The dissertation focuses on developing novel computational methods to improve the diagnosis of patients with rare or complex diseases. By systematically relating human phenotypes resulting from gene function loss or change to gene functions and anatomical/cellular locations, the candidate aims to enhance the prediction and prioritization of disease-causing variants. These methods, leveraging graph-based machine learning and biomedical ontologies, demonstrate significant improvements over existing approaches. The presentation will include a systematic evaluation of the methods, demonstrating their ability to compensate for incomplete data and their applications in biomedicine and clinical decision-making. This research contributes to more effective methods for predicting disease-causing variants and advancing precision medicine, offering promising prospects for improved diagnostics and patient care.

Ontologies are widely used in various domains, including biomedical research, to structure information, represent knowledge, and analyze data. Combining ontologies from different domains is crucial for systematic data analysis and comparison of similar domains. This requires ontology composition, integration, and alignment, which involve creating new classes by reusing classes from different domains, aggregating types of ontologies within the same domain, and finding correspondences between ontologies within the same or similar domain.

Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases, but also has a determinative genome location aspect.

Coffee Time: 15:30 - 16:00. Kernel matrices can be found in computational physics, chemistry, statistics, and machine learning. Fast algorithms for matrix-vector multiplication for kernel matrices have been developed, and is a subject of continuing interest, including here at KAUST. One also often needs fast algorithms to solve systems of equations involving large kernel matrices. Fast direct methods can sometimes be used, for example, when the physical problem is 2-dimensional. In this talk, we address preconditioning for the iterative solution of kernel matrix systems. The spectrum of a kernel matrix significantly depends on the parameters of the kernel function used to define the kernel matrix, e.g., a length scale.

Abstract

The increased availability of biomedical data, particularly in the public domain, offers

Bioinformatics experts, Don’t miss the opportunity to collaborate with researchers and field professionals in the BioHackathonMENA2023 event. BioHackathon events involve a large number of people that meet on-site to discuss ideas and implement projects in a collaborative manner during intensive coding sessions.

We propose a structured latent ODE model that explicitly captures system input variations within its latent representation. Building on a static latent variable specification, our model learns (independent) stochastic factors of variation for each input to the system, thus separating the effects of the system inputs in the latent space. This approach provides actionable modeling through the controlled generation of time-series data for novel input combinations (or perturbations). Additionally, we propose a flexible approach for quantifying uncertainties, leveraging a quantile regression formulation.

In this talk, I will first present how the application of phylogenetic and phylodynamic methods to whole genome sequencing data of multidrug resistant bacterial pathogens provided an in-depth understanding of the epidemiology and evolution of these strains on epidemiological time scales. I will then discuss the characterization of the genomic repertoire of bacterial traits using a combination of machine learning, whole genome sequencing and large-scale phenotypic assays. I will then present the leverage of predictive modelling to predict bacterial features, e.g. antimicrobial resistance, growth, and horizontal gene transfer, from genomic biomarkers. I will finally discuss how large-scale phenotypic assays enabled us to identity genes underlying morphogenesis and biofilm formation.

Biological systems are distinguished by their enormous complexity and variability. That is why mathematical modelling and computational simulation of those systems is very difficult, in particular thinking of detailed models which are based on first principles. The difficulties start with geometric modelling which needs to extract basic structures from highly complex and variable phenotypes, on the other hand also has to take the statistic variability into account.

Sakhaa Al-Saedi: We conduct a systematic genetic analysis of risk variants related to increasing the severity of COVID-19. It leads to a better understanding of its genetic basis and identifies the host genes to be targeted to tackle the COVID-19 pandemic and reduce its death toll. Azza Althagafi: We developed DeepSVP, a computational method to prioritize structural variants involved in genetic diseases by combining genomic and gene functions information. DeepSVP significantly improves the success rate of finding causative variants in several benchmarks and can identify novel pathogenic structural variants in consanguineous families.

Abstract

The life sciences have invested significant resources in the development and application

We developed and expanded novel methods for representation learning, predicting protein functions and their loss of function phenotypes. We use deep neural network algorithm and combine them with symbolic inference into neural-symbolic algorithms. Our work significantly improves previously developed methods for predicting protein functions through methodological advances in machine learning, incorporation of broader data types that may be predictive of functions, and improved systems for neural-symbolic integration. The methods we developed are generic and can be applied to other domains in which similar types of structured and unstructured information exist. In future, our methods can be applied to prediction of protein function for metagenomic samples in order to evaluate the potential for discovery of novel proteins of industrial value.  Also our methods can be applied to the prediction of loss of function phenotypes in human genetics and incorporate the results in a variant prioritization tool that can be applied to diagnose patients with Mendelian disorders.

In my research I aim to understand how formalized knowledge bases can be used to systematically structure and integrate biological knowledge, and how to utilize these formalized knowledge bases as background knowledge to improve scientific discovery in biology and biomedicine.  To achieve these aims, I develop methods for representing, integrating, and analyzing data and knowledge with the specific aim to make the combination of data and formalized knowledge accessible to data analytics and machine learning in bioinformatics. Biomedicine, and life sciences in general, are an ideal domain for knowledge-driven data analysis methods due to the large number of formal knowledge bases that have been developed to capture the broad, diverse, and heterogeneous data and knowledge.

Computational Bioscience Research Center at King Abdullah University of Science and Technology is pleased to announce the KAUST Research Conference on Digital Health 2020. To see the agenda of the conference Digital Health 2020 visit agenda page. To view ​frequently asked questions, visit FAQ page.

​Science to Watch is a science orientated movie series followed by a discussion about the movie as it relates to science.

In this talk, I will discuss our work to create computational standards, platforms, and methods to wrangle knowledge into simple, but effective representations based on semantic web technologies that are maximally FAIR - Findable, Accessible, Interoperable, and Reuseable - and to further use these for biomedical knowledge discovery. But only with additional crucial developments will this emerging Internet of FAIR data and services enable automated scientific discovery on a global scale.

KAUST Assistant professor Robert Hoehndorf will be giving a keynote presentation at the 4th International Workshop on Ontology Modularity, and Evolution @ JOWO 2019, Graz, Austria.

Abstract

The life sciences have invested sig

Prof. Rebholz-Schuhmann has long-term experience in semantics driven data analytics research, as well in life sciences as in other domains.

Contemporary drug-drug interactions  (DDIs)  research offers a  clinically impactful opportunity to identify  DDIs prior  to their occurrence;  however,  the clinical utility of current  DDI  identification systems have,  to date,  been greatly limited by the inability to accurately and concisely identify their pathway of interaction for the vast lists of identified computationally and clinically valid DDIs.

Malaria kills nearly one-half million people a year and over 1 billion people are at risk of becoming infected by the parasite. Plasmodial infections are difficult to treat for a myriad of reasons, but the ability of the organism to remain latent in hosts and the complex life cycles greatly contributed to the difficulty in treat malaria.

Biological knowledge is widely represented in the form of ontology-based annotations: ontologies describe the phenomena assumed to exist within a domain, and the annotations associate a biological entity with a set of phenomena within the domain.

Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products.

Abstract

Sequencing has identified millions