News

February 2024

• 

  AI tool predicts function of unknown proteins

  1 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

  1 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.

July 2023

• 

  PhD Dissertation Defense | Prioritizing Causative Genomic Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies

  1 min read · Mon, Jul 24 2023

  News

  Computer science biology artificial intelligence

  CBRC PhD Student Azza Althagafi successfully defends her dissertation under the supervision of Associate Professor Robert Hoehndorf. She has been a member of the Bio-Ontology Research Group (BORG) since 2016. Her research interest lies in the crossroads of computer science and biology, leveraging AI techniques to explore the human genome's intricacies and its link to various diseases.
• 

  PhD Dissertation Defense | Ontology design patterns and methods for integrating phenotype ontologies

  1 min read · Sun, Jul 23 2023

  News

  Ontologies Computer science artificial intelligence

  CBRC PhD student Sarah Alghamdi successfully defended her dissertation last week. She has been an essential member of the Bio-Ontology Research Group (BORG) since 2015.Her research interests include the applications of artificial intelligence and statistical methods to genomics and healthcare.

May 2023

• 

  Employee service awards 2023

  1 min read · Sun, May 28 2023

  News

  Congratulations to CBRC members Prof. Stefan Arold, Krishnakumar Sivakumar, Raik Grunberg, Senay Kafkas and Salim Bougouffa who received their 2023 KAUST employee service awards.
• 

  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".

December 2022

• 

  KAUST Commencement 2022 looks to a bright future

  1 min read · Sun, Dec 18 2022

  News

  King Abdullah University of Science and Technology (KAUST) celebrated its 13th Commencement on a cool, breezy evening, December 16, 2022, among approximately 380 graduating students and a full audience of supportive families, university community members and distinguished guests. This year CBRC saw many student candidates complete their Postdoctoral and Masters Degrees. CBRC congratulates all students on this great achievement and wishes you even more success in the future.

October 2022

• 

  BORG team win at the KAUST-NVIDIA GPU Hackathon 2022

  1 min read · Sun, Oct 16 2022

  News

  machine learning ontology artificial intelligence GPU

  Congratulations to Senay Kafkas, Maxat Kulmanov and Fernando Zhapa Camacho of the Bio-Ontology Research Group (BORG) on winning at the KAUST-NVIDIA GPU Hackathon 2022. The 8th edition of the Hackathon on Accelerating Scientific Applications using Graphical Processing Units (GPUs) was held at King Abdullah University of Science and Technology (KAUST), twelve teams of students and researchers enjoyed the opportunity to accelerate their codes in GPU’s under the guidance of expert mentors of NVIDIA, Codee, KAUST Supercomputing Lab (KSL) and KAUST core labs.
• 

  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

• 

  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".

December 2020

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  Alumna Imane Boudellioua (PhD ’19, MS ’12) receives KACST prize

  1 min read · Mon, Dec 21 2020

  News Spotlight

  Congratulations to Computer Science alumna Imane Boudellioua (Ph.D. ’19, MS ’12) for receiving a prize in the 19th edition of the annual KACST Almarai National Prize for Creative Scientific Work for Students (Ph.D. Level). As a Ph.D. student in the Computational Bioscience Research Center, Dr. Boudellioua worked in machine learning and data mining algorithms, with research targeting the potential to help patients with mysterious ailments find genetic causes for their undiagnosed disease.

August 2020

• 

  Former KAUST VSRP student wins Best Talk Award at ISMB 2020

  1 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

• 

  Studying COVID-19’s envelope protein

  1 min read · Tue, Jul 28 2020

  News

  COVID-19 human health genomics

  A likeness between genes of the SARS and COVID-19 viruses could inform research into potential treatments.
• 

  Robert Hoehndorf promoted to associate professor at KAUST

  1 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

  1 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

• 

  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

• 

  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

• 

  KAUST Research Conference: AI in Medicine

  1 min read · Mon, Feb 18 2019

  News

  artificial intelligence

• 

  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."

January 2019

• 

  Visualization of brain structures helps to model function

  1 min read · Thu, Jan 3 2019

  News

  bioscience

  Computer simulations and virtual reality are used by KAUST researchers and collaborators in France to visualize the energetic coupling between neurons and astrocytes and to improve understanding of brain metabolism. The human brain uses more energy than any other organ, accounting for around 20 percent of all glucose-derived energy. Neurons can’t meet their own energy requirements: they depend on supporting glial cells and the neurovascular system to supply various forms of sugar fuel. However, it is still unclear how this neuro-glio-vasculature network manages the brain’s energy demands

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.
• 

  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

• 

  Aerial Path Planning for Urban Scene Reconstruction: A Continuous Optimization Method and Benchmark

  1 min read · Tue, Oct 16 2018

  News

  optimization urban planning

  Small unmanned aerial vehicles (UAVs) are ideal capturing devices for high-resolution urban 3D reconstructions using multi-view stereo. Nevertheless, practical considerations such as safety usually mean that access to the scan target is often only available for a short amount of time, especially in urban environments. It, therefore, becomes crucial to perform both view and path planning to minimize flight time while ensuring complete and accurate reconstructions. In this work, we address the challenge of automatic view and path planning for UAV-based aerial imaging with the goal of urban
• 

  Award-winning algorithm takes search for habitable planets to the next level

  1 min read · Tue, Oct 16 2018

  News

  telescope astronomy NVIDIA PASC singular-value-decomposition-MOAO

  An international team of scientists, including KAUST high performance computing experts and astronomers from the Paris Observatory and the National Astronomical Observatory of Japan (NAOJ), in collaboration with NVIDIA, is taking the search for habitable planets and observation of first epoch galaxies to the next level.
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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.
• 

  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.
• 

  KAUST and KACST join forces to prevent infectious diseases

  1 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...

August 2018

• 

  CBRC goes to ECCB 2018

  1 min read · Thu, Aug 9 2018

  News

  Computational biology Nanopore Sequencing cwDTW algorithm ontology phenotypes SmuDGE

  The European Conference on Computational Biology (ECCB) is one of the most important conferences in the field of bioinformatics and computational biology. Held in a different European city annually, this year's conference will take place in the historic city of Athens, Greece on September 8-12, 2018.

July 2018

• 

  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

• 

  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.
• 

  Exploring science's fourth paradigm

  1 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.
• 

  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

• 

  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.​

December 2017

• 

  BORG students present research in KAUST Research Conference on Big Data Analyses in Evolutionary Biology

  1 min read · Tue, Dec 12 2017

  News

  ​Two students from the Bio-Ontology Research Group presented their research at KAUST Research Conference on Big Data Analyses in Evolutionary Biology.

November 2017

• 

  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

  1 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

• 

  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.
• 

  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

  1 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.

June 2017

• 

  CBRC participates in NATDP 2017

  1 min read · Sat, Jun 17 2017

  News

  comparative genomics proteins

  ​​​​​Five research groups from CBRC participated in this year's National Academic Talent Development Program (NATDP) Symposium on April 20. The Knowledge Mining Lab presented their research on Microbial Knowledge-based Expolaration Systems as well as Novel Computational Methods that Facilitate Development of Cyanofactories for Free Fatty Acid Production.

May 2017

• 

  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

  1 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.