshukairi, Y Aldabbagh, SA Adroub, T Mourier, KY Abumelha, et al., Outcome of Transplant Recipients Infected with Omicron BA. 1 and BA. 2: A Single-Center Retrospective Study in Saudi Arabia, Journal of Epidemiology and Global Health, 13 (1), 47-54, 2023, 10.1007/s44197-023-00084-6
  • R Culleton, A Pain, G Snounou, Plasmodium malariae: the persisting mysteries of a persistent parasite, Trends in parasitology, , 2022, 10.1016/
  • RJM Van Spanning, Q Guan, C Melkonian, J Gallant, L Polerecky, JF Flot, et al., Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem, Nature microbiology, 7 (12), 2089-2100, 2022, 10.1038/s41564-022-01252-3
  • B Franke-Fayard, C Marin-Mogollon, FJA Geurten, S Chevalley-Maurel, et al., Creation and preclinical evaluation of genetically attenuated malaria parasites arresting growth late in the liver, npj Vaccines, 7 (1), 139, 2022, 10.1038/s41541-022-00558-x
  • SG Gornik, V Flores, F Reinhardt, L Erber, DE Salas-Leiva, et al., Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes, Molecular Biology and Evolution, 39 (10), msac191, 2022, 10.1093/molbev/msac191
  • S Tajeri, L Momeux, B Saintpierre, S Mfarrej, A Chapple, T Mourier, et al., Theileria annulata histone deacetylase 1 (TaHDAC1) initiates schizont to merozoite stage conversion, Scientific Reports, 12 (1), 12710, 2022, 10.1038/s41598-022-15518-7
  • E Rivière, L Verboven, A Dippenaar, S Goossens, E De Vos, E Streicher, et al., Variants in bedaquiline-candidate-resistance genes: prevalence in bedaquiline-naive patients, effect on MIC, and association with Mycobacterium tuberculosis Lineage, Antimicrobial Agents and Chemotherapy, 66 (7), e00322-22, 2022, 10.1128/aac.00322-22
  • Q Guan, B Alhuthali, S Mfarrej, MA Halim, RS Almaghrabi, A Pain, Metagenomics-driven rapid diagnosis of an imported fatal case of rare amoebic meningoencephalitis, Journal of Travel Medicine, 29 (4), taab172, 2022, 10.1093/jtm/taab172
  • LR Runtuwene, N Sathirapongsasuti, R Srisawat, N Komalamisra, et al., Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing, BMC Research Notes, 15 (1), 44, 2022, 10.1186/s13104-022-05927-2
  • T Mourier, M Shuaib, S Hala, S Mfarrej, F Alofi, R Naeem, A Alsomali, et al., SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load, Nature communications, 13 (1), 601, 2022, 10.1038/s41467-022-28287-8
  • YC Wong, R Naeem, M Abd El Ghany, CC Hoh, A Pain, S Nathan, Genome-wide transposon mutagenesis analysis of Burkholderia pseudomallei reveals essential genes for in vitro and in vivo survival, Frontiers in cellular and infection microbiology, 12, 1891, 2022, 10.3389/fcimb.2022.1062682
  • A Kaushik, DP Roberts, A Ramaprasad, S Mfarrej, M Nair, DK Lakshman, et al., Pangenome analysis of the soilborne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB, Frontiers in microbiology, 13, 839524, 2022, 10.3389/fmicb.2022.839524
  • JL do Carmo Guimarães, A von Groll, G Unis, ER Dalla-Costa, et al., Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates, Tuberculosis, 131, 102137, 2021, 10.1016/
  • T Mourier, DAM de Alvarenga, A Kaushik, A de Pina-Costa, et al., The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching, BMC biology, 19, 1-17, 2021, 10.1186/s12915-021-01139-5
  • Q Guan, M Garbati, S Mfarrej, T AlMutairi, T Laval, A Singh, S Fagbo, et al., Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense, NAR genomics and bioinformatics, 3 (3), lqab070, 2021, 10.1093/nargab/lqab070
  • E Einarsson, I Lassadi, J Zielinski, Q Guan, T Wyler, A Pain, SG Gornik, et al., Development of the myzozoan aquatic parasite Perkinsus marinus as a versatile experimental genetic model organism, Protist, 172 (4), 125830, 2021, 10.1016/j.protis.2021.125830
  • K Guo, S Wustoni, A Koklu, E Díaz-Galicia, M Moser, A Hama, et al., Rapid single-molecule detection of COVID-19 and MERS antigens via nanobody-functionalized organic electrochemical transistors, Nature biomedical engineering, 5 (7), 666-677, 2021, 10.1038/s41551-021-00734-9
  • M Zeeshan, R Pandey, AK Subudhi, DJP Ferguson, G Kaur, R Rashpa, et al., Protein phosphatase 1 regulates atypical mitotic and meiotic division in Plasmodium sexual stages, Communications Biology, 4 (1), 760, 2021, 10.1038/s42003-021-02273-0
  • C Bi, G Ramos-Mandujano, Y Tian, S Hala, J Xu, S Mfarrej, CR Esteban, et al., Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing, Med, 2 (6), 689-700. e4, 2021, 10.1016/j.medj.2021.03.015
  • B Antony, J Johny, N Montagné, E Jacquin‐Joly, R Capoduro, K Cali, et al., Pheromone receptor of the globally invasive quarantine pest of the palm tree, the red palm weevil (Rhynchophorus ferrugineus), Molecular ecology, 30 (9), 2025-2039, 2021, 10.1111/mec.15874
  • A Ramaprasad, S Klaus, O Douvropoulou, R Culleton, A Pain, Plasmodium vinckei genomes provide insights into the pan-genome and evolution of rodent malaria parasites, BMC biology, 19, 1-22, 2021, 10.1186/s12915-021-00995-5


  • Post-doctoral fellow, Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, UK, 2001
  • Ph.D. University of Cambridge, U.K., 1996
  • M.Sc. Indian Agricultural Research Institute, 1992
  • B.Sc. Bidhan Chandra Krishi Viswavidyalaya, 1989

Scientific and Professional Membership

  • Fellow of Royal Society of Tropical Medicine and Hygiene (RSTMH), London, U.K. (2013- NOW)


  • Grant Award: 'COVID-19 Genomics - MENA': towards molecular surveillance of SARS-CoV-2 genomes during the vaccination period within the Middle East and North Africa, 2021
  • Distinguished Professorship, Global Center for Zoonosis Control, Hokkaido University, 2015
  • Senior Research Fellow (honorary) at Malaria Research Centre (MRC), University Malaysia Sarawak, Malaysia (2012- 2016)
  • Elected Fellow (FRSB) of Royal Society of Biology (London, U.K.)

Research Interests Keywords

Genome and transcriptome analysis Microbial genomics Apicomplexan parasites Evolution of obligate intracellular parasitism Mycobacteria Host-pathogen interactions Enteric pathogens Bioinformatics Apicomplexan parasites, genomics, gene editing,  confocal imaging epigenetics Host-pathogen relationship, Transcriptome Infectious diseases Microbial metagenomics & metatranscriptomics viral biology