22.4.2026. 15:15h, Faculty of Mathematics (online)

Shining light on structure and function in the dark protein universe

Dr Nicola Bordin

Tenure-Track Assistant Professor of Biochemistry, Università degli Studi di Padova, Italy

A meeting of the Bioinformatics seminar will be held on Wednesday, April 22nd, 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

The protein universe is vast, diverse, and still only partially explored, despite major advances in structure prediction and large-scale sequence analysis. A key challenge is the systematic characterization of this space in a way that captures structural diversity and the relationships between proteins at scale.

We will discuss a set of complementary approaches for exploring and organizing the protein universe. TED provides a large-scale structural decomposition of AlphaFold protein models into domains, defining a consistent vocabulary across hundreds of millions of structures. ContrasTED leverages contrastive learning to refine relationships between domains beyond traditional homology-based approaches. ProFam, a protein family language model, captures constraints within protein families and enables the generation of novel sequences consistent with those constraints.

Together, these approaches provide a framework for mapping, analysing, and engineering the protein universe.

Lecturer

Dr. Nicola Bordin did his Bachelor’s and Master in Biotechnology and Industrial Biotechnology at the University of Padua (Italy) with both dissertations in the fields of structural bioinformatics and functional genomics. He completed his PhD in Computational Biology and Bioinformatics on functional genomics in PVC bacteria at the Universidad Pablo de OIavide in Seville, Spain, under the supervision of Dr. Damien Devos. His fields of expertise are in algorithm design for protein function prediction, structure classification, sequence analyses and machine learning applied to protein data. After a period of postdoctoral research as senior researcher in the CATH team at University College London, where he developed novel algorithms for the functional classification of proteins and the structural classification of AlphaFold domains in CATH, he is currently a Tenure-Track Assistant Professor of Biochemistry at the University of Padua (Italy).

Seminar

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

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

    Video: Recorded lecture (MP4, 66min, 142MB)

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.

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.