Laboratory of Structural Genomics

Description

The main scientific interest of the Laboratory of Structural Genomics is the analysis of the sequence and 3D structure of the eukaryotic cell. In particular, we would like to better understand about the relationship of this structure and the fundamental processes such as transcription, replication or DNA repair.. Additionally, we explore how genome 3D structure varies across healthy and sick and among human populations. We use the latest high-throughput sequencing methods, including long-read sequencing like the Oxford Nanopore technology. Members of our laboratory are active participants of the 4DN consortium. In our studies, we analyze structural data obtained from ChIA-PET, Hi-C, Hi-ChIP, GAM experiments and other genomic data, e.g. ChIP-seq, RNA-seq, DNA-seq. Another important aspect of our work is the bioinformatic analysis of proteomic data. Specifically, we specialize in predicting interactions between proteins and small compounds using molecular docking, molecular dynamics simulations and machine learning. Furthermore, we predict proteins structure and function with the help of the homology modelling approach. As part of the IDUB agains COVID-19 grant, we focus our effort on predicting the interactions between the Spike proteins of the Coronaviridae family with their molecular partners, like ACE2 proteins. Our goal is to determine novel species belonging to that family that can jump from bats to humans and be a source of novel pandemics.

Services offered:

  • Long-read sequencing using Oxford Nanopore technology 
  • Bioinformatic analysis of proteomic and genomic data: 
    • Predicting free energy of binding for protein-ligand and protein-protein complexes 
    • Analyzing the influence of mutations on protein structure and function 
    • Homology modelling of proteins 
    • Genomic data analysis for humans and pathogens (COVID-19)

Equipment

  1. MinION Mk1C sequencing device (2 pc.)
  2. MinION Mk1B sequencing device (1 pc.)
  3. Access to a supercomputer at the MiNI department, WUT (4 servers, NVIDIA DGX-A100)

Projects

  1. Oxford Nanopore Technology long-read sequencing of selected families from the 1000 Genomes Project 
  2. Bat Coronaviruses as an emerging threat for 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 the use of long read DNA sequencing of ultracryosectioned nuclear profiles by laser microdissection. (IDUB BIOTECHMED-2, 2021–2023)

Employees

Skip to content