FORK SYSTEMS
2020
Dariusz Stępkowski, Marcin Studnicki, Grażyna Woźniak, Konrad J. Dębski
Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.
SERVICES
Thinking before coding...
We are solving problems with science and programming...
R / Python
Scientific Software Development
Consulting
Data analysis and bioinformatics software design
Data Analysis
Bioinformatics and Statistics
PCR primers
Design
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 doi.org/10.1126/sciadv.aat5979 (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) doi.org/10.18388/pb.2020_311 (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)
Software:
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).
Grants:
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.
Contact:
FORK SYSTEMS Konrad Dębski
Address:
ul. Broniewskiego 10
05-850 Duchnice
POLAND
NIP: 534 238 31 65
REGON: 364394936
PHONE: +48 502 725 679
MAIL: debski@fork.edu.pl
Bioinformatic Software Design is our passion. Data analysis is our hobby.
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Theme: Illdy.