Ilia Popov

Bioinformatics Institute, Bioinformatics for Biologists
Rostov State Medical University, Medical Doctor

Research experience 🔬

Bioinformatics Institute Research Project: The shadow of HIV 🦠

Data of WGS-based non-invasive prenatal testing (NIPT) or cell-free DNA testing contains exogenous DNA (bacterial and viral). This information is too fragmentary to conduct full microbiome studies, but still interesting for expanding NIPT functionality.
Being a retrovirus, HIV can not be directly detected in cell-free DNA data.
Steps of the study:

Extraction of unmapped reads
Assigning taxonomic labels
Creating residual virus and microbiome profiles of two datasets
Analysis of the HIV-positive sequencing data
Finding the differences in exogenous DNA composition between HIV- and HIV+ NIPT samples

Skills: Bash, bowtie2, Snakemake, Kraken2, KrakenTools, MaAsLin2.

Research Internship: Pediatric Nutritional Medicine and Intestinal Microbiology 🏥

Performed genome-based safety assessment of the probiotic strain Lpb. plantarum IS-10506.
Determined the multivariate association between clinical metadata and microbial meta-omics characteristics in a clinical study comparing gut microbiota profiles in stunted and normal children aged 36-45 months.

Skills: BAGEL4, CRISPRCasFinder, R, dplyr, ggplot2, tidyverse, tidyr, MaAsLin2.

Study projects 👨🏻‍💻

Beginner-level tools 🛠️

SequenceForge-Lite
Lightweight tool to work with biological sequences, providing various functionalities for filtering .fastq files and manipulating .fasta files
MyAwesomeEDA
Python module that provides a set of tools for exploring and analyzing your dataset

Bioinformatics Institute: study projects 📚

Projects completed during training at the Bioinformatics Institute:

Variant calling of Escherichia coli WGS
Variant calling of deep sequencing data (Influenza A virus (H3N2) hemagglutinin gene)
De novo assembly of Escherichia coli genome (TBD)
Tardigrade Ramazzottius varieornatus genome annotation and protein function prediction
Genotyping and SNP annotation of human 23andMe data
RNA-seq data analysis for differential gene expression of Saccharomyces cerevisiae after 30 minutes of fermentation
Ancient metagenomes analysis examining human dental calculus
Annotation of the immune repertoire derived from the T-cell population in a relatively healthy donor
Single-cell CITE-seq analysis detailing the cellular composition and transcriptional profiles within human bone marrow