Nikita Alexeev

PaReBrick identifies parallel rearrangements in bacterial genomes by analyzing synteny blocks and phylogenetic trees to detect events contributing to pathogenicity and adaptation.

This study analyzes genome rearrangements in Shigella and E. coli strains, finding high rearrangement rates and specific E3 ubiquitin ligases linked to pathogenicity.

This study produces chromosome-level genome assemblies for Anopheles coluzzii and Anopheles arabiensis using long-read sequencing and Hi-C scaffolding, improving reference-quality genomes and enabling identification of chromosomal inversion breakpoints.

This study evaluates twelve haplotype callers for NGS viral sequencing, finding they perform poorly under high genetic diversity, with PredictHaplo and PEHaplo showing better accuracy for HIV-like diversity levels.

This paper introduces a method to recover rearranged cancer chromosomes from karyotype graphs, demonstrating its effectiveness on a prostate cancer dataset.

The paper introduces a soft vertex classification method for identifying active modules in biological networks, providing confidence estimates and FDR control.