A5043105503- Bioinformatics and Genomic Networks
- Immune cells in cancer
- Gene expression and cancer classification
- Cardiomyopathy and Myosin Studies
- Gene Regulatory Network Analysis
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Muscle Physiology and Disorders
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Genetic Associations and Epidemiology
- Metabolomics and Mass Spectrometry Studies
- Immune Cell Function and Interaction
- Genomics and Phylogenetic Studies
- Nuclear Structure and Function
- GDF15 and Related Biomarkers
- Congenital limb and hand anomalies
- Mitochondrial Function and Pathology
- Phagocytosis and Immune Regulation
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Congenital heart defects research
- Fault Detection and Control Systems
ITMO University
2015-2024
Washington University in St. Louis
2015-2024
St Petersburg University
2011
Abstract Gene set enrichment analysis (GSEA) is an ubiquitously used tool for evaluating pathway in transcriptional data. Typical experimental design consists comparing two conditions with several replicates using a differential gene expression test followed by preranked GSEA performed against collection of hundreds and thousands pathways. However, the reference implementation this method cannot accurately estimate small P-values, which significantly limits its sensitivity due to multiple...
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly such into high-quality, finished sequences remains challenging. Many tools are available, but they differ greatly in terms their performance (speed, scalability, hardware requirements, acceptance newer read technologies) final output (composition assembled sequence). More importantly, it largely unclear how best assess the quality sequences. Assemblathon competitions...
Transcriptomic profiling became a standard approach to quantify cell state, which led the accumulation of huge amount public gene expression datasets. However, both reuse these datasets or analysis newly generated ones requires significant technical expertise. Here, we present Phantasus: user-friendly web application for interactive provides streamlined access more than 96,000 datasets, as well allows user-uploaded Phantasus integrates an intuitive and highly JavaScript-based heatmap...
Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands metabolites. Such profiles, when analyzed together with transcriptional can reveal novel insights underlying biological processes. While a number conceptual approaches have been developed data integration, easily accessible tools integrated analysis mammalian and are lacking. Here we present GAM ('genes metabolites'): web-service network focused on identification the...
RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed global produce computational artifacts. To remedy this, created the End Sequence Analysis Toolkit (ESAT). As a test, first compared and bulk using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). predicted by telescripting model transcriptional bursts, ESAT detected an...
The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one the key physiological characteristics immune system. Here, we focus on understanding metabolic variability MNPs through network analysis applied to three large-scale transcriptional datasets: introduce (1) an ImmGen MNP open-source dataset 337 samples 26 tissues; (2) a myeloid subset Phase I (202 samples); and (3) mouse single-cell RNA sequencing (scRNA-seq) (51,364 cells) assembled based Tabula Muris Senis. To...
Abstract The population of Russia consists more than 150 local ethnicities. ethnic diversity and geographic origins, which extend from eastern Europe to Asia, make the uniquely positioned investigate shared properties inherited disease risks between European Asian ancestries. We present analysis genetic phenotypic data a cohort 4,145 individuals collected in three metro areas western Russia. show presence multiple admixed ancestry clusters spanning primarily high identity-by-descent sharing...
Mutations in FLNC for a long time are known connection to neuromuscular disorders and only recently were described association with various cardiomyopathies. Here, we report new clinical phenotype of filaminopathy four unrelated patients early-onset restrictive cardiomyopathy (RCM) combination congenital myopathy due mutations (NM_001458.4:c.3557C>T, p.A1186V, rs1114167361 three probands c.[3547G>C; 3548C>T], p.A1183L, rs1131692185 one proband). In all cases, concurrent was confirmed by...
The standard of care for ovarian cancer comprises cytoreductive surgery, followed by adjuvant platinum-based chemotherapy plus taxane therapy and maintenance with the antiangiogenic compound bevacizumab and/or a PARP inhibitor. Nevertheless, there is currently no clear clinical indication use bevacizumab, highlighting urgent need biomarkers to assess response bevacizumab. In present study, based on novel RNA-seq dataset (n=181) previously published microarray-based (n=377), we have...
Abstract Transcriptomic profiling became a standard approach to quantify cell state, which led accumulation of huge amount public gene expression datasets. However, both reuse these datasets or analysis newly generated ones requires significant technical expertise. Here we present Phantasus – user-friendly web-application for interactive provide streamlined access more than 84000 datasets, as well allows user-uploaded integrates an intuitive and highly JavaScript-based heatmap interface with...
We present the results of depression Genome-wide association studies study performed on a cohort Russian-descent individuals, which identified novel at chromosome 7q21 locus. Gene prioritization analysis based already known risk genes indicated MAGI2 (S-SCAM) as most probable gene from locus and potential susceptibility for disease. Brain gut expression patterns were main features highlighting functional relatedness to previously genes. Local genetic covariance analysis, expression, provided...