Overview

Title: Modelling microbial pathways using multi-omics data

Study program: Biomedical Technology and Bioinformatics

Supervisor: doc. Mgr. Ing. Karel Sedlář, Ph.D.

Topic description:

Modelling of various signalling pathways became an integral part of holistic approach used in understanding of diverse microogranisms, especially after the emergence of frameworks allowing integration of multi-omics data.

This PhD project focuses on expanding our knowledge how particular omics technologies, e.g. genome sequencing, transcriptome sequencing, HPLC, mass spectrometry, etc., can be integrated into static and dynamic models describing behaviour of diverse organisms and their interactions with the environment. It particularly offers opportunities to explore interactions of antimicrobial agents, e.g., fungal pigments, with microbes causing food spoilage, e.g., bacteria from the genus Clostridium.

The project will be conducted at the Department of Biomedical Engineering, with anticipated collaboration with national (Department of Biotechnology, UCT Prague) and international partners from academia (LMU Munich, Germany; HZAU, China) and private sector (VTT, Finland).

Your task:

  • To develop a software solution for the inference of static and dynamic models of microbial interactions.

  • To set rules for integrating data from diverse omics technologies.

  • To publish results in scientific journals and international conferences.

Requirements:

  • Master’s degree in a relevant field, e.g., systems biology, bioinformatics, microbiology.

  • Strong programming skills, preferably Python or R.

  • Familiarity with different omics technologies.

  • Good communication skills in English.

  • A keen interest in modern biotechnology and bioinformatics.

We offer:

  • Collaboration within an active and interdisciplinary team – Bioinformatics and Systems Biology Lab (BioSys_BUT).

  • Project (Czech Science Foundation) co-funded position (financial support beyond the state scholarship).

  • Opportunities for professional development, including participation in international conferences, workshops, and specialized training.

For more information about this topic please contact Karel Sedlar – sedlar@vut.cz

Relevant publications:

https://doi.org/10.1021/acs.jafc.5c08401

https://doi.org/10.1016/j.csbj.2024.01.013

Application portal: https://www.vut.cz/eprihlaska/

Application deadline: April 30, 2026

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