Robert Hoehndorf

July 2026

• 

  Vanesa Gamez Baez earns MSc on multi-omics fidelity of colorectal cancer organoids

  2 min read · Mon, Jul 6 2026

  News

  Vanesa Gamez Baez has completed her MSc with a thesis that uses a genome, transcriptome and proteome framework to test how faithfully patient-derived organoids from Saudi colorectal cancer patients recall the original tumors.

June 2026

• 

  New publication uses ontology reasoning to evaluate genome-scale function annotations

  2 min read · Tue, Jun 30 2026

  News

  Our new paper in Briefings in Bioinformatics uses the Gene Ontology, GO-Plus and logical constraints to evaluate whether genome-scale function annotations are complete, coherent and consistent.
• 

  New publication: INDIGENA predicts disease–gene associations from phenotype ontologies

  1 min read · Mon, Jun 1 2026

  News

  A new paper in Bioinformatics introduces INDIGENA, an inductive method that ranks candidate genes for a disease from its phenotypes using graph embeddings of phenotype ontologies, and that generalises to diseases never seen during training.

September 2025

• 

  AI speeds up human embryo model research

  1 min read · Thu, Sep 11 2025

  News Clip News

  genome genome sequencing precision medicine genetics smart health AI AI for healthcare

  Deep-learning tool outperforms human experts at classifying lab-grown embryo-like structures, enabling advances in developmental biology and drug discovery.

January 2025

• 

  AI tool maps hidden links between diseases

  1 min read · Wed, Jan 15 2025

  News Clip News

  AI for healthcare AI Natural Language Processing bioinformatics

  Understanding how diseases trigger one another could lead to better treatments, prevention strategies and improved genetic risk prediction.

February 2024

• 

  AI tool predicts function of unknown proteins

  2 min read · Sun, Feb 18 2024

  News

  artificial intelligence bioinformatics biotechnology

  Powered by logic and large language models, DeepGO-SE predicts the biological role of proteins and could be used to aid drug discovery.

October 2023

• 

  A new approach to rare disease diagnosis

  2 min read · Mon, Oct 23 2023

  News

  bioinformatics artificial intelligence

  An innovative AI-based tool leverages varied symptom descriptions, along with evidence from the scientific literature and genomic datasets, to pinpoint disease-associated gene variants.

May 2023

• 

  MS Thesis Defense | Learning 3D structures for protein function prediction

  1 min read · Tue, May 9 2023

  News

  bioinformatics protein function prediction Computer science artificial intelligence

  Student Nurul Muttakin from the Bio-Ontology Research Group (BORG) under the supervision of Assoc. Prof. Robert Hoehndorf successfully defends his Masters thesis. He presented his research on the topic " Learning 3D structures for protein function prediction".
• 

  MS Thesis Defense | Predicting Regulatory and Phenotypic Effects of Non-coding Variants

  1 min read · Mon, May 8 2023

  News

  Student Hatoon Ali from the Bio-Ontology Research Group (BORG) under the supervision of Prof. Robert Hoehndorf successfully defends her Masters thesis. She presented her research on the topic " Predicting Regulatory and Phenotypic Effects of Non-coding Variants".

October 2022

• 

  Appointment of Prof. Xin Gao as Interim Director and Prof. Robert Hoehndorf as Interim Associate Director of CBRC

  1 min read · Mon, Oct 3 2022

  News

  The Computational Bioscience Research Center (CBRC) is pleased to announce that Professor Xin Gao has assumed the position of Interim Director and Professor Robert Hoehndorf as Interim Associate Director of the CBRC. Both professors assumed their roles on September 15, 2022.

September 2022

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  How much do model organism phenotypes contribute to the computational identification of human disease genes?

  1 min read · Sun, Sep 4 2022

  News

  Ontologies phenotype ontologies gene-disease associations

  PhD Student Sarah M Alghamdi from the Bio-Ontology Research Group (BORG) explains how phenotype ontologies help in identifying disease genes through phenotype comparison. Her research was picked as a highlight in the July 2022 issue of Disease Models and Mechanisms Journal.

April 2022

• 

  MS Thesis Defense: Embedding Ontologies using Category Theory Semantics by Fernando Zhapa Camacho

  1 min read · Sun, Apr 10 2022

  News

  Computer science

  Fernando Patricio Zhapa Camacho an M.S./Ph.D. candidate in the KAUST Bio-Ontology research group under the supervision of Professor Robert Hoehndorf successfully defended his thesis "Embedding Ontologies using Category Theory Semantics".

March 2022

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  MS Thesis Defense: Description Logic EL++Embeddings with Intersectional Closure by Xi Peng

  1 min read · Thu, Mar 31 2022

  News

  machine learning Knowledge representation and reasoning

  Xi Peng MS Student under the supervision of Professor Robert Hoehndorf successfully defended his thesis "Description Logic EL++Embeddings with Intersectional Closure"
• 

  MS Thesis Defense: Rare variant collapsing analysis on UK Biobank by Yang Liu

  1 min read · Thu, Mar 31 2022

  News

  bioinformatics machine learning

  Yang Liu, M.S./Ph.D. candidate in the Bio-Ontology research group under the supervision of Professor Robert Hoehndorf successfully defended her thesis "Rare variant collapsing analysis on UK Biobank".

August 2020

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  Former KAUST VSRP student wins Best Talk Award at ISMB 2020

  2 min read · Tue, Aug 18 2020

  News

  bio-ontology ISCB ISMB genome artificial intelligence

  Runar Reve, a former KAUST Visiting Student Research Program (VSRP) student, recently received the International Society for Computational Biology’s (ISCB) Bio-Ontologies COSI – Best Talk Award at the 28th Conference on Intelligent Systems for Molecular Biology (ISMB) 2020.

July 2020

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  Robert Hoehndorf promoted to associate professor at KAUST

  4 min read · Wed, Jul 1 2020

  News

  bioinformatics biomedical data artificial intelligence

  KAUST faculty member Robert Hoehndorf was recently promoted from the rank of assistant professor to associate professor. Hoehndorf’s promotion caps a year-long process where the German researcher’s scientific and scholarly output was measured and evaluated by internal and external reviews.

June 2020

• 

  KAUST Prospective student: Fernando Patricio Zhapa Camacho

  2 min read · Thu, Jun 25 2020

  News

  Natural Language Processing

  Fernando is a 23-year-old Information Technology graduate fromYachay Tech University in Urcuquí, Ecuador. He has planned to continue his academic career at KAUST under the supervision of Professor Robert Hoehndorf.

January 2020

• 

  Algorithm turns cancer gene discovery on its head

  1 min read · Mon, Jan 20 2020

  News

  human health Computer science cancer

  A method for finding genes that spur tumor growth takes advantage of machine learning algorithms to sift through reams of molecular data collected from studies of cancer cell lines, mouse models and human patients.

December 2019

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  Abeer Almutairi succesfully defends her master's thesis | Unsupervised Method for Disease Named Entity Recognition

  1 min read · Mon, Dec 2 2019

  News

  ​Abeer Almutairi, a student under the supervision of Professor Robert Hoehndorf, defended her Master's thesis "Unsupervised Method for Disease Named Entity Recognition" on November 4, 2019.
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  Mona Alshahrani Ph.D. Defense | Knowledge Graph Representation Learning: Approaches and Applications in Biomedicine

  1 min read · Sun, Dec 1 2019

  News

  Mona Alshahrani a Ph.D. candidate under the supervision of Professor Robert Hoehndorf Defended her Ph.D. thesis "Knowledge Graph Representation Learning: Approaches and Applications in Biomedicine."

October 2019

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  Symbol of change for AI development

  1 min read · Sun, Oct 20 2019

  News

  artificial intelligence Computer science

  Bridging the knowledge gap in artificial intelligence requires an embedding function that helps step between different types of "thinking."

September 2019

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  Database to support infectious disease research

  1 min read · Wed, Sep 11 2019

  News

  machine learning artificial intelligence human health Computer science

  Linking disease pathogens to clinical signs and symptoms through a database could support research into the molecular mechanisms of infectious diseases.

February 2019

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  Imene Boudellioua defended her PhD thesis

  1 min read · Tue, Feb 5 2019

  News

  On 5 February, Imene successfully defended her Ph.D. thesis titled "Semantic Prioritization of Novel Causative Variants."

November 2018

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  Sara Althubaiti defends her Master's thesis

  1 min read · Tue, Nov 6 2018

  News

  cancer driver mutation bioinformatics text mining machine learning

  Sara Althubaiti, a student under the supervision of Assistant Professor Robert Hoehndorf, defended her Master's thesis on November 5, 2018.
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  Azza Althagafi defends her Master's thesis

  1 min read · Fri, Nov 2 2018

  News

  bioinformatics artificial intelligence genomics

  Azza Althagafi, a student under the supervision of Assistant Professor Robert Hoehndorf, defended her Master's thesis on November 1, 2018.

October 2018

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  Mona Alshahrani defends her thesis proposal

  1 min read · Tue, Oct 16 2018

  News

  data integration machine learning human bioinformatics

  Mona Alshahrani, a Ph.D. candidate under the supervision of Assistant Professor Robert Hoehndorf, defended her thesis proposal on October 10, 2018.
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  National Infectious Disease Initiative Workshop brings researchers to KAUST

  1 min read · Mon, Oct 8 2018

  News

  infectious disease

  Representatives from the KAUST Computational Bioscience Research Center (CBRC), King Abdulaziz City for Science and Technology (KACST), King Saud University (KSU), Taibah University, National Guard Health Affairs (NGHA) and the Saudi Arabia Ministry of Health (MOH) met on October 1 to iron out details of a national initiative to fight infectious diseases.
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  KAUST and KACST join forces to prevent infectious diseases

  2 min read · Mon, Oct 1 2018

  News

  The KAUST Computational Bioscience Research Center (CBRC) and King Abdulaziz City for Science and Technology (KACST) have collaborated under the umbrella of the National Infectious Disease Initiative to enrich research...

July 2018

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  Maxat Kulmanov defends his thesis proposal

  1 min read · Tue, Jul 31 2018

  News

  bioinformatics artificial intelligence neural network Semantic web machine learning

  Maxat Kulmanov, a Ph.D. candidate under the supervision of Assistant Professor Robert Hoehndorf, defended his thesis proposal on July 31, 2018.

May 2018

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  BORG members to present at ISMB 2018

  1 min read · Sun, May 27 2018

  News

  ​​Three members of the Bio-Ontology Research Group will be presenting their work at the International Society for Computational Biology conference in Chicago, U.S.A.
• 

  Meshari Alazami defends his thesis proposal

  1 min read · Tue, May 22 2018

  News

  machine learning bioinformatics structural biology systems biology

  Meshari Alazami, a Ph.D. student under the supervision of Associate Professor Xin Gao, successfully defended his thesis proposal on May 22, 2018. His topic, "Towards Rational Design of Biosynthesis Pathways", was well received by committee members Associate Professor Xin Gao, Distinguished Professor Takashi Gojobori and Assistant Professor Robert Hoehndorf.
• 

  Exploring science's fourth paradigm

  5 min read · Mon, May 7 2018

  News

  computational and statistical interface big data

  The recent KAUST Research Conference: Computational and Statistical Interface to Big Data brought together leading computer science researchers and statistical experts to discuss the current state and future of data science. Held on campus from March 19 to 21, the conference covered such data science topics as succinct data representation and storage; big data visualization; parallel and distributed algorithms for inference and optimization; and analysis of large graphs and networks.
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  Sarah Alghamdi defends her master's thesis

  1 min read · Sun, May 6 2018

  News

  artificial intelligence bioinformatics computational methods data mining

  Sarah Alghamdi successfully defended her master's thesis on April 10, 2018. Her project, entitled "Ontology Design Patterns for Combining Pathology and Anatomy: Application to Study Ageing and Longevity in Inbred Mouse Strains", was well-received by a panel of professors that included Professor Vladimir Bajic, Associate Professor Xin Gao and Assistant Professor Robert Hoehndorf.

April 2018

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  Assistant Professor Robert Hoehndorf awarded Center Partnership Fund

  1 min read · Thu, Apr 19 2018

  News

  ​CBRC was awarded three Center Partnership Funds by the KAUST Office of Sponsored Research on April 1, 2018.​

November 2017

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  Job Opportunity - Ph.D. or M.S./Ph.D. student

  1 min read · Wed, Nov 15 2017

  News

  ​The student will work on combining methods from Symbolic Artificial Intelligence (formal logics, rule-based systems) with machine learning and statistical approaches to data mining, and apply these methods to biomedical datasets. Major application areas include understanding molecular mechanisms underlying traits, phenotypes, and disease, and identifying ways to perturb biological systems through bioactive compounds (drugs).​
• 

  Job Opportunity - Postdoctoral Researcher

  2 min read · Wed, Nov 15 2017

  News

  ​The postdoctoral researcher will work on the development and application of Artificial Intelligence methods in bioinformatics and computational biology, with a particular focus on combining symbolic AI approaches (e.g., ontologies, knowledge graphs, rule-based systems) with machine learning methods.​​​
• 

  Professor Robert Hoehndorf discusses artificial intelligence in 2001: A Space Odyssey

  1 min read · Thu, Nov 2 2017

  News

  Professor Robert Hoehndorf was a guest speaker at the Science to Watch screening of 2001: A Space Odyssey. He gave a presentation about artificial intelligence and its implications in the movie.

October 2017

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  Professor Robert Hoehndorf will be a guest speaker at upcoming Science to Watch

  1 min read · Sun, Oct 22 2017

  News

  ​Professor Robert Hoehndorf will be a guest speaker at the upcoming Science to Watch Film and Forum. Science to Watch is a science orientated movie series followed by a discussion about the movie as it relates to science. The objective of the series is to increase public awareness about science, to stimulate curiosity about the research conducted here at KAUST, and at the same time enjoy a good movie with friends, including pizza and popcorn. The post-movie discussion is guided by a KAUST scientist working in the area.
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  Congratulations to Ph.D. student Maxat Kulmanov for new publication

  1 min read · Thu, Oct 5 2017

  News

  ​Ph.D. student Maxat Kulmanov's paper, "DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier" was recently published in Bioinformatics.

August 2017

• 

  The awesome scope of big data

  2 min read · Sun, Aug 6 2017

  News

  big data artificial intelligence computational methods health protein structures biology

  Sifting through huge amounts of data may bring a better understanding of whale shark social structures, protein targets for drug therapies and disease-causing genes.

May 2017

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  BORG at ISMB/ECCB

  1 min read · Tue, May 30 2017

  News

  ​​Meet members of the BORG at ISMB/ECCB this year in Prague. We will present one tutorial on ontologies in biology and biomedicine, one poster presentation at the Bio-Ontologies SIG, one flash talk at the Function SIG, and one oral presentation in the Variant Interpretation SIG.​
• 

  One size does not fit all: an innovative analytical tool will help pave the way for tailor made health care

  2 min read · Wed, May 24 2017

  News

  genetic mutation drug effects genomeFit

  It is estimated that each year, around eight million children worldwide are born with a serious genetic condition that is either life-threatening or debilitating. These disorders are caused by underlying mutations affecting the genetic makeup contained in our cells, and according to experts, half of the variations responsible for these diseases are still unknown. Because of the lack of information on these disorders, physicians are often unable to pinpoint the exact molecular cause of the disease or opt for the most appropriate treatment.
• 

  A new publication "Semantic prioritization of novel causative genomic variants" has been released

  1 min read · Thu, May 4 2017

  News

  PVP

  A new publication by Professor Robert Hoehndorf and Ph.D. student Imane Boudellioua from the Bio-Ontology Research Lab, as well as the University of Cambridge collaborator Paul Schofield has been released.

April 2017

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  Algorithm scours datasets to diagnose medical mysteries

  1 min read · Sat, Apr 29 2017

  News

  bioscience Computer science algorithm

  A new tool uses genetic and clinical information to find the root cause of unexplained illnesses.

March 2017

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  PhD Student positions available

  1 min read · Mon, Mar 27 2017

  News

  We have two openings for Ph.D. student positions available on the interface between Linked Data, ontologies, and machine learning.
• 

  Professors discuss big data and human health in latest Sci-Café

  1 min read · Mon, Mar 13 2017

  News

  machine learning big data artificial intelligence comparative genomics biomedical data human health

  ​Professors Takashi Gojobori, Xin Gao and Robert Hoehndorf spoke about big data and human health at the Sci-Café event held on February 27. Their talk, which was moderated by James Calvin, Vice President for Academic Affairs, aimed to answer the question, "Can Big Data Solve My Health Problems?" This event was open to all members of the KAUST community.

October 2016

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  ​PhenomeNET method wins at Ontology matching workshop

  1 min read · Tue, Oct 25 2016

  News

  ontology phenotype ontologies PhenomeNET

  CBRC congratulates Professor Robert Hoehndorf and Postdoctoral Fellow Miguel Angel Rodriguez Garcia for being one of the winners of the Ontology Alignment Evaluation Initiative challenge sponsored by Pistoia Alliance, presented in the Ontology Matching Workshop that is co-located with ISWC 2016 in Kobe, Japan.
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  Professor Robert Hoehndorf's PhenomeNET method wins at Ontology matching workshop

  1 min read · Sun, Oct 23 2016

  News

  artificial intelligence bioinformatics biomedical data PhenomeNET

  Professor Robert Hoehndorf and Postdoctoral Fellow Miguel Angel Rodriguez Garcia are the winners of the Ontology Alignment Evaluation Initiative Challenge sponsored by Pistoia Alliance.

September 2016

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  CS Graduate Seminar: Symbolic AI in Bioinformatics

  1 min read · Tue, Sep 20 2016

  News

  Professor Robert Hoehndorf recently held a seminar on Symbolic AI in Bioinformatics on September 19, 2016.

August 2016

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  BORG members at ECCB 2016

  1 min read · Tue, Aug 16 2016

  News

  ​BORG will be present at ECCB. We will present a tutorial on bio-ontologies and their role in analyzing personal genome data, and members of our group will attend the main conference. If you want to learn more about bio-ontologies, please attend our tutorial. If you want to learn more about our work, find us at ECCB!

July 2016

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  Group website online

  1 min read · Sat, Jul 23 2016

  News

  On our new website, you can find ​out about current members of the group and our activities.​

July 2015

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  Disease researchers have a way with words

  1 min read · Sat, Jul 25 2015

  News

  Computer science bioscience computing biology biomedicine

  Specialized word search method sheds light on phenotypic similarity of diseases.