Our Projects
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.
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.
CytoMeth
CytoMeth tool compiles a set of open source software named in the Roche pipeline guidelines to perform SeqCap Epi data analysis. The pipe includes read quality assessment, read filtering, mapping to a reference genome, removal of PCR duplicates, assessment of coverage statistics, analyse methylation and variant calling and filtering as well as some additional functionalities added to improve the process and facilitate obtaining the processed results. Here, to obtain methylomes for brain tumor samples we used SeqCap Epi CpGiant Methylation panel and performed bisulphite conversion followed by Illumina NGS sequencing and CytoMeth tool analysis.
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.
Unveiling a group of epigenetic regulatory elements associated with breast cancer development
The aim of this study is to identify mechanisms that regulate the expression of breast cancer specific genes that could be mediated by transcription factors (TFs), DNA methylations within transcription factor binding sites and miRNAs.