Elena Nikolaevna Ilina

The paper assesses peptide proteotypicity in-house for targeted proteomics by synthesizing and verifying peptides from three plasma proteins.

Snappy identifies DNA methylation sites in bacteria using Oxford Nanopore reads without requiring control samples or motif enrichment heuristics.

AliMarko identifies eukaryotic viruses in metagenomic data using reference mapping, de novo assembly, and HMM, with tools to reduce false positives and visualize results.

Snapper is a high-sensitive algorithm for detecting methylation motifs from Oxford Nanopore reads, showing improved enrichment sensitivity over existing tools and identifying new methylation sites in H. pylori.

FunFun evaluates the functional content of fungi or mycobiomes using ITS sequencing data to annotate functional capabilities.

The paper identifies and genetically characterizes a novel MERS-related coronavirus from bats, suggesting potential for hedgehogs to act as intermediate hosts.

The paper identifies reproducible stool metagenomic biomarkers associated with positive melanoma immunotherapy outcomes across multiple studies.

The paper analyzes the respiratory tract microbiota in COVID-19 patients to find associations between microbiota composition and disease severity.

BioCAT is a tool that identifies biosynthetic gene clusters for nonribosomal peptides using structure-based search and improves upon existing methods with position-specific scoring and ensemble modeling.

The paper introduces GCB, a tool for visualizing and analyzing prokaryote genome variability, identifying regions of high complexity associated with genomic rearrangements and horizontal gene transfer.

The paper introduces RECAST, a computational tool to analyze metagenomic data from FMT studies, identifying colonizing and non-colonizing microbes and their associations with resistance genes.

Phigaro annotates prophage regions in genome and metagenome assemblies, producing prophage genome maps and taxonomic annotations.

This study uses whole genome sequencing to analyze gut microbiota changes after Helicobacter pylori eradication therapy, finding reduced alpha-diversity, shifts in metabolic potential, and increased antibiotic resistance genes.