| 2025–ongoing | KAUST Smart Health Initiative 2024 round (SHI2024) | PI |
| 2025–2026 | Personalized cancer treatment prediction (KCSH Pathway to Impact 2025) | PI |
| 2024–ongoing | KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme) | PI |
| 2024–2026 | A public Saudi pangenome as reference for genomics in the Middle East | PI |
| 2023–2026 | Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11) | PI |
| 2023–2026 | Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications | PI (co-PI) |
| 2023–2025 | Enabling desert revegetation by AI-tailored soil microbiome fortification | CoI |
| 2023–2023 | Enabling mangrove restoration by AI-tailored microbiome fortification | CoI |
| 2022–2024 | Metagenomics-based surface prospecting | PI |
| 2022–2025 | Evolutionary potential of corals to adapt to climate warming | CoI |
| 2022–2024 | Computational methods for functional metagenomics: from protein functions to multi-scale interactions | PI |
| 2021–2023 | IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information | PI |
| 2021–2023 | Development of Algorithms for Biotechnology and Biomedical Applications | PI |
| 2019–2021 | CompleX: Variant Prioritization in Complex Disease | PI |
| 2019–2021 | Improving health of Saudi population | PI |
| 2019–2019 | Whole genome sequencing of rare disease patients | PI |
| 2018–2021 | Sequencing and computational analysis of MRSA samples | PI |
| 2018–2019 | Improvement of genetic variant prioritization technology | PI |
| 2018–2020 | Bio2Vec: Smart analytics infrastructure for the life sciences | PI |
| 2018–2020 | The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish | CoI |
| 2016–2018 | Data integration and ontologies for microbial cell factories | WP-lead |
