A5063808562- Gene expression and cancer classification
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- Cardiac electrophysiology and arrhythmias
- Bacteriophages and microbial interactions
- Esophageal Cancer Research and Treatment
- Molecular Biology Techniques and Applications
- Cardiomyopathy and Myosin Studies
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Diagnosis and treatment of tuberculosis
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Cardiovascular Effects of Exercise
- Epilepsy research and treatment
- Advanced biosensing and bioanalysis techniques
- Vitamin D Research Studies
- vaccines and immunoinformatics approaches
- Genetics and Neurodevelopmental Disorders
- RNA Research and Splicing
- Probiotics and Fermented Foods
- Health and Well-being Studies
Nazarbayev University
2016-2025
Center for Life Sciences
2014
National Center for Biotechnology
2012-2013
Al-Farabi Kazakh National University
2012
EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive heterogeneity transcriptional programs. Here, we combine independent component analysis single-cell RNA sequencing data from diverse types and model systems with time-resolved mapping EWSR1-FLI1 binding sites open chromatin regions characterize dynamic cellular processes associated...
Independent Component Analysis (ICA) is a method that models gene expression data as an action of set statistically independent hidden factors. The output ICA depends on fundamental parameter: the number components (factors) to compute. optimal choice this parameter, related determining effective dimension, remains open question in application blind source separation techniques transcriptomic data.
The success of DNA analytical methods, including long-read sequencing, depends on the availability high-quality, purified DNA. Previously, we developed a method and device for isolating high-molecular-weight (HMW) sequencing using high-salt gel electroelution trap. Here, present an improved version this purifying nucleic acids with high yield purity from even most challenging biological samples. proposed is significant improvement over previously published procedure, offering simple, fast,...
Long-read sequencing technologies require high-molecular-weight (HMW) DNA of sufficient purity and integrity, which can be difficult to obtain from complex biological samples. We propose a method for purifying HMW that takes advantage the fact DNA's electrophoretic mobility decreases in high-ionic-strength environment. The begins with separation various impurities by electrophoresis an agarose gel-filled channel. After separation, high-salt gel block is placed ahead band interest, leaving...
Background: Tuberculosis (TB) and vitamin D deficiency remain major public health problems in Kazakhstan. Due to the high incidence of pulmonary tuberculosis country based on importance modulation immune response association its with many conditions, aim our research was study status, VDR TLR gene polymorphisms, epidemiology Methods: A case-control included 411 individuals diagnosed TB 686 controls no family history tuberculosis. Concentrations serum (25-(OH)D) levels were measured by...
Low vitamin D status is linked to disturbance in cognitive performance. This study explored possible ways how composition and functional capacity of the gut microbiome affects metabolism, directing serum (VitD) levels memory impairmets. It was found that composition, characterized by an increase relative abundance Enterococcus correlated with deficiency and, as consequence, impairments. A key mechanism identified differential utilization short-chain fatty acids (SCFAs) produced bacteria...
Abstract Objectives The data presented in this study were collected with the aim of obtaining complete genomes specific strains Bacillus bacteria, namely, licheniformis T5. This strain was chosen based on its enzymatic activities, particularly amylolytic activity. In study, nanopore sequencing technology employed to obtain genome sequences strain. It is important note that these represent a focused objective within larger research context, which involves exploring biochemical features...
Matrix factorization (MF) methods are widely used in order to reduce dimensionality of transcriptomic datasets the action few hidden factors (metagenes). MF algorithms have never been compared based on between-datasets reproducibility their outputs similar independent datasets. Lack this knowledge might a crucial impact when generalizing predictions made study others.We systematically test several collected from same cancer type (14 colorectal, 8 breast and 4 ovarian datasets). Inspired by...
Background Tuberculosis (TB) is a major public health emergency in many countries, including Kazakhstan. Despite the decline incidence rate and having one of highest treatment effectiveness world, TB remains high Social environmental factors along with host genetics contribute to pulmonary tuberculosis (PTB) incidence. Due Kazakhstan, our research aimed study epidemiology PTB Materials methods 1,555 participants were recruited case–control study. The data was taken during an interview....
Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization Mycobacterium strains obtained from Kazakhstani patients with pre-extensively drug-resistant diagnosed Kazakhstan.Whole-genome sequencing was performed on 10 M. different regions Kazakhstan. All had high-confidence resistance mutations according grading system previously established by World Health Organization. The genome analysis using...
We developed a comprehensive multiplexed set of primers adapted for the Oxford Nanopore Rapid Barcoding library kit that allows universal SARS-CoV-2 genome sequencing. This primer is designed to up any variants pool whole-genome sequencing using single- or double-tiled amplicons from 1.2 4.8 kb with Nanopore. also applicable tasks like targeted proposed here an optimized protocol synthesize cDNA Maxima H Minus Reverse Transcriptase specific primers, which has high yields template RNA and...
Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer in Central Asia, often diagnosed at advanced stages. Understanding population-specific patterns ESCC crucial for tailored treatments. This study aimed to unravel ESCC’s genetic basis Kazakhstani patients and identify potential biomarkers early diagnosis targeted therapies. from Kazakhstan were studied. We analyzed histological subtypes conducted in-depth transcriptome sequencing. Differential gene...
Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these of different origins is essential for understanding the evolution and adaptation a given organism. These repeating patterns have manifold signatures structures with varying degrees homology, making their identification challenging. To address this challenge, we developed new algorithm software that can rapidly accurately detect any repeated sequences de novo homology genomic interspersed or...
Many genome-scale studies in molecular biology deliver results the form of a ranked list gene names, accordingly to some scoring method.There is always question how many top-ranked genes consider for further analysis, example, order creating diagnostic or predictive signature disease.This usually approached from statistical point view, without considering any biological properties they are related each other functionally.Here we suggest new method selecting number such that this set forms...
Abstract Muscular dystrophy is a condition potentially predisposing for cancer; however, currently, only Myotonic patients are known to have higher risk of cancer. Here, we searched link between facioscapulohumeral ( FSHD ) and cancer by comparing published transcriptome signatures various malignant tumours found significant enrichment cancer‐related genes among the differentially expressed in . The analysis has shown that gene expression profiles myoblasts myotubes resemble Ewing's sarcoma...
Severe acute respiratory syndrome (SARS-CoV-2) is responsible for the worldwide pandemic, COVID-19. The original viral whole-genome was sequenced by a high-throughput sequencing approach from samples obtained Wuhan, China. Real-time gene main parameter to manage outbreaks because it expands our understanding of virus proliferation, spread, and evolution. Whole-genome critical SARS-CoV-2 variant surveillance, development new vaccines boosters, representation epidemiological situations in...
Tuberculosis (TB) is an infectious disease that remains essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) TB increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known novel potential genetic variants are associated with drug resistance Mycobacterium tuberculosis (Mtb). There limited reports data...
Left ventricular assist device (LVAD) implantation is one of the mechanical circulatory support (MCS) treatments for advanced heart failure (HF) patients. MCS has emerged as a lifesaving therapy that improves patients' quality life. However, remains limited by paradoxical coagulopathy accompanied thrombosis and bleeding. The mechanisms are increasingly being defined, but MCS-related bleeding, which related to shear-mediated alteration platelet function, poorly understood. Complications might...