LABORATORY OF BIOINFORMATICS

Head: Michał Dąbrowski

 

Degrees:

2012 DSc, Nencki Institute of Experimental Biology

1998 PhD, Medical University of Warsaw

1994 MD, Medical University of Warsaw

 

Research trainings:

2014 Science Infrastructure Management Support (Poland, USA, Germany; IBM, Fraunhofer- Gesellschaft, TUDresden, MPI-CBG)

 

Professional employments:

2014-present Head of the Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, PAS

2003-2014 Associate professor, Nencki Institute of Experimental Biology, PAS

2000-2003 Postdoc, Katholieke Universiteit Leuven, Belgium

1998-2000 Specialist Hospital in Kościerzyna

 

Honors and fellowships:

2014 Award for outstanding scientific achievements of The Division II of the Polish Academy of Sciences for the year 2014 (awarded to the team headed by Bożena Kamińska)

2010 Jerzy Konorski Award (awarded for the paper by Marta B. Wiśniewska et al.)

2004 Marie-Curie European Reintegration Grant

2001 Marie-Curie European Fellowship

1998 Honours for the PhD dissertation

Staff: Agata Charzyńska, Aleksandra Cabaj (PhD student), Adam Jarmuła, Jan Ludwiczak (PhD student), Shamba Sankar Mondal (PhD student)

 

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 the areas of Bioinformatics related to Systems Biology and to foster collaboration.

Our main focus of interest is Regulatory Genomics: i.e. transcription and its genome-wide regulation at cis-regulatory, epigenetic and structural level.

As a core laboratory, we also provide support for high-throughput methods (microarrays, next-generation sequencing and mass spectrometry), in a wide context of Systems Biology. Our expertise includes integration of genomic, epigenomic and expression data using database, statistical and machine learning tools, as well as molecular modeling and molecular dynamics, to address biologically motivated questions, in particular in the context of mammalian cell biology and neurobiology. The main form of our activity are collaborative projects with experimental groups, in which we are responsible for the bioinformatics part.

 

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

 

Current research activities:

  • Application of DNase I-seq to identify transcription factors participating in alternative microglia activation in response to factors secreted by glioma
  • Mutations in regulatory regions of epigenetic genes in gliomas
  • Molecular mechanisms of HIF switch in human endothelium
  • Regulation of transcription of genes from the Grainyhead-like family in human cells, in the context of cancer
  • Crystal structures and molecular docking in the search for nematode-specific inhibitors of thymidylate synthase
  • Evaluating the influence of C-termini on the motion and interaction between two motor domains and stack in the Ncd protein, by molecular modeling
  • Evaluation of the human thymidylate synthase – dihydrofolate reductase complex as a novel target for anticancer drugs.

 

Recent publications:

 

Nagaraj S., Laskowska-Kaszub K., Dębski K.J., Wojsiat J., Dąbrowski M., Gabryelewicz T., Kuźnicki J., Wojda U. (2017) Profile of 6 microRNA in blood plasma distinguish early stage Alzheimer's disease patients from non-demented subjects. Oncotarget, doi:10.18632/oncotarget.15109.

 

Ellert-Miklaszewska A., Wiśniewski P., Kijewska M., Gajdanowicz P., Pszczółkowska D., Przanowski P., Dąbrowski M., Maleszewska M., Kamińska B. (2016) Tumour-processed osteopontin and lactadherin drive the protumorigenic reprogramming of microglia and glioma progression. Oncogene, 35(50): 6366-6377.

 

Bednarczyk J., Dębski K.J., Bot A.M., Łukasiuk K. (2016) MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy. Sci Rep, 6: 33736.

 

Antosiewicz A., Jarmuła A., Przybylska D., Mosieniak G., Szczepanowska J., Kowalkowska A., Rode W., Cieśla J. (2016) Human dihydrofolate reductase and thymidylate synthase form a complex in vitro and co-localize in normal and cancer cells. J Biomol Struct Dyn, 5: 1-17.

 

Dąbrowski M., Dojer N., Krystkowiak I., Kamińska B., Wilczyński B. (2015) Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. BMC Bioinformatics, 16: 140.