Laboratory of Bioinformatics and Genome Structure

The Laboratory of Bioinformatics and Genome Structure was established in 2022 in the Centre for Advanced Materials and Technologies CEZAMAT and is a part of the Department of Microbiology, Molecular genetics, and Genomics. In our work, we perform bioinformatic analysis of proteomic data to expand our understanding of how proteins evolve and interact with other molecules, both endo- and exogenous. We specialize in predicting interactions between proteins and small compounds using molecular docking, molecular dynamics simulations, and machine learning. In the IDUB against COVID-19 grant, we focus on predicting the interactions between the Spike proteins from the Coronaviridae family members with their molecular partner – ACE2 protein. Our goal is to determine novel species belonging to that family that can switch hosts from bats to humans. This event might result in novel pandemics. Another important aspect of our work is the analysis of chromatin 3D structure. As a part of the grant “NanoGAM: a method of studying the three-dimensional structure of the genome, through the use of long-read DNA sequencing of ultracryosectioned nuclear profiles by laser microdissection”, we identify chromatin regions that show alteration in the pattern of interactions between experiments like Hi-C and GAM. These regions are next depicted in greater detail using their sequence and various epigenetic marks obtained from publicly available data. We also analyse DNA-seq, RNA-seq and ChiP-seq experiments. 

1. MinION Mk1B sequencing device
2.  MinION Mk1C sequencing device
3. Qubit 4 Fluorometer

1. Oxford Nanopore Technology long-read sequencing of selected families from the 1000 Genomes Project 
2. Bat Coronaviruses as an emerging threat to the human population, IDUB against Covid-19 grant(IDUB against COVID-19, 2020–2022)
3. NanoGAM: a method of studying the three-dimensional structure of the genome, through long-read DNA sequencing of ultracryosectioned nuclear profiles by laser microdissection. (IDUB BIOTECHMED-2, 2021–2023)

• Teresa Szczepińska, PhD – Head of the Laboratory
• Sachin Gadakh – bioinformatician