The Tsoy Group

I’m a group leader of the Computational Genomics and Transcriptomics group (cgat-group.de). My main research interest is mechanisms of pathological conditions such as diseases with complex phenotypes and drug side effects and the role of alternative splicing. I graduated from Lomonosov Moscow State University (Moscow, Russia) and did PhD in Kharkevich Institute in Moscow in Professor Mikhail Gelfand's lab. There I studied the evolution of transcriptional regulatory networks in bacteria. During my PhD, I shortly stayed at Stowers Institute for Medical Research (Kansas-City, USA), and at Okinawa Institute of Science and Technology (Okinawa, Japan) where I went on working on the regulation of bacterial metabolic pathways. As a research scientist, I worked at the Skolkovo Institute of Science and Technology (Moscow) on 3D chromatin structure analysis. In 2019, I joined the group of Professor Jan Baumbach at the Technical University of Munich, and continued working with the group at the University of Hamburg.

I’m a PhD candidate at CoSy.Bio since April 2021 after finishing my M.Sc. Computer Science at TUM. Before, I gained some experience with ligand binding site prediction using CNNs and Class Activation maps at Rostlab and with single cell analysis in human T-cell immunology at Zielinski Lab. At the Chair of Experimental Bioinformatics at TUM I worked on exon-specific differences in microRNA regulation due to alternative splicing for my Master’s thesis. Currently I'm excited to research the application of deep learning methods for extracting splice junctions from RNAseq data with low sequencing depth.

Since April 2023, I have joined CoSy.Bio as a postdoc. My primary research interest is employing interpretable machine learning techniques to gain new biological insights. I did my PhD under the guidance of Professor Mikhail Gelfand at IITP RAS (Moscow, Russia). My doctoral research was focused on investigating the role of mRNA secondary structure in mRNA editing of cephalopods. Additionally, I worked as a junior researcher at the Skolkovo Institute of Science and Technology and contributed to several projects in the fields of bacterial genomics and human alternative splicing research.

I am a research associate at the CoSy.Bio lab since April 2023, working on the DrugSiderAI and PosyMed projects. I earned a B.Sc. in Electrical Engineering from IAU and an M.Sc. in Biomedical Engineering from AUT. During my master’s program, I gained experience in signal processing and machine learning (ML) methods for biomedical applications. Following my graduation, I conducted research on applying ML techniques to transcriptomic data, with the aim of advancing personalized medicine. Additionally, I focused on network-based approaches and gained experience working with graph convolutional neural networks to capture the complex relationships in biological data. My primary research interest lies at the crossroads of applying network-based ML to the field of medicine. I am excited to continue exploring this field and contributing to cutting-edge research as part of the CoSy.Bio team.

I'm a master's student at the University of Maastricht, studying Drug Development and Neurohealth. In January 2023 I will be returning to Cosy.Bio to work on my master's thesis under the supervision of Dr. Olga Tsoy and Lena Hackl. I will be looking at tissue-specific andbloodbased biomarkers in cardiomyopathies. In 2021/2022, I first joined CoSy.Bio to work on the thesis for my MSc degree in Systems Biology (Maastricht University), under the supervision of Dr. Olga Zolotareva, working towards a federated implementation of a DNA methylation microarray data analysis workflow. Before this, I obtained a BSc (Hons) degree in Forensic Science at Anglia Ruskin University.

I am a master's student in bioinformatics at the Technical University of Munich (TUM) and Ludwig Maximilian University of Munich (LMU). For my BSc thesis I evaluated domain-domain interaction prediction methods and used the PPIDM method to infer new interactions. I will join the CoSy.Bio team from January 2024 as a HIWI and will be working to update DIGGER and NEASE, with a focus on making the tools easily available online