On June 28, Dmytro Fishman defended his PhD thesis on “Developing a data analysis pipeline for automated protein profiling in immunology”. In this work, Dmytro and his collaborators explored the dynamics of autoimmune diseases as well as developed a software tool that simplifies similar research in the future.

Proteins are essential elements of all living organisms. A significant number of life-critical functions depend on these tiny yet important molecules. The amount of proteins in an organism’s cells is strictly regulated, as an excessive amount or sudden shortage can cause unwanted consequences. Abnormal protein levels can be a sign of serious sickness. Therefore, an ability to accurately assess protein amounts in the body can be the key to the understanding of disease mechanisms.

One of the most popular approaches for measuring the presence of proteins in a person (e.g. from blood) is called protein microarray. This platform allows to measure hundreds or even thousands of proteins at the same time enabling researchers to study the interplay between proteins and diseases. One of the main challenges of using protein microarray platform is being able to apply correct computational methods to analyse and interpret the experimental data that it produces. Despite a multitude of computational methods developed for existing similar microarray-based platforms, protein microarrays differ from them in a number of important ways, rendering such methods unusable. Therefore, methods tailored specifically to protein microarrays are absolutely necessary to make most of what this technology has to offer as well as help biologists and doctors to use these methods. This was precisely the focus of Dmytro’s PhD thesis.

Over the series of studies, Dmytro, his supervisors and collaborators firstly implemented and then tested various relevant computational methods for analysing protein microarray data. A focal point of this PhD work is the protein microarray web-explorer (PAWER) – an R-based web-tool, developed to enable semi-automatic protein microarray analysis. PAWER incorporates all the relevant computational methods. Its intuitive user interface and step-by-step workflow are designed to help perform protein microarray analysis with ease. All the studies were published in well-established international peer-reviewed journals.