Prof. Dariusz Plewczynski, PhD has established two laboratories: (a) experimental Laboratory of Functional and Structural Genomics at the Centre of New Technologies, University of Warsaw, and (b) computational Laboratory of Bioinformatics and Computational Genomics at the Faculty of Mathematics and Information Sciences, Warsaw University of Technology. Our aim is to understand the sequence-structure-function molecular paradigm in the context of spatial and temporal behavior of nucleome. Therefore, we address both computationally (statistical and biophysical algorithms) and experimentally (Hi-C, ChIA-PET, HiChIP) the relation between sequence, epigenomics and the three-dimensional structure of Human genomes.

We focus on the statistically relevant relation of the chromatin spatial conformation with the DNA sequence diversity at the human population scale, both natural and pathological. In particular, I examine the relationship between structural variants observed in different worldwide populations and the cohorts of patients, changes in the number of copies of genes and regulatory regions; and their spatial localisation in the spatio-temporal (4D) dynamical structure of a cell nucleus. We have proposed recently novel 3D epigenome folding algorithm that predicts three-dimensional conformation and its changes by combination of machine learning trained on epigenomic information (ChIP-seq) from different cell types, and biophysical polymer modelling. Finally, We are interested in the dependence of the expression of selected genes on their location in three-dimensional space during activation process (in neurons, B-cells and T-cells), or application of drug therapy (eg. chemotherapy).

Selected publications

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummiesGenomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic WindowsFrom DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effectSuper-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopyMultiNet: A Diffusion-Based Approach to Assign Directionality in Protein Interactions Using a Consensus of Eight Protein Interaction DatasetsConsensus-Based Identification and Comparative Analysis of Structural Variants and Their Influence on 3D Genome Structure Using Long- and Short-Read Sequencing Technologies in Polish FamiliesMulti-scale phase separation by explosive percolation with single-chromatin loop resolutionConsensuSV—from the whole-genome sequencing data to the complete variant listPrediction of chromatin looping using deep hybrid learning (DHL)3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genomeEnhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactionsThe dynamic role of cohesin in maintaining human genome architecturecudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modellingThe Identification of Chromatin Contact Domains (CCD) in Human Genomes from ChIA-PET Data Using Graph MethodsccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.Chromatin topology reorganization and transcription repression by PML-RAR? in acute promyeloid leukemia.Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.