Theses

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

  • Mohammad 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