Fields of research in lab


Areas For Scientific Synergies

Three dimensional Genomics, 4DNucleome related projects, the higher order chromatin organization; Hi-C / ChIA-PET / Hi-ChIP experiments and data analysis, chromatin looping, topologically associating domains, compartmentalization of nucleus, lamina and subnuclear structures interactions with chromatin; genome wide association studies (GWAS), structural variants identification and functional analysis (including deletions, duplications, insertions, inversions, and translocations), next generation sequencing, short (Illumina) and long-reads (Oxford Nanopore, PacBio) DNA sequencing and data analysis, ChIP-seq data analysis from the 3D structure perspective; Big Data, statistical learning, massive dataset analysis, Computational Genomics and bioinformatics in population-level genomic data for medical applications and fundamental research in Life Sciences, structural and functional analysis of “omics” data; biophysical simulations , polymer modeling, DNA, RNA and proteins structure prediction, protein-protein, protein-DNA, protein-RNA and RNA-DNA interactions: prediction and analysis of biomolecular interactions networks; whole-cell systems biology modeling;

Three-dimensional Human Genome structure at the population scale: computational algorithm and experimental validation for lymphoblastoid cell lines of selected families from 1000 Genomes

Project TEAM - Laboratory of Functional and Structural Genomics CeNT

Analysis of mechanisms of drug resistance to trastuzumab in HER2 overexpressing breast cancer based on gene expression changes in selected cell lines

Anna Rusek

Contacts of structural chromatin domains investigated by GAM method. A scientific internship at the laboratory of Professor Ana Pombo in Berlin.

The scientific goal of the project is to develop bioinformatic methods to study contacts between chromatin structural domains. In Professor Ana Pombo’s laboratory, I will gain access to newly created data from the GAM method for embryonic human stem cells (hESC-H1 cell line).

Identification of structural variants in human genome using long-read Next Generation Sequencing with the Oxford Nanopore technology

The main aim of our research project is the increase of the competences of the applicant, in the area of understanding of experimental technologies, such as Oxford Nanopore long read sequencing. Another aim is the generation of experimental data (which isn’t accessible to date as public data), for the purpose of subsequent bioinformatics research and the submission of research grants. The research project which is assumed to be submitted as a proposal (up to 12 months), assumes the creation of bioinformatics tools and web services for the purpose of analysis of the human genome (and others), for the analysis of the correspondence between rare diseases and structural variants (SV) occurrence. The data being sequenced are to be originated from 1000 genomes families (parents and children). DNA had been isolated from peripheral blood (according to the protocols used in the 1000 Genomes project). With the methodology used in 1000 Genomes consortium and basing upon our own algorithms the main types of structural variants will be identified.

Co-financing of the internship at the 4D Nucleome Center at the Jackson Laboratory for Genomic Medicine

Michał Łaźniewski

Genome-wide chromatin interactions in the mouse brain in vivo – establishment and validation of Hi-C protocol

Agnieszka Kraft

Modeling and analysis of the spatial structure and dynamics of chromatin in the cell nucleus

Przemysław Szałaj

Methods of integrating multi-scale biological information in artificial learning systems

Julian Zubek

Performing cohesin HiChIP experiments for mother–father–child trio from 1000 Genome Project

Karolina Jodkowska