11.12.2024. 18:15h, Faculty of Mathematics (online)

A bioinformatics strategy for the discovery of host-based biomarkers from human cell-free DNA in blood plasma

Dr. Alessandra Vittorini Orgeas

Hungarian Centre of Excellence for Molecular Medicine, Szeged, Hungary

    Video: Recorded lecture (MP4, 62min, 154MB)

A meeting of the Bioinformatics seminar will be held on Wednesday, December 11th, starting at 18:15, 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 for this meeting we will switch to the Zoom platform instead of the usual Webex.

Abstract

Human cell-free DNA molecules in the bloodstream originate from various tissues and can be easily isolated and analysed. Although the biogenesis of these molecules is still not well understood, their abundance, size, genetic and epigenetic alterations are associated with many benign and malignant diseases. A large number of samples can be collected easily and quickly through a routine blood draw. In addition, high-throughput sequencing technologies (NGS) have made it possible to generate substantial amounts of complex genomic data. This has led to a great interest in cell-free DNA in clinical settings, due to its potential role as a biomarker. However, this potential can only be exploited if supported by a computational platform that simplifies the execution of the analysis and makes it efficient, reproducible and portable across different platforms. To address the complexity of this analysis, we have implemented a computational pipeline for the discovery of host-based genetic biomarkers of infectious diseases and beyond that addresses some of the well-known challenges associated with traditional pipelines as well as less well-known challenges associated with the output data of NGS methods. In this talk, I will summarize the challenges faced in the development of this pipeline and offer a solution based on the results of our previous studies and the particular characteristics of our dataset. Finally, I will describe the workflow of the pipeline and explain the function of each module into which it is decomposed. Finally, I will describe the workflow of the pipeline and explain the function of each module into which it is decomposed. The pipeline is currently in the testing phase, but we believe that it could serve as a model for future projects of this kind.

Lecturer

Alessandra Vittorini Orgeas is an interdisciplinary scientist with a strong academic and research background in biophysics, mathematical physics, and bioinformatics. She holds two PhDs: one in Mathematical Physics from the University of Melbourne (2019) and another in Materials for Health, Environment, and Energy from the University of Rome Tor Vergata (2013). Alessandra also earned a Master’s Degree in Biophysics and a Bachelor’s in Physics, both with top honors, from the University of Rome La Sapienza.

Alessandra has gained valuable academic research experience at internationally recognized institutions, including Leibniz Universität Hannover (Germany) and the Institut national de la recherche scientifique (INRS) in Canada. Her work has been published in leading scientific journals such as Nature Materials and Journal of Physics A.

After a period of work in IT consulting, Alessandra returned to research and is currently a Postdoctoral Researcher at HCEMM Nonprofit kft. in Hungary. As part of the Circulating Nucleic Acids Biomarkers Core Group, she investigates novel methods for using nucleic acids as biomarkers to diagnose infectious diseases and other malignancies.

Seminar

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

27.11.2024. 18:15h, Faculty of Mathematics (online)

3D Genomics Based on Sequencing

Prof. Dr. Yuriy Orlov

Centre for Information Technologies and Medical Data Analysis, First Moscow State Medical University of the Ministry of Health of the Russian Federation

    Video: Recorded lecture (MP4, 63min, 250MB)

A meeting of the Bioinformatics seminar will be held on Wednesday, November 27th, starting at 18:15, 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 for this meeting we will switch to the Zoom platform instead of the usual Webex.

Abstract

Genome sequencing technologies allow studying chromosome contacts using new approaches. Here we compare 3D genomics methods: Hi-C (high order 3C - Chromosome Conformation Capture) and ChIA-PET (Chromatin Interactions Analysis – Paired End Tags) methods. Histone modification profiles and transcription binding sites profiles are complemented by information on distant chromosome interaction. We discuss gene expression regulation mechanisms from the point of view of chromosome contacts.

Lecturer

Yuriy L. Orlov is professor of the Russian Academy of Sciences, chair of Centre for Information Technologies and Medical Data Analysis, First Moscow State Medical University of the Ministry of Health of the Russian Federation. He delivers lectures on bioinformatics at the Institute of Digital Biodesign and Life Systems Modeling, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia. He has worked at the Genome Institute of Singapore, developing ChIP-seq data analysis models and then ChIA-PET method, first published in Nature in 2009.

Seminar

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

13.11.2024. 18:15h, Faculty of Mathematics (online)

AI in Medicine: Unveiling Current Applications and Exploring New Frontiers

Dr. Ivan Lorencin

Faculty of Informatics, Juraj Dobrila University of Pula, Croatia

    Video: Recorded lecture (MP4, 64min, 88MB)

A meeting of the Bioinformatics seminar will be held on Wednesday, November 13th, starting at 18:15, 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.

Abstract

Artificial intelligence (AI) has the potential to significantly transform medicine, enhancing diagnostic accuracy, patient care, and healthcare processes. This lecture explores the use of various AI technologies, including deep learning, large language models (LLMs), and computer vision, within medical applications. Emphasis is placed on how AI aids in the analysis of medical texts, the generation of medical reports, diagnostics from imaging, and predictive health risk assessments. By leveraging semantic segmentation, AI can precisely detect and classify tumor masses, while robotic surgery applications demonstrate improvements in precision and patient outcomes. The lecture will also address the role of AI in automating healthcare administration and accelerating drug discovery. Ethical considerations, such as transparency, data privacy, and bias prevention, are highlighted as crucial factors for trustworthy AI deployment.

Lecturer

Ivan Lorencin is an Assistant Professor at the Faculty of Informatics, Juraj Dobrila University of Pula, where he currently serves as Vice Dean for Business Cooperation and Science. He was elected to the scientific rank of Research Associate in the fields of Electrical Engineering, Mechanical Engineering, and Computer Science, and is also an editor of the journal "Mathematics." He is the author and co-author of over 100 scientific papers, more than 30 of which are published in Q1 and Q2 journals. He is actively involved in multiple AI-related projects as a project leader or team member. Besides his academic career, Ivan is also a partner and AI R&D specialist at the Croatian-Serbian startup dAIgnostics, focusing on the development of artificial intelligence solutions for medical applications, and serves as the CEO and founder of Ant Intelligence, an AI development and consulting firm.

Seminar

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