Teaching

Theses produced by BORG members at KAUST. Author names link to their BORG profile.

PhD theses

• Yang Liu (2026, Bioengineering) — Reference Bias and Variant Interpretation in Human Disease Genomics — defended 2026-04-27
• Fernando Zhapa-Camacho (2026, Computer Science) — Neuro-symbolic methods for embedding ontologies, and applications in life sciences — defended 2026-04-26
• Sumyyah Toonsi (2025, Computer Science) — Data Driven Mining of Causal Disease Relations to Enhance Disease Centric Predictions — defended 2025-05-15
• Rund Tawfiq (2025, Bioengineering) — Computational Methods for Functional Characterization of Microbial Communities — defended 2025-11-17
• Sarah Alghamdi (2023, Computer Science) — Ontology design patterns for integrating phenotype ontologies — defended 2023-07-20
• Azza Althagafi (2023, Computer Science) — Prioritizing Causative Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies — defended 2023-07-20
• Maxat Kulmanov (2020, Computer Science) — Prediction of protein functions and phenotypes — defended 2020-04-06
• Imane Boudellioua (2019, Computer Science) — Semantic Prioritization of Novel Causative Variants — defended 2019-02-05
• Mona Alshahrani (2019, Computer Science) — Multi-modal learning on biological knowledge graphs — defended 2019-11-03

MSc theses

• Mohammed Ashhad (2026, Bioengineering) — Machine learning methods for survival analysis: from outcome-conditioned data synthesis to decoupled ranking and calibration — defended 2026-05-03
• Asaad Mohammedsaleh (2026, Computer Science) — Genome-Scale Protein Function Adjustment using Constraint Optimization — defended 2026-04-29
• Safana Bakheet (2025, Bioengineering) — An Inductive, Supervised Gene-Disease Associations Method — defended 2025-05-04
• Sawsan Al Boeisa (2025, Bioengineering) — Differential Effects of p38 MAPK Inhibition on Chemoresistance in Patients with Colorectal Cancer — defended 2025-11-17
• Mahdi Bu Ali (2025, Computer Science) — Automated Theorem Proving with Large Language Models in Lean: An Exploration of Specialized In-Context Learning and General-Purpose Hierarchical Architectures — defended 2025-05-12
• Daulet Toibazar (2024, Bioengineering) — Context-aware protein function prediction in bacterial genomes — defended 2024-07-23
• Maria G Gomez Castillo (2024, Bioengineering) — Heatstroke multi-omics analysis — defended 2024-07-24
• Amal Alhelal (2024, Bioengineering) — Protein functional domain identification methodology — defended 2024-05-07
• Melissa Rios Zertuche (2024, Bioscience) — Establishment and Evaluation of a Computational Workflow for the Design and Optimization of Nanobodies — defended 2024-07-22
• Md Nurul Muttakin (2023, Computer Science) — 3D conformation-based protein function prediction — defended 2023-04-30
• Hatoon Al Ali (2023, Bioengineering) — Predicting effects of non-coding genomic variants — defended 2023-05-01
• Shahad Qatan (2022, Computer Science) — Predicting Protein Functions From Interactions Using Neural Networks and Ontologies — defended 2022-11-09
• Kexin Niu (2022, Bioscience) — De novo genome-scale prediction of protein-protein interaction networks using ontology-based background knowledge — defended 2022-07-04
• Yang Liu (2022, Bioengineering) — Rare variant collapsing analysis on UK Biobank
• Xi Peng (2022, Computer Science) — Description Logic EL++ Embeddings with Intersectional Closure — defended 2022-03-29
• Fernando Zhapa-Camacho (2022, Computer Science) — Embedding Ontologies using Category Theory Semantics
• Zhenwei Tang (2022, Computer Science) — Towards Quality and General Knowledge Representation Learning — defended 2022-04-05
• Sakhaa Alsaedi (2020, Computer Science) — Evaluating the Application of Allele Frequency in the Saudi Population Variant Detection — defended 2020-04-07
• Abeer Almutairi (2019, Computer Science) — Unsupervised Method for Disease Named Entity Recognition — defended 2019-11-04
• Sumyyah Toonsi (2019, Computer Science) — Automatic annotation of protein functions through text mining
• Sarah Alghamdi (2018, Computer Science) — Ontology design patterns for aging mouse ontologies
• Sara Althubaiti (2018, Computer Science) — Ontology-based identification of cancer driver genes — defended 2018-11-05
• Azza Althagafi (2018, Computer Science) — Simulation and visualization of human genomes