Teaching

Course listings, doctoral and master’s theses supervised, and postdoctoral researchers. Group-member profiles and current activity live on the Bio-Ontology Research Group site.

PhD Theses Supervised

• Yang Liu (2022–2026) — Reference Bias and Variant Interpretation in Human Disease Genomics
• Fernando Zhapa-Camacho (2022–2026) — Neuro-symbolic methods for embedding ontologies, and applications in life sciences
  Now: KAUST (Postdoctoral Fellow)
• Sumyyah Toonsi (2020–2025) — Data Driven Mining of Causal Disease Relations to Enhance Disease Centric Predictions
  Now: Effat University (Assistant Professor)
• Rund Tawfiq (2021–2025) — Computational Methods for Functional Characterization of Microbial Communities
  Now: Sano Centre Krakow (Postdoctoral researcher)
• Sarah Alghamdi (2018–2023) — Ontology design patterns for integrating phenotype ontologies
  Now: King Abdulaziz University (Assistant Professor)
• Azza Althagafi (2019–2023) — Prioritizing Causative Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies
  Now: Taif University (Assistant Professor)
• Maxat Kulmanov (2015–2020) — Prediction of protein functions and phenotypes
  Now: KAUST (Research Scientist)
• Imane Boudellioua (2015–2019) — Semantic Prioritization of Novel Causative Variants
  Now: King Fahd University of Petroleum and Minerals (Assistant Professor)
• Mona Alshahrani (2015–2019) — Multi-modal learning on biological knowledge graphs
  Now: Jubail University College (Assistant Professor)

Master’s Theses Supervised

• Mohammad Ashhad (2025–2026) — Machine Learning Methods for Survival Analysis: From Outcome-Conditioned Data Synthesis to Decoupled Ranking and Calibration
  Now: PhD student, Computer Science, KAUST
• Asaad Mohammedsaleh (2025–2026) — Genome-Scale Protein Function Adjustment using Constraint Optimization
• Safana Bakheet (2024–2025) — An Inductive, Supervised Gene-Disease Associations Method
• Sawsan Al Boeisa (2024–2025) — Differential Effects of p38 MAPK Inhibition on Chemoresistance in Patients with Colorectal Cancer
• Mahdi Bu Ali (2024–2025) — Automated Theorem Proving with Large Language Models in Lean: An Exploration of Specialized In-Context Learning and General-Purpose Hierarchical Architectures
• Daulet Toibazar (2022–2024) — Context-aware protein function prediction in bacterial genomes
• Maria G Gomez Castillo (2022–2024) — Heatstroke multi-omics analysis
• Amal Alhelal (2022–2024) — Protein functional domain identification methodology
• Melissa Rios Zertuche (2023–2024) — Establishment and Evaluation of a Computational Workflow for the Design and Optimization of Nanobodies
• Md Nurul Muttakin (2022–2023) — 3D conformation-based protein function prediction
• Hatoon Al Ali (2021–2023) — Predicting effects of non-coding genomic variants
• Shahad Qatan (2021–2022) — Predicting Protein Functions From Interactions Using Neural Networks and Ontologies
• Kexin Niu (2021–2022) — De novo genome-scale prediction of protein-protein interaction networks using ontology-based background knowledge
• Yang Liu (2021–2022) — Rare variant collapsing analysis on UK Biobank
• Xi Peng (2021–2022) — Description Logic EL++ Embeddings with Intersectional Closure
• Fernando Zhapa-Camacho (2021–2022) — Embedding Ontologies using Category Theory Semantics
• Zhenwei Tang (2021–2022) — Towards Quality and General Knowledge Representation Learning
• Sakhaa Alsaedi (2019–2020) — Evaluating the Application of Allele Frequency in the Saudi Population Variant Detection
• Abeer Almutairi (2018–2019) — Unsupervised Method for Disease Named Entity Recognition
• Sumyyah Toonsi (2019) — Automatic annotation of protein functions through text mining
• Sarah Alghamdi (2017–2018) — Ontology design patterns for aging mouse ontologies
• Sara Althubaiti (2017–2018) — Ontology-based identification of cancer driver genes
• Azza Althagafi (2017–2018) — Simulation and visualization of human genomes

Postdoctoral Researchers

• Fernando Zhapa-Camacho (2026–present) — from KAUST (PhD)
• Tengwei Song (2025–present)
• Ashraf Kibraya (2020–2021)
• Maxat Kulmanov (2020–2021) — from KAUST (PhD)
  Now: KAUST (Research Scientist)
• Miguel Angel Rodriguez Garcia (2016–2018) — from University of Murcia
  Now: King Juan Carlos University (Research Scientist)

Courses

• 2026: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2026: Instructor for Neurosymbolic AI, Computer Science Program, King Abdullah University of Science and Technology.
• 2025: Instructor for Applications of AI in Bioinformatics, Computer Science Program, King Abdullah University of Science and Technology.
• 2025: Instructor for Algorithms in Bioinformatics, Computer Science Program, King Abdullah University of Science and Technology.
• 2025: Co-Instructor for Foundations of Bioengineering, Bioengineering Program, King Abdullah University of Science and Technology.
• 2024: Co-Instructor for Foundations of Bioengineering, Bioengineering Program, King Abdullah University of Science and Technology.
• 2024: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2024: Instructor for Neurosymbolic AI, Computer Science Program, King Abdullah University of Science and Technology.
• 2023: Instructor for Data Analytics, Computer Science Program, King Abdullah University of Science and Technology.
• 2022: Instructor for Algorithms in Bioinformatics, Computer Science Program, King Abdullah University of Science and Technology.
• 2022: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2021: Co-Instructor for Foundations of Bioengineering, Bioengineering Program, King Abdullah University of Science and Technology.
• 2021: Instructor for Data Analytics, Computer Science Program, King Abdullah University of Science and Technology.
• 2021: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2020: Instructor for Algorithms in Bioinformatics, Computer Science and Bioengineering Programs, King Abdullah University of Science and Technology.
• 2020: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2019: Instructor for Introduction to Artificial Intelligence, Computer Science Program, King Abdullah University of Science and Technology.
• 2018: Instructor for Applied Ontology, Computer Science Program, King Abdullah University of Science and Technology.
• 2017-2018: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2016--2017: Instructor for Applied Ontology, Computer Science Program, King Abdullah University of Science and Technology.
• 2015--2016: Instructor for Knowledge Representation and Reasoning, Computer Science Program, King Abdullah University of Science and Technology.
• 2015: Organizer for Computer Science Graduate Seminar, Computer Science Program, King Abdullah University of Science, and Technology.
• 2014: Instructor in Object-Oriented Programming, Software Engineering College, Northeastern University, Shenyang, China.
• 2013-2014: Instructor in Professional And Personal Development, Department of Computer Science, Aberystwyth University.
• 2013: Instructor in Object-Oriented Programming, Software Engineering College, Northeastern University, Shenyang, China.
• 2013: Co-instructor in Machine learning, Department of Computer Science, Aberystwyth University.
• 2005-2008: Co-instructor for seminars on Ontology in medical information systems, Department of Computer Science, University of Leipzig.
• 2006-2007: Instructor and co-organizer for seminars on Computer science and society and Information, Department of Computer Science, University of Leipzig.