Laboratory of Bioinformatics

Head: Michał Dąbrowski

 

Staff: Aleksandra Cabaj, Agata Charzyńska, Konrad Dębski, Shamba Sankar Mondal*

*PhD student delegated from the Laboratory of Molecular Neurobiology

 

Research profile:

 

The mission of our laboratory is to provide world-class bioinformatics support to experimental groups at the Nencki Institute. Our strategy is to focus on areas of Bioinformatics related to Systems Biology and to foster collaboration.

 

Our main area of interest is Regulatory Genomics: i.e. transcription and its genome-wide regulation, at cis-regulatory, epigenetic, and chromatin structure level. As a core laboratory, we also provide support for high-throughput methods in a wider context of Systems Biology, such as: microarrays, next-generation sequencing (NGS) and mass spectrometry. Our core expertise is manipulation of large genomic and expression data and application of database and machine learning methods, in scripting languages environment (R, Python, Mathematica, SQL), to address biologically motivated questions, especially in the context of mammalian cell biology and neurobiology. We maintain the Nencki Genomics Database – resource of regulatory regions and motifs in human, mouse and rat.

 

More information can be found under this link: http://bioinfo.nencki.gov.pl/

 

Recent publications:

 

Miszczuk D, Dębski KJ, Tanila H, Lukasiuk K, Pitkänen A. Traumatic brain injury increases the expression of Nos1, Abeta clearance, and epileptogenesis in APP/PS1 mouse model of Alzheimer's disease. Mol Neurobiol. 2015 Dec 15. PubMed PMID: 26671618.

 

Kuzniewska B, Nader K, Dabrowski M, Kaczmarek L, Kalita K. Adult Deletion of SRF Increases Epileptogenesis and Decreases Activity-Induced Gene Expression. Mol Neurobiol. 2015 Jan 31. [Epub ahead of print] PubMed PMID: 25636686.

 

Nagalski A, Puelles L, Dabrowski M, Wegierski T, Kuznicki J, Wisniewska MB. Molecular anatomy of the thalamic complex and the underlying transcription factors. Brain Struct Funct. 2015 May 12. [Epub ahead of print] PubMed PMID: 25963709.

 

Dabrowski M, Dojer N, Krystkowiak I, Kaminska B, Wilczynski B. Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. BMC Bioinformatics. 2015 May 1;16:140. doi: 10.1186/s12859-015-0573-5. PubMed PMID: 25927199; PubMed Central PMCID: PMC4436866.

 

Wei Y, Mondal SS, Mouawad R, Wilczyński B, Henry RW, Arnosti DN. Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis. G3 (Bethesda). 2015 May 20;5(7):1503-15. doi: 10.1534/g3.115.019166. PubMed PMID: 25999584; PubMed Central PMCID: PMC4502384.

 

Dabrowski M, Dojer N, Zawadzka M, Mieczkowski J, Kaminska B. Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems. BMC Syst Biol. 2010 Jun 17;4:86. doi: 10.1186/1752-0509-4-86. PubMed PMID: 20565733; PubMed Central PMCID: PMC2902439.