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

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.

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

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

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.

26.11.2025. 15:15h, Faculty of Mathematics (online)

Computational genomics at scale: Open-source frameworks for cancer omics and gene regulation

Prof. Dr. Aziz Khan

Mohamed bin Zayed University of Artificial Intelligence (MBZUAI), Abu Dhabi, United Arab Emirates

A meeting of the Bioinformatics seminar will be held on Wednesday, November 26th, 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

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

Abstract

Advances in cancer research rely on scalable and reproducible computational frameworks for analyzing genomic data. This seminar will introduce open-source tools and infrastructures for interrogating diverse cancer genomes. First, I will highlight open resources for studying gene regulation and the regulatory genome. Next, I will present the scalable bioinformatics infrastructure we built at Stanford to enable reproducible, large-scale cancer genomics, supporting initiatives such as the Human Tumor Atlas Network (HTAN) and Metastasis Research Network (MetNet). Finally, I will share our recent HTAN pre-cancer colon atlas using familial adenomatous polyposis (FAP) as a model.

Lecturer

Aziz Khan is an Assistant Professor of Computational Biology at the Mohamed bin Zayed University of Artificial Intelligence (MBZUAI) in Abu Dhabi, where he leads the Computational Biology and Cancer Regulatory Genomics (https://khanlab.bio/) Lab. His research focuses on deciphering gene regulation and the non-coding genome in cancer and precision medicine, using scalable computational and machine learning approaches. His lab develops open-source tools and integrative frameworks to interpret large-scale, multi-omics data.

Aziz earned his PhD in Bioinformatics from Tsinghua University and completed his postdoctoral research at the University of Oslo’s NCMM. Before joining MBZUAI, he was a senior research scientist at Stanford Cancer Institute, where he led core efforts in cancer genomics infrastructure and contributed to large multi-institutional initiatives, including the Human Tumor Atlas Network (HTAN) and the Metastasis Research Network (MetNet). He has developed widely used computational resources such as JASPAR, Intervene, and UniBind, and has taught and advocated for open, transparent, and reproducible science as a Carpentries Instructor and former eLife/ASAPbio Ambassador. His work bridges AI, genomics, and systems biology, with a mission to enable reproducible, collaborative, and globally impactful science.

Seminar

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