Researcher biography

Dr Magdalena Antczak is a Postdoctoral Research Fellow in Professor Di Yu's research lab, based in the Translational Research Institute and specialising in T-cell Immune Mechanism, Monitoring and Modulation. Dr Antczak's current research project involves investigating the evolution of the common gamma chain family of cytokines and their receptors, focusing on protein structure and protein-protein interactions.

Dr Antczak obtained her PhD in Computational Biology from the University of Kent, the United Kingdom, in 2021. During her PhD, she conducted meaningful research with the main focus being identifying protein function and variation. Her findings have contributed to an increased understanding of the fundamental cellular functions, as well as mechanisms in which cancer cells develop resistance to various anti-cancer drugs.

One of her projects involved studying unknown functions in the first minimal synthetic bacterial cell, which contains only the genes essential to survive in a medium full of nutrients and self-replicate in a reasonable time. She established the function of 133 out of 149 previously unknown genes by combining results from various protein function prediction methods and making manually curated predictions for the functions.

The second focus of her PhD research involved studying drug resistance mechanisms in cancer cell lines. Within this project, she co-designed and co-built a pipeline to detect drug resistance markers among variants identified in the cell lines. She then used this pipeline to detect variants that drive resistance to an MDM2-inhibitor, nutlin-3, in acute myeloid leukaemia cell lines and four tubulin-binding agents in neuroblastoma cell lines which resulted in identifying several mechanisms of drug resistance.

The third focus of her PhD research has been assessing novel methods of predicting protein function. The main objective has been to bridge the gap between the increasing number of protein sequences that lack experimental annotation. She has predicted the function for over 100,000 proteins using our in-house method Gene Ontology Annotation Tool (GOAT), which combines information from proteins' close and distant homologues, domains and conserved residues using a machine learning algorithm - Support Vector Machine (SVM).

Finally, she has collaborated on developing a web server that aims to identify amino acid positions that differ between SARS-CoV and SARS-CoV-2 but were highly conserved in each of them and increase understanding of differences in the behaviour of the two viruses, including the higher transmission of SARS-CoV-2.

As a bioinformatics researcher at the University of Kent, Dr Antczak has been mentoring new laboratory members with a biology background. She has also been a demonstrator at the bioinformatics practical sessions for second and third-year undergraduate students.