Dmitry Shtokalo

Dmitry Shtokalo
AcademGene Ltd. · Research & Development

PhD

About

67
Publications
3,523
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506
Citations
Citations since 2017
47 Research Items
314 Citations
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20172018201920202021202220230102030405060
20172018201920202021202220230102030405060

Publications

Publications (67)
Article
Full-text available
Background Despite proven therapeutic effects in inflammatory conditions, the specific mechanisms of phytochemical therapies are not well understood. The transcriptome effects of Traumeel (Tr14), a multicomponent natural product, and diclofenac, a non-selective cyclooxygenase (COX) inhibitor, were compared in a mouse cutaneous wound healing model t...
Preprint
Full-text available
Background: Despite proven therapeutic effects in inflammatory conditions, the specific mechanisms of phytochemical therapies are not well understood. The transcriptome effects of Tr14 (Traumeel), a multicomponent natural product, and diclofenac, a non-selective cyclooxygenase (COX) inhibitor, were compared in a mouse cutaneous wound healing model...
Article
Full-text available
Background A variety of DNA-based methods have been applied to identify genetic markers of attention deficit hyperactivity disorder (ADHD), but the connection to RNA-based gene expression has not been fully exploited. Methods Using well defined cohorts of discordant, monozygotic twins from the Michigan State University Twin Registry, and case-cont...
Article
Full-text available
Motivation: The transcriptomic data are being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are the data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details abou...
Article
Full-text available
In vitro cellular models are promising tools for studying normal and pathological conditions. One of their important applications is the development of genetically engineered biosensor systems to investigate, in real time, the processes occurring in living cells. At present, there are fluorescence, protein-based, sensory systems for detecting vario...
Preprint
Full-text available
Background: A variety of DNA-based methods have been applied to identify genetic markers of attention deficit hyperactivity disorder (ADHD), but the connection to RNA-based gene expression has not been fully exploited. Using well defined cohorts of discordant, monozygotic twins from the Michigan State University Twin Registry, and case-controlled A...
Preprint
Full-text available
Background: A variety of DNA-based methods have been applied to identify genetic markers of attention deficit hyperactivity disorder (ADHD), but the connection to RNA-based gene expression has not been fully exploited. Using well defined cohorts of discordant, monozygotic twins from the Michigan State University Twin Registry, and case-controlled A...
Preprint
Full-text available
Background: A variety of DNA-based methods have been applied to identify genetic markers of attention deficit hyperactivity disorder (ADHD), but the connection to RNA-based gene expression has not been fully exploited. Methods: Using well defined cohorts of discordant, monozygotic twins from the Michigan State University Twin Registry, and case-co...
Preprint
Full-text available
The in vitro cellular models are promising tools for studying normal and pathological conditions. One of their important applications is the development of genetically engineered biosensor systems to investigate the processes occurring in living cells in real time. Today, there are fluorescence protein based sensory systems for detecting various su...
Preprint
Full-text available
Motivation The transcriptomic data is being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details about the s...
Preprint
The hydrocephalus can be either an independent disease or a concomitant symptom of a number of pathologies, therefore representing an urgent issue in the present-day clinical practice. Deep Learning is an evolving technology and the part of a broader field of Machine Learning. Deep learning is currently actively researched in the field of radiology...
Article
Full-text available
Reprogramming of somatic cells to a pluripotent state is a complex, multistage process that is regulated by many factors. Among these factors, non-coding RNAs and microRNAs (miRNAs) have been intensively studied in recent years. MiRNAs play an important role in many processes, particularly in cell reprogramming. In this study, we investigated the r...
Article
Generation of patient-specific induced pluripotent stem cells (iPSCs) and their subsequent differentiation into cardiomyocytes opened new opportunities for studying pathogenesis of inherited cardiovascular diseases. One of these diseases is hypertrophic cardiomyopathy (HCM) for which no efficient therapy methods have been developed so far. In this...
Article
Full-text available
Aim of the study. Aim of the study was to estimate the occurrence of pathogenic mutations in the BRCA1 gene in Russian breast cancer patients. Material and methods . Complete coding sequence of the BRCA1 gene of 445 early onset breast cancer patients (under 40 years) from Novosibirsk region (Russia) were analyzed by targeted Next Generation Sequenc...
Conference Paper
Full-text available
Background Anti-inflammatory agents are used widely in treating numerous pain and inflammatory conditions. With a focus on the COX/LOX pathways in cutaneous wound repair in mice, the therapeutic activities of Tr14 (Traumeel), a multicomponent/multitarget natural product, and diclofenac (NSAID), a non-selective cyclooxygenase (COX) inhibitor were co...
Conference Paper
Background Anti-inflammatory agents are used widely in treating numerous pain and inflammatory conditions. With a focus on the specialised pro-resolving mediators (SPM) pathways in cutaneous wound repair in mice, the therapeutic activities of Tr14 (Traumeel), a multicomponent/multitarget natural product, and diclofenac (NSAID), a non-selective cycl...
Article
Full-text available
Self-renewal of cultured pluripotent stem cells is a complex process, which includes multiple functional and regulatory levels. Transcription factors, their target genes, chromatin modifiers, signaling pathways, and regulatory noncoding RNAs are involved in the maintaining of self-renewal. Studies of molecular and genetic bases of maintaining self-...
Data
The effect of partial-thickness abrasion and Tr14 treatment on IL6, IL8, and IL10 mRNA levels. The levels of 3 well-characterized interleukins is shown over time after injury of the mouse skin. Control wounds treated with saline (S), are compared to wounds treated with Tr14 as a combination of injections and topical treatment as specified (IO, labe...
Data
The top 100 differentially expressed in control wounds compared to the unwounded, 0 h time point. RNA-seq data was analyzed to identify transcripts affected by abrasive wounding of the mouse skin at the specified time points. Differentially expressed transcripts were identified by statistical comparison using Welch's test (P-value). The fold change...
Data
The effect of Tr14 treatment on transcripts in the Epithelial Cell Differentiation GO. Details are similar to Supplementary Figure 4 except that both up and down-regulated transcripts in the Epithelial Cell Differentiation GO were analyzed.
Data
(A–G) Tagwise dispersion plots of wound-related transcripts in untreated control mice at specified times after injury. RNA-seq data, expressed as RPKM, was analyzed for differential expression between the 0 h, unwounded, and specific time points afterward. The log2 RPKM gene expression for each transcript (red or blue circle) is ratioed between sam...
Data
The schematic workflow of RNA sequencing using the SeqLL true Single Molecule Sequencing (tSMS) method. Total RNA from RNAlater-preserved skin samples at the wound site was isolated by Trizol, and then depleted of ribosomal RNA (riboRNA) prior to fragmentation for RNA-seq. The fragments are tailed with polyA to allow capture by polyT strands on the...
Data
Graphic Representation of the intensity of the Response to Wounding GO category at specific time points of the wound healing response. Details of total transcripts affected (hits), total transcripts in pathway, hits expected by chance, and p-value, for the Response to wounding/Wound Healing GO category, at each time point.
Data
The effect of Tr14 treatment on transcripts in the Response to Wounding GO. Upregulated transcripts were calculated between Tr14 vs. saline-treated controls at each of the time points specified as described in Materials and Methods except a p-value threshold of 0.01 was applied. The upregulated transcripts were analyzed for preferential enrichment...
Data
Overall study design, describing the time points, treatment groups, and individual samples sequenced in the study.
Data
Differentially expressed transcripts in Tr14-treated wounds compared to control. RNA-seq data was analyzed to identify transcripts modulated by Tr14 during wound repair. The transcripts with the p < 0.0005 and a fold-change > 1.41 are shown for each of the time points from 12 to 192 h. For each time point, the RPKM values are shown for each sample...
Data
Gene ontology (GO) categories for differentially expressed genes affected by Tr14 treatment of wounds over time. RNA-seq data was analyzed to identify transcripts modulated by Tr14-IO during wound repair, as shown in Supplementary Table 3. The transcripts were then organized using DAVID (Huang da et al., 2009) into Gene Ontologies that covered thos...
Data
Raw data for RNA sequencing analysis of mouse wound repair. The raw RPKM data for gene expression for all groups, animals, and time points is reported in the following tables. (A) Reports the (U) group of placebo treated animals, (B) reports the (S) saline injected control group, (C) reports the (I) Traumeel injection group, and (D) reports the (IO...
Article
Full-text available
Wound healing involves an orchestrated response that engages multiple processes such as hemostasis, cellular migration, extracellular matrix synthesis, and in particular, inflammation. Using a murine model of cutaneous wound repair, the transcriptome was mapped from 12 hours to 8 days post-injury, and in response to a multicomponent, multi-target n...
Article
Full-text available
MicroRNAs (miRNAs) constitute a class of small noncoding RNAs that plays an important role in the post-transcriptional regulation of gene expression. Much evidence has demonstrated that miRNAs are involved in regulating the human and mouse pluripotency. Nevertheless, to our knowledge, miRNAs in the pluripotent stem cells of one of the most commonly...
Conference Paper
Background Anti-inflammatory agents are used widely in treating numerous inflammatory conditions. The effect of Tr14, a multitargeted natural product, was compared to diclofenac, a non-selective cyclooxygenase inhibitor, on cutaneous wound repair in mice. Objectives To compare the effect of diclofenac with Tr14 on the transcriptome after cutaneous...
Article
Full-text available
Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we...
Article
Full-text available
The accurate and thorough genome-wide detection of adenosine-to-inosine editing, a biologically indispensable process, has proven challenging. Here, we present a discovery pipeline in adult Drosophila, with 3,581 high-confidence editing sites identified with an estimated accuracy of 87%. The target genes and specific sites highlight global biologic...
Article
Full-text available
The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs. Here we identify 2,147 vlincRNAs covering 10 percent of...
Article
The analysis of the differential expression of genes has been the key goal of many molecular biology methods for decades and will remain with us for decades to come. It constitutesa fundamental resource at our disposal for determining the relationship between products of transcription, biology and disease. The completed genome sequencing of many co...
Article
The HuR protein regulates the expression of thousands of cellular transcripts by modulating mRNA splicing, trafficking, translation, and stability. Although it serves as a model of RNA-protein interactions, many features of HuR's interactions with RNAs remain unknown. In this report, we deployed the cryogenic RNA immunoprecipitation technique to an...
Article
Full-text available
Background The function of RNA from the non-coding (the so called “dark matter”) regions of the genome has been a subject of considerable recent debate. Perhaps the most controversy is regarding the function of RNAs found in introns of annotated transcripts, where most of the reads that map outside of exons are usually found. However, it has been r...
Data
Full-text available
Figure S1. A scheme of the strategy to partition intronic coordinates in the cases of overlapping transcripts. Boxes –exons, lines – introns. Regions 1–4 were used to calculate the average read density of the corresponding introns.
Data
Figure S3. Examples of DE bins detecting regions around annotated miRNAs, found both in an intron (mir-135b, A) and an interegenic region (mir-146a, B).
Data
Table S3. Details of RT-PCR analysis in selected mouse introns.
Data
Figure S2. An example of DE bins specifically detecting a specific up-regulated isoform of Adora3 locus.
Data
Table S1. Correlation of specified introns of Prkca and Slc24a3 with their corresponding exons.
Data
Table S2. Properties of individual mouse introns.
Article
The results are presented of studying a mathematical model of linear biomolecular synthesis which accounts for the reversibility of attaching a monomer to a growing molecule and some spontaneous termination of the synthesis. A previous model of a synthesis ignored the influence of reversibility and sinks. It is shown that if the rate of the monomer...
Article
Full-text available
Composite Module Analyst (CMA) is a novel software tool aiming to identify promoter-enhancer models based on the composition of transcription factor (TF) binding sites and their pairs. CMA is closely interconnected with the TRANSFAC® database. In particular, CMA uses the positional weight matrix (PWM) library collected in TRANSFAC® and therefore pr...

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