Day and Night at PMF 2023: “Find me!” shouted the malignant cell – Bioinfo

Day and Night at PMF 2023: "Find me!" shouted the malignant cell

April 26, 2023

Tumor cells are hard to detect because they are few, small, and hidden among healthy cells. In the workshop, participants used single-cell RNA sequencing to analyze gene activity and identify whether cells came from mutated brain or bone tumors.

Authors: Miran Grgić, Marta Paladin, Petra Struški, Barbara Maračić

Menthors: Paula Štancl, Doris Repušić

Tumor cells are difficult to detect because they are few in number, very small, and hidden among normal tissue cells. Fortunately, scientists have developed a method that allows for the “reading” (so-called sequencing) of all mRNA molecules present in an individual cell. This method enables precise determination of gene activity levels in each cell, making it possible to identify hidden tumor cells.

The aim of the workshop is to introduce participants to the method of single-cell RNA sequencing and the analysis of the resulting data for identifying different cell types. Participants stepped into the role of bioinformaticians for a day, analyzing data to determine whether cells originated from mutated brain or bone tumors.

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Kristian Vlahoviček

Group leader and Full Professor of Bioinformatics at the Faculty of Science, University of Zagreb

While studying molecular biology at the University of Zagreb he developed a strong interest in applying computational methods and approaches to biosciences. For his master thesis he worked on a problem in X-ray crystallography and developed a program for absorption correction of scattered X-ray data. He obtained his PhD in Bioinformatics/Biochemistry, still pursuing his structural biology interests, working on a computational prediction of structural and physicochemical properties of DNA. He spent 10 years as a research fellow at the International Center for Genetic Engineering and Biotechnology in Trieste, Italy, where he also worked on computational prediction and classification of protein domains using machine learning approaches.

In 2002 he established a computational biology group at the Zagreb University, where he moved permanently in 2006 with the EMBO Young Investigators Programme installation grant, and directed the scientific interests towards the newly emerging field of genomics. His bioinformatics group develops computational tools and uses machine learning techniques to tackle open questions in developmental genomics and metagenomics.

In 2011 he became full professor at the Faculty of Science at Zagreb University. He had several international appointments, including a 4-year adjunct professorship at the University of Oslo, Norway and a two-year adjunct professorship at the University of Skövde, Sweden. From 2008 to 2012 he served as the head of the Division of Biology, Faculty of Science at University of Zagreb and was responsible for managing a division of ~150 staff.

He is involved in teaching four graduate-level courses: Bioinformatics, Algorithms and programming, Statistics and machine learning and Computational genomics. During his time as a group leader more than 30 doctoral and master students graduated under his supervision. Some of his graduates continued with PhD and postdoctoral training at prestigious universities around the world, including LMB Cambridge, UK; EMBL, Heidelberg, Germany; RIKEN, Japan and ETH, Zurich, Switzerland.

His scientific track-record includes more than 60 publications in high-level journals and talks in many renowned institutions throughout the world. His research topics are: developmental and differentiation genomics, metagenomics, population genomics and glycomics, origins of multicellularity, epigenomics of cancer, development of computational methods and application of machine learning in genomics and molecular biology.

He is the reviewer in a number of scientific journals, as well as national and international funding bodies and programmes, such as ESF Programme, EC FP7, H2020, and Horizon Europe Programmes, Estonian National Funding Agency, Hungarian National Funding Agency, Flanders Research Foundation, The Netherlands ZonMw Vidi Programme, Croatian National Funding Agencies. He reviewed program applications for Croatian pre-accession and accession structural funds.

Prof. Vlahoviček is a Fellow of the Academia Europaea, and a member of several professional societies, at the national and international level. Professor Vlahoviček is a strong proponent of science reforms in Croatia and evidence-based policy making. He served in the steering committee of Croatia’s highly successful science funding body, the Unity through Knowledge Fund (UKF) and has participated in several strategy-drafting panels at the university and national level. He also served as the Member of the Steering Committee of the Ruđer Bošković Institute, a leading Croatian research entity in natural sciences, with ~900 staff.