A5036803162- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Mitochondrial Function and Pathology
- Diet and metabolism studies
- Glycosylation and Glycoproteins Research
- Advanced Chemical Sensor Technologies
- RNA Research and Splicing
- Computational Drug Discovery Methods
- Cancer-related gene regulation
- Microbial Metabolic Engineering and Bioproduction
- Nutritional Studies and Diet
- Advanced Biosensing Techniques and Applications
- Vitamin C and Antioxidants Research
- Analytical Chemistry and Chromatography
- HER2/EGFR in Cancer Research
- Probiotics and Fermented Foods
Institute of Biomedical Chemistry
2015-2024
Bioinformatics Institute
2017-2021
Sechenov University
2021
Kursk State Medical University
2019
The continuous improvement of proteomic techniques, most notably mass spectrometry, has generated quantified proteomes many organisms with unprecedented depth and accuracy. However, there is still a significant discrepancy in the reported numbers total protein molecules per specific cell type. In this article, we explore results studies Escherichia coli, Saccharomyces cerevisiae, HeLa cells terms copy cell. We observe up to ten-fold difference between values. Investigating possible reasons...
Obesity is a socially significant disease that characterized by disproportionate accumulation of fat. It also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers pathological processes linked to obesity especially vital for young individuals, given their increased potential lifestyle modifications. By comparing the genetic, proteomic, metabolomic profiles individuals categorized as underweight, normal, overweight, obese, we aimed...
A gene-centric approach was applied for a large-scale study of expression products single chromosome. Transcriptome profiling liver tissue and HepG2 cell line independently performed using two RNA-Seq platforms (SOLiD Illumina) also by Droplet Digital PCR (ddPCR) quantitative RT-PCR. Proteome shotgun LC-MS/MS as well selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) cells. On the basis SRM/SIS measurements, protein copy numbers were estimated Chromosome 18 (Chr 18)...
Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, set of human genes a known function remains far from complete. This especially true for hundreds mitochondria-associated genes, which are under-characterized and lack clear functional annotation. However, advent multi-omics profiling methods coupled systems algorithms, cellular role many such can be elucidated. Here, we report pathways associated TOMM34, Translocase Outer Mitochondrial...
This work continues the series of quantitative measurements proteins encoded by different chromosomes in blood plasma a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and gene-centric approach, which is basis for implementation international Chromosome-centric Human Proteome Project (C-HPP), were applied measurement human plasma. Analyses carried out frame C-HPP each protein-coding gene four chromosomes: 18, 13, Y, mitochondrial....
Diarrhea is one of the manifestations novel coronavirus disease (COVID-19), but it also develops as a complication massive antibiotic therapy in this disease. This study aimed to compare these types diarrhea.We included patients with COVID-19 cohort and excluded chronic diarrhea, laxative use, those who died during first day hospitalization.There were 89 (9.3%), 161 (16.7%), 731 (75.7%) early viral, late antibiotic-associated, without respectively. Late diarrhea lasted longer (6 [4-10] vs 5...
Despite tremendous efforts in genomics, transcriptomics, and proteomics communities, there is still no comprehensive data about the exact number of protein-coding genes, translated proteoforms, their function. In addition, by now, we lack functional annotation for 1193 where expression was confirmed at proteomic level (uPE1 proteins). We re-analyzed results AP-MS experiments from BioPlex 2.0 database to predict functions uPE1 proteins splice forms. By building a protein-protein interaction...
Both biological and technical variations can discredit the reliability of obtained data in omics studies. In this note, we investigated effect prolonged cultivation HepG2 hepatoma cell line on its metabolomic profile. Using GC × GC-MS approach, determined degree metabolic variability across cells cultured uniform conditions for 0, 5, 10, 15, 20 days. Post-processing revealed substantial changes relative abundances 110 metabolites among samples under investigation. Our findings have...
Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. Isoform switching, the process where alter of various splice forms (isoforms) a gene, plays critical role cellular function adaptation. Our study provides comprehensive analysis prevailing across ten most studied human cell lines using public RNAseq data. We analyzed occurrence found substantial justification revising canonical sequences...
The development of commercially available panels for human blood plasma screening via selected reaction monitoring (SRM) offers reliable, cost-efficient and highly-standardized discovery validation protein biomarkers. However, detection by SRM can be hampered interfering peptide fragment ions. To estimate the influence interference on detection, we performed different types sample preparation implemented measurements well-characterized targets approved US Food Drug Administration.We used...
Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount MS data. Nowadays, routine manual search does not satisfy "speed" modern science any longer. In our work, necessity single-thread analysis bulky data emerged during interpretation HepG2 proteome profiling results for proteoforms searching. We compared contribution each eight engines (X!Tandem, MS-GF[Formula: see text], Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an...
This manuscript collects all the efforts of Russian Consortium, bottlenecks revealed in course C-HPP realization, and ways their overcoming. One main is insufficient sensitivity proteomic technologies, hampering detection low- ultralow-copy number proteins forming "dark part" human proteome. In frame MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination shotgun technology selected reaction monitoring with two-dimensional alkaline...
Obesity is a frightening chronic disease, which has tripled since 1975. It not expected to slow down staying one of the leading cases preventable death and resulting in an increased clinical economic burden. Poor lifestyle choices excessive intake “cheap calories” are major contributors obesity, triggering type 2 diabetes, cardiovascular diseases, other comorbidities. Understanding molecular mechanisms responsible for development obesity essential as it might result introducing anti-obesity...
Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number encoded by human Chr18 genes. Within half a year, since January 2020 version NextProt, entries in MP+uPE1 datasets changed, mainly due to achievements antibody-based proteomics. Assuming that proteome is closely related transcriptome scaffold, quantitative PCR, Illumina HiSeq, Oxford Nanopore Technology were applied characterize liver samples three male donors comparison with HepG2 cell...