Muhammad Shuaib

Research Scientists

Research Scientist





He obtained Ph.D in Molecular and Cellular Biology from the University of Strasbourg in 2012, and continued his postdoctoral work at the Institute of Genetics and Molecular and Cellular Biology (IGBMC), where he studied the role of histone variants in the epigenetic specification of centromeric chromatin. After joining KAUST in 2014 as a research scientist, he first pioneered in establishing epigenomic laboratory with Prof. Valerio Orlando. In his research at KAUST, he has been using genome-wide approaches combined with biochemical and molecular biology tools to investigate the role of long non-coding RNAs and RNAi proteins in 3D genome organization and gene expression regulation. He joined the Pathogen Genomic Laboratory (Prof. Arnab Pain group) on July 1, 2020. His current research interests include:

  1. Host-pathogen epigenomic interactions
  2. Host 3D genome and transcriptome remodeling upon infection
  3. Role of non-coding RNAs and RNA-protein interactions in Apicomplexan parasites

Research Interests

Dr. Shuaib's current research interests include host-pathogen epigenomic interactions, functional genomics, and non-coding RNA. 

Selected Publications

  • Shuaib M*, Adroub S, Mourier T, et al. (2023). Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations onthe inflammatory immune response in COVID-19 severity. Genome Medicine 15, 54. (*Corresponding author)
  • 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 Microbiology8, 2154–2169 (2023) 10.1038/s41564-023-01497-6.
  • Mourier, T*., Shuaib, M*., Hala, S*. et al. (2022). SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsidmutations in host response and increased viral load. Nature Communications 13, 601 . (*Equal first author)
  • Fallatah, B*., Shuaib, M*., Adroub, S.A., Paytuví-Gallart, A., Della, Valle. F., Nadeef, S., Lanzuolo, C., Orlando, V. (2021). Ago1 controls myogenic differentiation by regulating eRNA mediated CBP guided epigenome reprogramming. Cell Report. 37 (9): 110066. (*Equal first author)
  • Shuaib, M., Parsi, K.M., Adroub, S.A., Thimma, M., Hideya, K., Seridi, L., Carninci, P., and Orlando, V. (2019). NuclearAGO1 regulates gene expression by affecting chromatin architecture in human cells. Cell Systems. 9 (5): 446-458.e6.
  • Liu, P., Shuaib, M., Zhang, H., Nadeef, S., and Orlando, V. (2019). Ubiquitin ligases HUWE1 and NEDD4 cooperativelycontrol signal dependent PRC2-Ezh1 a/b mediated adaptive stress response pathway in skeletal muscle cells. Epigenetics & Chromatin 12, 78 (2019) doi:10.1186/s13072-019-0322-5.
  • Roulland, Y., Ouararhni, K., Naidenov, M., Ramos, L., Shuaib, M., Syed, S.H., Lone, I.N., Boopathi, R., Fontaine, E., Papai,G., Tachiwana, H., Gautier, T., Skoufias, D., Padmanabhan, K., Bednar, J., Kurumizaka, H., Schultz, P., Angelov, D.,Hamiche, A., Dimitrov, S. (2016). The flexible ends of CENP-A nucleosome are required for mitotic fidelity. Molecular Cell. 63 (4): 674-85.
  • Goutte-Gattat*, D., Shuaib, M*., Ouararhni, K*., Gautier, T., Skoufias, D.A., Hamiche, A., and Dimitrov S. (2013).Phosphorylation of the CENP-A amino-terminus in mitotic centromeric chromatin is required for kinetochorefunction. Proc Natl Acad Sci USA. 110 (21): 8579-8584. (*Equal first author)
  • Shuaib, M., Ouararhni, K., Dimitrov, S., Hamiche, A. (2010). HJURP binds CENP-A via a highly conserved N-terminaldomain and mediates its deposition at centromeres. Proc Natl Acad Sci USA. 107(4): 1349-1354.
  • Drané, P., Ouararhni, K., Depaux, A., Shuaib, M., and Hamiche, A. (2010). The death-associated protein DAXX is anovel histone chaperone involved in the replication-independent deposition of H3.3. Genes & Development. 24(12): 1253-1265.


Ph.D in Molecular and Cellular Biology from the University of Strasbourg, 2012

Research Interests Keywords

Host-pathogen interactions epigenetics functional genomics Non-coding RNAs