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. We perform bioinformatic analysis while aiming to understand different aspects of molecular biology:

1) Functional analysis of 3D genome structure, as an analysis of a selection of gene interactions in 3D to determine and analyze those that are involved in the regulation of a specialized biological process, is an important part of understanding the role of chromatin interactions. We are proposing tools to (i) measure 3D genome structure changes between different cells and conditions (ii) to look for the enrichment of GO terms in contacts of genes – GO-a-GO (iii) associate chromatin modifications with different 3D chromatin structures.

2) Differential gene expression and functional analysis in studies of: (i) a universal platform for rapid testing of protective vaccines against COVID-19 and other viral diseases, (ii) treatment for patients with fungal infections, (iii) the action mode of combined therapy and development of new and effective methods of treating cancer patients.

3) Metagenomics analysis of environmental samples.

4) Data analysis from experiments exploring new aspects of chromatin organization. Application of machine learning for association of chromatin marks with the new structures.

5) Building predictive models for tumor classification and personalized treatment of patients with soft tissue sarcomas.


  1. Prof. Monika Staniszewska, Laboratory of Pathogens’ Biology and Molecular Diagnostics, CEZAMAT WUT
  2. Prof. Andrew Belmont, University of Illinois at Urbana-Champaign, USA
  3. Dr. Aleksander Jankowski, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw
  4. Pola Łomża-Kalinowska, MSc, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology
  5. Dr. Aneta Borkowska, Prof. Piotr Rutkowski, Maria Skłodowska-Curie National Research Institute of Oncology
  6. Prof. Agnieszka Adamczyk-Woźniak, Faculty of Chemistry, Warsaw University of Technology
  7. Dr. Heng-Chang Chen, Quantitative Virology Laboratory, Łukasiewicz – PORT, Wrocław


  1. MinION Mk1B and 2x Mk1C Oxford Nanopore sequencing devices
  2. LENOVO ThinkStation P620, AMD Ryzen Threadripper PRO 5945WX 12-Cores, 24 threads, Clock 4.1GHz (Max. 4.5GHz), 5x2TB, 128 GiB RAM, NVIDIA RTX A2000 12GB


RND IB PW – “A tool for functional analysis of groups of gene pairs and its application to gene pairs determined by chromatin contacts” – 2023-2024, Teresa Szczepińska – leader

LIDER POB BIB 2 – “Diagnostyka biomarkerów mięsaków tkanek miękkich w stratyfikacji pacjentów i monitorowaniu wyników leczenia – medycyna spersonalizowana (ONCOTRACE) 2024-2025, Sachin Gadakh – co-investigator

NCN OPUS 25 – “Molecular profiling of soft tissue sarcomas in tumor and peripheral blood in terms of response to treatment and early detection of recurrence or dissemination” – 2024-2026, Teresa Szczepińska – co-investigator


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