25.3.2026. 15:15h, Faculty of Mathematics (online)

Single cell omics for personalized medicine in the age of artificial intelligence

Dr. Eduardo Beltrame

Mohamed bin Zayed University of Artificial Intelligence (MBZUAI), Abu Dhabi, UAE

A meeting of the Bioinformatics seminar will be held on Wednesday, March 25th, starting at 15:15, in online classroom. Teachers and students of doctoral and master studies in computer science, mathematics, biology and other related disciplines are invited to join us.

LINK: https://zoom.us/j/2183428158?pwd=ouAZtpLrbPnOBsKjQiarS9Rh59fyqF.1&omn=99579912618

Please note that the seminar time has been moved to Wednesday, 15:15 CET this semester.

Abstract

One of the most exciting consequences of the accessibility of single cell omics technologies is their use in new experimental designs. Beyond atlases, longitudinal studies with many timepoints are also yielding unprecedented volumes and formats of data, with hundreds of millions of cells publicly available. Driven by steadily decreasing sequencing costs and streamlined experimental workflows, single cell omics technologies are now widely used from basic biological research to drug discovery and clinical studies.

I will present an overview of the emerging data and AI-models landscape in the field, together with novel clinical study designs enabled by lowering cost and complexity barriers, and current prospects from AI virtual cells to new developments in precision medicine and diagnostics. I will discuss emerging research directions for working with these growing volumes of single cell omics data at the newly established Computational Biology program at the Mohamed bin Zayed University of Artificial Intelligence in Abu Dhabi, and exciting opportunities at the intersection of artificial intelligence applied to biological data.

Lecturer

Eduardo da Veiga Beltrame is an Assistant Professor of Computational Biology at the Mohamed bin Zayed University of Artificial Intelligence (MBZUAI) in Abu Dhabi, where he is responsible for coordinating the new master’s and PhD programs in Computational Biology. His main research interest is the development of methods and tools to work with biological data generated by single-cell omics and their applications in precision medicine.

He holds a Ph.D. in Bioengineering from Caltech, where his primary line of research focused on developing experimental and computational methods and tools for single-cell RNA sequencing and its application to biological questions. Before joining MBZUAI, he was head of bioinformatics at ImYoo, a biotechnology startup spun out of Caltech research that conducts decentralized studies of the immune system using single-cell omics. Prior to ImYoo, Beltrame was a founding scientist at Retro Biosciences, a biotechnology startup dedicated to developing therapies for aging-related diseases.

His academic page is: https://mbzuai.ac.ae/study/faculty/eduardo-beltrame/

Seminar

The organizer of the seminar is BIRBI. The heads of the seminar are Prof. dr Nataša Pržulj and dr Jovana Kovačević.

17.12.2025. 15:15h, Faculty of Mathematics (online)

Evolutionary costs and benefits of organismal complexity: insights from a cross-species analysis

Dr. Yury Barbitoff

Institute of Bioinformatics Research and Education and JetBrains Research, Belgrade, Serbia

    Video: Recorded lecture (MP4, 71min, 121MB)

A meeting of the Bioinformatics seminar will be held on Wednesday, December 17th, starting at 15:15, in online classroom. Teachers and students of doctoral and master studies in computer science, mathematics, biology and other related disciplines are invited to join us.

Please note that the seminar time has been moved to Wednesday, 15:15 CET this semester.

Abstract

Reconstruction of the complex network of genotype-to-phenotype relationships is a pivotal task of modern genetics. High-throughput methods have facilitated the investigation of the network of genotype-to-phenotype relationships of the whole-phenome scale (i.e., simultaneously studying hundreds or even thousands of traits). Pleiotropy, a phenomenon of multiple phenotypic effects of the same genetic alteration, is one of the most important features of genotype-to-phenotype networks. Pleiotropy is commonly considered one of the hallmarks of organismal complexity, and theoretical models predict that it should negatively affect adaptation of an organism to the environment. We have recently conducted a series of studies aimed at dissecting the functional determinants and evolutionary consequences of pleiotropy for different species and types of traits. We found that the same mechanisms appear to be driving pleiotropic effects in different species, despite the low concordance of individual gene-trait relationships between those species. Across different types of traits, highly pleiotropic genes emerge as ones with the broadest expression profile, greatest number of protein-protein interactions, and involvement in a large number of processes. Perhaps more importantly, our results show that the high degree of pleiotropy tends to enhance both positive and negative natural selection across different species and trait domains. These results suggest that organismal complexity has both its costs and benefits for the species, and are in line with the expectations drawn from the more advanced theoretical models.

Lecturer

Yury Barbitoff is a research group leader at the Institute of Bioinformatics Research and Education (IBRE) and a Senior Researcher at JetBrains Research working in Belgrade, Serbia. At IBRE, Yury’s research group focuses on studying human genome variation, with an emphasis on systemic analysis of genotype-to-phenotype relationships and evolutionary processes shaping the landscape of genetic variation across human genes. Yury obtained his Ph.D. in Genetics from St. Petersburg State University in 2023. From 2018 to 2022, Yury has been directing research efforts at the Bioinformatics Institute (St. Petersburg, Russia), and has been the leading contributor to large-scale human population genomics endeavors, such as the construction of the RUSeq database of protein-coding genetic variation in Russia.

Seminar

The organizer of the seminar is BIRBI. The heads of the seminar are Prof. dr Nataša Pržulj and dr Jovana Kovačević.

3.12.2025. 15:15h, Faculty of Mathematics (online)

Charting the Unknown: AI-Powered Classification and Discovery Across the Protein Universe

Prof. Dr. Joana Pereira

VIB Center for AI and Computational Biology and Department Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium

A meeting of the Bioinformatics seminar will be held on Wednesday, December 3rd, starting at 15:15, in online classroom. Teachers and students of doctoral and master studies in computer science, mathematics, biology and other related disciplines are invited to join us.

Please note that the seminar time has been moved to Wednesday, 15:15 CET this semester.

Abstract

The protein universe remains only partly charted, with countless families and functions yet to be uncovered. By harnessing large-scale datasets of protein sequences and structures, we recently introduced an unsupervised representation of this space that identifies functionally meaningful clusters across millions of proteins. This data-driven framework enables systematic prioritization and characterization of uncharacterized families, generating candidates for experimental validation. Through this approach, we revealed new biology at scale, including unrecognized prokaryotic defense systems and a previously undescribed repetitive protein fold, the β-flower.

Although the biological role of proteins adopting the β-flower fold remains unknown, we demonstrate that these sequences are remarkably diverse at both sequence and structural levels. They are predominantly encoded in metagenomic datasets, with expression patterns that are not yet understood. Importantly, experimentally determined structures confirm the existence of the β- flower fold, offering opportunities for engineering repetitive, soluble β-barrel–like architectures. Together, these results highlight the transformative potential of AI-guided discovery and establish the foundation for a dynamic, ever-expanding atlas of the protein universe, accelerating efforts to decode molecular functions, trace evolutionary trajectories, and inspire protein design across the tree of life.

Lecturer

Joana Pereira leads the “Protein Evolution and Function Models” group at the VIB Center for AI and Computational Biology in Leuven and is an Assistant Professor at KU Leuven’s Department of Cellular and Molecular Medicine (since February 2025). She is an expert in computational structural biology and protein evolution, with a doctorate in Chemistry from the University of Hamburg and EMBL, and a background in biochemistry. She has over seven years of postdoctoral experience at the Max Planck Institute in Tübingen and the Biozentrum in Basel. Her research integrates structural bioinformatics, complex network analysis, and deep learning to study the structure, diversity, and evolution of the protein universe, in close collaboration with experimental labs, especially on prokaryotic systems

Seminar

The organizer of the seminar is BIRBI. The heads of the seminar are Prof. dr Nataša Pržulj and dr Jovana Kovačević.