Our Projects

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Atlas of brain regulatory regions and regulatory networks - a novel system biology approach to pathogenesis of selected neurological disorders
This is a five year interdisciplinary project founded by National Science Centre (NCN) and developed in consortium with Nencki Institute of Experimental Biology and University of Warsaw, Faculty of Mathematics, Informatics and Mechanics. Our group focus on regulatory regions detection that significantly affects overall survival of glioma patients. Using feature selection and machine learning methods on molecular data we seek to discover the functions disorders of the assigned regulatory regions.

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Monte Carlo Feature Selection and Interdependency Discovery (MCFS-ID)
MCFS-ID is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. The R package called 'rmcfs' is publicly available on CRAN repository.

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Methylation patterns affecting the overall survival of glioma patients
In this project we are focused on detection of putative interactions between gene expression values and DNA methylations beta-values as well as to obtaining a ranking of significant features that accurately discern short (up to 400 days) and long (over 400 days) overall survival of glioma patients. In the further steps of the project we will try to unveil the function of the detected significant features and informative interactions.

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A coarse-grained model of protein - nanoparticles interactions for simulating the transport of drug molecules to their targets.
The main goal of this project is to extend the coarse-grained UNRES (United RESidue) model for protein simulations to treat protein- and peptide-nanotube systems. Two nanotube models will be designed (i) the continuous-tube, (ii) the granular model where each benzene ring will be represented a spheroidal interaction site located in its center. The second goal of this project is to simulate the adsorption of histidine- and tryptophan-rich peptides on nanotubes known as the corona effect and to simulate the interactions of nanotubes with the toll-like receptors.