Dariusz Stępkowski, Marcin Studnicki, Grażyna Woźniak, Konrad J. Dębski

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy. 


Thinking before coding...

We are solving problems with science and programming...

R / Python

Scientific Software Development


Data analysis and bioinformatics software design

Data Analysis

Bioinformatics and Statistics

PCR primers


Our Team

Konrad J. Dębski

Biologist and Senior Bioinformatics Software Developer, TTMS bioinformatical software expert by order of Roche Polska, developing and maintaining R systems for scientific data management and visualization and Python systems for data harmonization.


My scientific achievements was possible only due to my wife Karoline and great scientists with whom I was able to work with especially:

  • Katarzyna Łukasiuk
  • Michał Dąbrowski
  • Krzysztof Pawłowski

Aleksandra Cabaj

Biotechnologist by education and bioinformatitian by choice, involved mostly in chromosome conformation research and primer design for diagnostics. Enjoys torturing herself with huge NGS datasets. ;)

Scientific Papers:

The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental temporal lobe epilepsy

K. J. Debski*, N. Ceglia*, A. Ghestem*, A. I. Ivanov*, G. E. Brancati, S. Bröer, A. M. Bot, J. A. Müller, S. Schoch, A. Becker, W. Löscher, M. Guye, P. Sassone-Corsi, K. Lukasiuk, P. Baldi and C. Bernard (* These authors contributed equally to this work.
Science Advances  09 Oct 2020: Vol. 6, no. 41, eaat5979 (2020)

Dieta jako czynnik ryzyka choroby Alzheimera (Diet as a risk factor for Alzheimer’s disease)

Postępy Biochemii (Advances in Biochemistry)  Tom 66 Nr 1 (2020) (2020)

Proportions of macronutrients, including specific dietary fats, in prospective anti-Alzheimer’s diet

Marcin Studnicki, Konrad J. Dębski, Dariusz Stępkowski

Scientific Reports volume 9, Article number: 20143 (2019)

Open chromatin landscape of rat microglia upon proinvasive or inflammatory polarization

Piotr Przanowski, Shamba S. Mondal, Aleksandra Cabaj, Konrad J. Dębski, Bartosz Wojtas, Bartłomiej Gielniewski, Beata Kaza, Bozena Kaminska, Michal Dabrowski

GLIA doi: 10.1002/glia.23686 (2019)

Global pentapeptide statistics are far away from expected distributions

Jarosław Poznański, Jan Topiński, Anna Muszewska, Konrad J. Dębski, Marta Hoffman-Sommer, Krzysztof Pawłowski & Marcin Grynberg

Scientific Reports volume 8, Article number: 15178 (2018)

The circadian hippocampus and its reprogramming in epilepsy: impact for chronotherapeutics.

Konrad Debski, Nicholas Ceglia, Antoine Ghestem, Anton Ivanov, Giulio Emilio Brancati, Sonja Broer, Anna Bot, Alexander Muller, Susanne Schoch, Albert Becker, Wolfgang Loscher, Paolo Sassone-Corsi, Katarzyna Lukasiuk, Pierre Baldi, Christophe Bernard 

bioRvix (2017)

Transcriptional regulation of CacyBP/SIP gene and the influence of increased CacyBP/SIP level on gene expression pattern in colorectal cancer HCT116 cells.

Beata Kądziołka, Konrad J. Dębski, Paweł Bieganowski, Wiesława Leśniak, Anna Filipek

IUBMB Life doi:10.1002/iub.1698 (2017)

CI Thermometer: Visualizing Confidence Intervals in Correlation Analysis.

Agnieszka Wnuk, Konrad J. Debski, Marcin Kozak

IEEE Computer Graphics and Applications doi:10.1109/MCG.2017.4031058 (2017)

Chronically dysregulated NOTCH1 interactome in the dentate gyrus after traumatic brain injury.

Noora Puhakka, Anna Maria Bot, Niina Vuokila, Konrad Jozef Debski, Katarzyna Lukasiuk, Asla Pitkänen

PLoS ONE (2017)

Profile of 6 microRNA in blood plasma distinguish early stage Alzheimer’s disease patients from non-demented subjects.

Siranjeevi Nagaraj, Katarzyna Laskowska-Kaszub, Konrad J. Dębski, Joanna Wojsiat, Michał Dąbrowski, Tomasz Gabryelewicz, Jacek Kuźnicki and Urszula Wojda

Oncotarget (2017)

MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy.

Joanna Bednarczyk, Konrad J. Dębski, Anna M. Bot & Katarzyna Lukasiuk

Scientific Reports (2016)

Gene Set Enrichment Analysis and Ingenuity Pathway Analysis of Metastatic Clear Cell Renal Cell Carcinoma Cell Line.

Mohammed Imran Khan MSc., Konrad J. Dębski, Michał Dabrowski, Anna M. Czarnecka, Cezary Szczylik 

American Journal of Physiology – Renal Physiology (2016)

Should we trust graphs’ default settings in the R packages?

Wnuk A., Dębski K.J. 

Communications in Biometry and Crop Science 11, 114–126. (2016)

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.

Konrad J. Dębski, Asla Pitkanen, Noora Puhakka, Anna M. Bot, Ishant Khurana, KN Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El-Osta, Katarzyna Lukasiuk, Katja Kobow.

Scientific Reports (2016)

Traumatic Brain Injury Increases the Expression of Nos1, Aβ Clearance, and Epileptogenesis in APP/PS1 Mouse Model of Alzheimer’s Disease.

Diana Miszczuk, Konrad J. Dębski, Heikki Tanila, Katarzyna Lukasiuk, Asla Pitkänen.

Molecular Neurobiology (2015)

Alterations in miRNA Levels in the Dentate Gyrus in Epileptic Rats.

Anna Maria Bot, Konrad Józef Dębski, Katarzyna Lukasiuk.

PLoS ONE (2013)

Nencki Genomics Database – Ensembl funcgen enhanced with intersections, user data, and genome-wide TFBS motifs.

Krystkowiak I., Lenart J., Debski K., Kuterba P., Petas M., Kaminska B., Dabrowski M.

Database (2013)

Diversity of Phytophthora infestans from Poland.

M. Chmielarz, S. Sobkowiak, K. Dębski, D. E. L. Cooke, M. B. Brurberg, J. Śliwka

Plant Pathology (2013)

Development of somatic hybrids Solanum × michoacanum Bitter. (Rydb.) (+) S. tuberosum L. and autofused 4x S. × michoacanum plants as potential sources of late blight resistance for potato breeding.

P. Smyda, H. Jakuczun, K. Dębski, J. Śliwka, R. Thieme, M. Nachtigall, I. Wasilewicz-Flis, E. Zimnoch-Guzowska

Plant Cell Reports (2013)

Diploidalne klony z kolekcji źródłem odporności na wirusy ziemniaka.

Wasilewicz-Flis I., Strzelczyk-Żyta D., Dębski K., Hara A., Jakuczun H.

Zeszyty Problemowe Postępów Nauk Rolniczych (2010 z. 555: 657-666)


Set of tools used to analyse DNASeq data:

Open chromatin landscape of rat microglia upon proinvasive or inflammatory polarization

Piotr Przanowski, Shamba S. Mondal, Aleksandra Cabaj, Konrad J. Dębski, Bartosz Wojtas, Bartłomiej Gielniewski, Beata Kaza, Bozena Kaminska, Michal Dabrowski

GLIA doi: 10.1002/glia.23686 (2019)

ccChooser can be used to developing and evaluation of core collections for germplasm collections (entire collection). This package used to develop a core collection for biological resources like genbanks. A core collection is defined as a sample of accessions that represent, with the lowest possible level of redundancy, the genetic diversity (the richness of gene or genotype categories) of the entire collection. The establishing a core collection that represents genetic diversity of the entire collection with minimum loss of its original diversity and minimum redundancies is an important problem for gene-banks curators and crop breeders. ccChooser establish core collection base on phenotypic data (agronomic, morphological, phenological).


Nr: 2014/13/N/NZ2/00587*
Funding agency: National Science Centre
Grant type: PRELUDIUM
Panel: NZ2
Title: Searching for common features in DNA methylation and its influence on gene expression in three different animal models of temporal lobe epilepsy.
Principal Investigator: Konrad J. Dębski
Supervisor: Katarzyna Łukasiuk
Amount: 100 000 PLN
Duration: 2015-01-27 / 2017-01-26

Publication: Konrad J. Dębski et al., (2016) Scientific Reports

* The grant was obtained and accomplished at the Nencki Institute PAS.


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Bioinformatic Software Design is our passion. Data analysis is our hobby.








Theme: Illdy.

Data Analysis
Software Development