Přehled

Title: Computational analysis of bioremediation capacity in microbial communities

Study program: Biomedical Technology and Bioinformatics

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

Topic description:

Thanks to their diversity, non-model bacteria represent an inexhaustible resource for microbial biotechnology. While tools, including the computational ones, to study pure bacterial cultures are developed to at least a certain point, their counterparts for mixed cultures are underdeveloped or completely missing.

This PhD project is focused on computational methods for a comprehensive analysis of microbial consortia in order to reveal their functional capacity for industrial biotechnology, bioremediation, and production of value added chemicals, primarily bioplastics. It also offers opportunities to set up comprehensive computational pipeline to analyse diversity of a selected mixed bacterial culture, to set up a metagenome of this community, and to match its observed behaviour through analyses of other omics data revealing running biological and metabolic processes.

The project will be conducted at the Department of Biomedical Engineering, with anticipated collaboration with national (Faculty of Chemistry, BUT; Masaryk University) and international partners (HES-SO Valais Wallis, Switzerland; LMU Munich, Germany).

Your task:

  • To develop a computational tool to mine and integrade information from diverse omicst techniques.

  • To develop a unique software solution for short NGS as well as long TGS reads to cover all currently used sequencing technologies.

  • To publish results in scientific journals and international conferences.

Requirements:

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

  • Strong programming skills, preferably Python or R.

  • Familiarity with sequencing techniques.

  • 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.

Relevant publications: (optional)

https://doi.org/10.4137/EBO.S38546

https://doi.org/10.71150/jm.2411006

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

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

Application deadline: April 30, 2026

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