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 funded by the National Science
Centre (NCN) and developed by a consortium
comprising the Nencki Institute of Experimental Biology and the Faculty of
Mathematics, Informatics and Mechanics at the University of Warsaw. Our group focuses
on detecting regulatory regions that significantly affect the overall survival of
glioma patients. Using feature-selection and machine-learning methods on molecular
data, we seek to discover functional disorders associated with the identified
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 pipeline includes read quality
assessment, read filtering, mapping to a reference genome, removal of PCR duplicates,
assessment of coverage statistics, methylation analysis, 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.