Rare disease

Improvement of genetic variant prioritization technology

Engineering improvements to the semantic variant-prioritization pipeline (PhenomeNet, DeepPVP). Period: 2018–2019 Funding KAUST Center Partnership Fund — Grant ID: FCS/1/3657-01-01 (PI) — USD 9,500 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Paul N Schofield — CoI (University of Cambridge) Georgios V Gkoutos — CoI (University of Birmingham) Vladimir Bajic — CoI (Former KAUST CBRC director (retired)) Publications acknowledging this project (4) (2020) Semantic similarity and machine learning with biomedical ontologies (2019) Formal axioms in biomedical ontologies improve

Whole genome sequencing of rare disease patients

Pilot rare-disease whole-genome sequencing and analysis, in collaboration with KAUST Health. Period: 2019–2019 Funding KAUST OSR Director's Award, Digital Health Initiative — Grant ID: REP/1/4133-01-01 (PI) — USD 138,600 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Topics: Rare disease

Improving health of Saudi population

Health informatics and precision-medicine pipelines tailored to Saudi-population genetic and phenotypic data. Period: 2019–2021 Funding KAUST Center Competitive Fund — Grant ID: URF/1/1976-31-01 (PI) — USD 324,000 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Sakhaa Alsaedi — MSc (alumnus) Yang Liu — MSc (alumnus) Publications acknowledging this project (5) (2020) Semantic similarity and machine learning with biomedical ontologies (2019) Formal axioms in biomedical ontologies improve analysis and interpretation of associated data (2018) Formal axioms in biomedical

CompleX: Variant Prioritization in Complex Disease

Semantic methods for prioritising causative variants in complex (polygenic / oligogenic) disease using phenotype ontologies and gene network embeddings. Period: 2019–2021 Funding KAUST Competitive Research Grant — Grant ID: URF/1/3790-01-01 (PI) — USD 240,000 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Paul N Schofield — CoI (University of Cambridge) Georgios V Gkoutos — CoI (University of Birmingham) Imane Boudellioua — PhD (alumnus) (King Fahd University of Petroleum and Minerals (Assistant Professor)) Mona Alshahrani — PhD (alumnus) (Jubail University College

IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

Neuro-symbolic methods integrating biomedical networks and ontologies for quantitative analysis of disease phenotypes and variants. Period: 2021–2023 Funding KAUST Competitive Research Grant — Grant ID: URF/1/4355-01-01 (PI) — USD 239,999 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Paul N Schofield — CoI (University of Cambridge) Georgios V Gkoutos — CoI (University of Birmingham) Sarah Alghamdi — PhD (alumnus) Azza Althagafi — PhD (alumnus) Sumyyah Toonsi — PhD (alumnus) Fernando Zhapa-Camacho — PhD (alumnus), MSc (alumnus) (KAUST) Xi Peng — MSc (alumnus) Zhenwei Tang —
smart health peptide leukemia

Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications

Disease modelling using biomimetic peptide scaffolds and patient-derived leukemic cells for precision medicine applications. Period: 2023–2026 Funding KAUST Smart Health Initiative — Grant ID: REI/1/4938-01-01 (PI (co-PI)) — USD 200,000 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Charlotte Hauser — PI (KAUST (Biological & Environmental Sciences)) Yang Liu — PhD (alumnus) Sawsan Al Boeisa — MSc (alumnus) Publications acknowledging this project (3) (2022) Causal Knowledge Graphs: Leveraging Background Knowledge for Causal Inference at Scale (2022) Causal Knowledge Graphs
coe genai bcb

KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)

Generative-AI methods applied to BCB-themed health and wellness within the KAUST Center of Excellence for Generative AI. Sub-WBS FCC/1/5940-07-02. Period: 2024–ongoing Funding KAUST Center of Excellence for Generative AI (CoE) — Grant ID: FCC/1/5940-07-02 (PI) Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Mahdi Bu Ali — MSc (alumnus) Publications acknowledging this project (10) (2025) Lattice-based $\mathcalALC$ ontology embeddings with saturation (2024) Neuro-symbolic AI in Life Sciences (2023) DeepGOMeta: Functional Insights into Microbial Communities with Deep Learning
kcsh pathway to impact

Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)

Personalized cancer treatment prediction work funded through KCSH Pathway to Impact 2025. Sub-WBSes FCC/1/5932-10-02, FCC/1/5932-11-01, FCC/1/5932-12-10. Period: 2025–2026 Funding KAUST Center for Smart Health, Pathway to Impact Grant Program 2025 — Grant ID: FCC/1/5932-10-02 (PI) Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Publications acknowledging this project (2) (2022) Causal Knowledge Graphs: Leveraging Background Knowledge for Causal Inference at Scale (2022) Causal Knowledge Graphs: Leveraging Background Knowledge for Causal Inference at Scale Topics: Neuro
smart health saudi pangenome

A public Saudi pangenome as reference for genomics in the Middle East

Builds an open Saudi pangenome reference to support genomics applications in the Middle East, including rare-disease variant interpretation. Period: 2024–2026 Funding KAUST Smart Health Initiative — Grant ID: REI/1/5659-01-01 (PI) — USD 210,000 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Malak Althagafi — CoI (Emory University) Yang Liu — PhD (alumnus) Publications acknowledging this project (7) (2024) Predicting protein functions using positive-unlabeled ranking with ontology-based priors Supplementary Material (2022) Context-based protein function prediction in