Konrad Dębski

Konrad Dębski
Fork Systems

M

About

31
Publications
7,651
Reads
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474
Citations
Additional affiliations
May 2016 - present
FORK SYSTEMS
Position
  • Developer
November 2014 - July 2016
Nencki Institute of Experimental Biology
Position
  • Bioinformatician
April 2012 - October 2014
Nencki Institute of Experimental Biology
Position
  • Bioinformatician
Education

Publications

Publications (31)
Article
Full-text available
Gene and protein expressions display circadian oscillations, which can be disrupted in diseases in most body organs. Whether these oscillations occur in the healthy hippocampus and whether they are altered in epilepsy are not known. We identified more than 1200 daily oscillating transcripts in the hippocampus of control mice and 1600 in experimenta...
Article
Full-text available
Chroniczne spożywanie niezdrowej diety jest jedną z przyczyn chorób cywilizacyjnych i wpływa znacząco na średnią długość życia społeczeństw. Wpływ diety na zdrowie jest niezwykle skomplikowany ze względu na chemiczną różnorodność jej składu. Dieta dostarcza ponad 26 tysięcy składników i jeszcze większej liczby ich metabolitów. Wśród tej różnorodnoś...
Article
Full-text available
Here we present a novel life-long whole-population study, which enabled us to predict a diet that, in terms of macronutrient proportions, may be prophylactic against Alzheimer’s Disease (AD). The method is based on the existence of oscillations in the correlation between historical per capita personal income (PCPI) and age-adjusted death rates (AAD...
Article
Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. Herein, we report a comprehensive, replicated, false discovery rate-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for rat microglia. We compared the open chromatin landscapes in untreated primary microglial cultures and c...
Article
Full-text available
The relationships between polypeptide composition, sequence, structure and function have been puzzling biologists ever since first protein sequences were determined. Here, we study the statistics of occurrence of all possible pentapeptide sequences in known proteins. To compensate for the non-uniform distribution of individual amino acid residues i...
Article
Full-text available
The CacyBP/SIP protein is expressed at a particularly high level in brain, spleen, and various tumors. In this work, we have studied transcriptional regulation of the CacyBP/SIP gene and the influence of increased CacyBP/SIP level on gene expression in colorectal cancer HCT116 cells. We have shown that E2F1, EGR1, and CREB transcription factors bin...
Article
Correlation analysis is one of the most popular statistical methods. Despite that, the way research reports correlation is often misleading. The difficulty increases with the amount of information that must be read and interpreted. The proposed CI thermometer makes correlation matrices much easier to read and provides information that would be diff...
Working Paper
Full-text available
Gene and protein expression displays circadian oscillations in numerous body organs. These oscillations can be disrupted in diseases, thus contributing to the disease pathology. Whether the molecular architecture of cortical brain regions oscillates daily and whether these oscillations are modified in brain disorders is less understood. We identifi...
Article
Full-text available
Traumatic brain injury (TBI) can result in several dentate gyrus-regulated disabilities. Almost nothing is known about the chronic molecular changes after TBI, and their potential as treatment targets. We hypothesized that chronic transcriptional alterations after TBI are under microRNA (miRNA) control. Expression of miRNAs and their targets in the...
Data
Cellular function categories among the regulated mRNAs. Spreadsheet of results exported from IPA. (XLS)
Data
Diseases or functions annotation for NOTCH1 targets. Spreadsheet of results exported from IPA. (XLS)
Data
miRNA expression changes after TBI. Spreadsheet containing results after statistical analysis. (XLS)
Data
Gene expression changes after TBI. Spreadsheet containing results after statistical analysis. (XLS)
Article
Full-text available
Alzheimers disease (AD) is the most common age-related dementia. Among its major challenges is identifying molecular signatures characteristic for the early AD stage in patients with Mild Cognitive Impairment (MCI-AD), which could serve for deciphering the AD pathomechanism and also as non-invasive, easy-to-access biomarkers. Using qRT-PCR we compa...
Article
Full-text available
The aim of the present study was to examine involvement of MBD3 (methyl-CpG-binding domain protein 3), a protein involved in reading DNA methylation patterns, in epileptogenesis and epilepsy. We used a well-characterized rat model of temporal lobe epilepsy that is triggered by status epilepticus, evoked by electrical stimulation of the amygdala. St...
Article
Full-text available
In recent years, genome-wide RNA expression analysis has become a routine tool that offers a great opportunity to study and understand the key role of genes that contribute to carcinogenesis. Various microarray platforms and statistical approaches can be used to identify genes that might serve as prognostic biomarkers and be developed as antitumor...
Article
Full-text available
Nowadays, we cannot imagine conducting analysis and creating any graph without support of various computer programs. They make researchers' work easier. No matter how good their computer skills are, it is always nice to have some help, and that is what default settings usually are for. It is believed that using default settings of graphical softwar...
Article
Full-text available
This study tested the hypothesis that acquired epileptogenesis is accompanied by DNA methylation changes independent of etiology. We investigated DNA methylation and gene expression in the hippocampal CA3/dentate gyrus fields at 3 months following epileptogenic injury in three experimental models of epilepsy: focal amygdala stimulation, systemic pi...
Article
Full-text available
To test the hypothesis that an amyloidogenic genetic background predisposes to worsening of post-TBI outcome, we investigated whether traumatic brain injury (TBI) in amyloid precursor protein (APP)/PS1 mice aggravates epileptogenesis and/or enhances somatomotor and cognitive impairment. To elaborate the mechanisms of worsening outcomes, we studied...
Article
Full-text available
A collection of 96 Polish isolates of Phytophthora infestans sampled in the years 2006, 2008 and 2009 were analysed using phenotypic and genotypic markers. Mating type, virulence, resistance to metalaxyl, mitochondrial haplotype and polymorphism at 12 simple sequence repeat (SSR) loci were determined. The majority of isolates were of the A1 mating...
Article
Full-text available
The aim of this study was to characterize changes in miRNA expression in the epileptic dentate gyrus. Status epilepticus evoked by amygdala stimulation was used to induce epilepsy in rats. The dentate gyri were isolated at 7 d, 14 d, 30 d and 90 d after stimulation (n=5). Sham-operated time-matched controls were prepared for each time point (n=5)....
Article
Full-text available
Key message Phytophthora infestans resistant somatic hybrids of S. × michoacanum (+) S. tuberosum and autofused 4 x S. × michoacanum were obtained. Our material is promising to introgress resistance from S. × michoacanum into cultivated potato background. Abstract Solanum × michoacanum (Bitter.) Rydb. (mch) is a wild diploid (2n = 2x = 24) potato s...
Article
Full-text available
We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we pr...

Questions

Question (1)
Question
I have microarrays normalized with RMA algorithm (Affy GeneChip Rat 2.0 ST) and older microarrays RG U34A which were normalized with MAS5 algorithm (I have no raw data so I cannot reanalyze them just with RMA). Now I want to compare results (gene lists) and I think that a good idea is to normalize RG U34A with RMA algorithm.
Do you have any experience ?