Přehled
Title: New computational approaches in recruiting bacterial genomes from metagenomes
Study program: Biomedical Technology and Bioinformatics
Supervisor: Ing. Markéta Jakubíčková, Ph.D.
Topic description:
Recent advances in sequencing technologies have enabled routine sequencing of metagenomic samples from various environments, significantly expanding our ability to identify and analyze bacterial species within these systems. In the past, all newly described bacteria had to be isolated and their cultures made publicly available, which posed a significant challenge since many microbial species are uncultivable using current techniques. However, this requirement has been changed by the SeqCode initiative, which introduced a nomenclatural code allowing the description of prokaryotes directly from sequencing data, thereby greatly expanding the possibilities for their classification and study. To confirm their existence, computational methods such as bacterial recruitment are used, enabling the detection of specific bacteria in metagenomic databases. However, there is currently no standardized methodology for this technique, and commonly used approaches, often relying on BLAST, may lead to false-positive results due to shared genetic segments among different species. Therefore, this research aims to find a method for quantification as precise as possible. The methodology will involve processing both short NGS and long TGS sequencing reads to cover all currently used sequencing technologies. The proposed method could contribute to the more efficient detection of novel microorganisms and help to understand better their role in clinical and environmental metagenomes. The project will be primarily carried out at the Department of Biomedical Engineering, with expected collaboration with the Center for Molecular Biology and Genetics, FN Brno, and Mendel University in Brno. PhD students will complete six-month internships at prestigious partner universities abroad as part of their studies. DBME provides doctoral students with a stipend and/or a part-time contract beyond the state stipend when joining a grant project or engaging in teaching.
Your task:
- Develop advanced computational methods for bacterial genome recruitment.
- Present your research at international conferences and publish in scientific journals.
- Write and submit applications for junior research funding (e.g., PhD Talent, IGA, etc.).
Requirements:
- Proficiency in programming (e.g., Python, R); experience with Linux-based environments and Bash scripting is an advantage.
- Basic experience with bioinformatics tools and software applications.
- Strong analytical thinking and ability to work independently as well as in a research team.
- English proficiency allowing effective communication, writing, and presenting.
We offer:
- Participation in GAČR and AZV projects addressing current and relevant scientific challenges.
- Being part of a progressive and growing research team (BioSys_BUT).
- Opportunity to present research findings at prestigious international conferences.
- Flexible working hours, the possibility of home office, and team-building activities.
For more information about this topic please contact Markéta Jakubíčková – jakubickova@vut.cz
Relevant publications:
How to apply:
Please apply and submit your motivation letter and CV via university website from April 1 to April 30, https://www.vut.cz/eprihlaska/cs/zadani/vybrat-obor/fakulta/5
Funding:
Funding is provided as a combination of part-time or full-time research projects and/or regular scholarships.
