Here you can find some of the projects carried out during my studies in Bioinformatics Institute. Each folder contains a detailed report, a jupiter notebook with step-by-step description of actions and possibly some additional scripts.
And here is some brief description of each work.
Microbial resistance to antibiotics is a major problem in the treatment of bacterial infections and there are plenty of ways for bacteria to become resistant to a particular antibiotic. These small changes make it challenging for the immune system to recognize and effectively neutralize new strains of influenza. As a result, the flu vaccine may ofer reduced protection against these drifted strains, leading to increased susceptibility within the population.
In this project, I worked with real sequencing data from a strain of E. coli resistant to the antibiotic ampicillin and the job was to analyze that sequencing data to locate the mutations responsible for giving E. coli its antibiotic resistance property and propose possible mechanisms of antibiotic resistance in each case, and then I was to make recommendations for alternative antibiotics a doctor could use to treat each strain.
Skills: Shot-gun sequencing data analysis, variant calling, SNP annotation, data interpretation, alignements visualisation
Like others RNA viruses, influenza exists as heterogeneous populations of closely related genetic variants. These variations are called quasispecies. Even though a person was vaccinated to develop immunity to a certain viral strain, the small changes within quasispecies make it challenging for the immune system to recognize and effectively neutralize new strains of influenza. As a result, the flu vaccine may ofer reduced protection against these drifted strains.
The goal of this practical work was to check out the hypothesis that a small portion of the known virus population mutated and evolved while replicating inside the roommate’s cells.
Skills: deep sequence data, awk one-liners, epitope mapping, sequencing errors detection
In April 2011, hundreds of people in Germany were hospitalized with hemolytic uremic syndrome (HUS), a deadly blood disease that often starts as food poisoning with bloody diarrhea and can lead to kidney failure. German health officials immediately informed the World Health Organization about the incident, but they had no idea that it was the beginning of the deadliest E. coli outbreak in recent history, caused by a mysterious strain that we will call E. coli X.
In this project, I followed in the footsteps of the bioinformaticians investigating the outbreak by assembling the genome of the deadly E. coli X strain and tried to determine how it became pathogenic.
Skills: de novo genome assambly, comparative genomics-based gene annotation, alignements visualisation
Tardigrades (also known as water bears, pudgy wudgies, or moss piglets) are microscopic animals capable of withstanding some of the most severe environmental conditions, including radiation. Scientists tried to explain tardigrades' radiation withstand with the fact that they are able to enter the dehydrated state (and survive in up to five years), and this state provides fewer reactants for ionizing radiation. But later it was shown that when hydrated, they still remain highly resistant to shortwave UV radiation in comparison to other animals. But how? In this project we tried to analyze their genome and understand this secret.
Skills: functional annotation, protein localisation prediction, DNA-bound proteins detection
The goal of this project was to imagine that we are in the not-too-distant-future, where transhumanism has been widely accepted, and we are allowed to use CRISPR-Cas9 on humans and I you just could order a DIY kit to make any corrections to your DNA (actually, you can order it now, but just for E. coli). What would I change?
Skills: SNP annotation (ClinVar, SnpEff/SnpSift, GWAS catalog), variant effect prediction
The goal of the project was to see in-detail the changes in RNA expression during the fermentation process in in yeast cells.
Skills: splice-junction aware alignment, guided transcript assembly, differential expression analysis