PhD Student: Procedure no. DSMBBC​/Comparative analysis of Mortierellomycota genomes

Institute of Biochemistry and Biophysics Polish Academy of Sciences

Organisation/Company Institute of Biochemistry and Biophysics Polish Academy of Sciences Department Laboratory of Fungal Bioinformatics Research Field Biological sciences » Biology Researcher Profile First Stage Researcher (R1) Positions PhD Positions Country Poland Final date to receive applications 7 Jan 2026 - 23:58 (Europe/Warsaw) Type of Contract Temporary Job Status Full-time Hours Per Week 40 Offer Starting Date 2 Mar 2026 Is the job funded through the EU Research Framework Programme?

Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Fungi are important for the health and human economy as pathogens of crops, fermenting organisms, with additional use in bioreactors. In our previous projects, we have linked the distribution of diverse gene classes to the ecology of fungi [1] and predicted the presence of traits that were considered absent from fungi [2]. Currently, only homologs of defined and relatively conserved protein families are widely used for genomic comparative studies.

However, we have experience in studying diverse fungal traits, including transposons, horizontally transferred genes [1] and diversified protein families. The main idea of the project is to explore the properties of a fungal phylum that has both biotechnological potential as oil producers [3] and puzzling ecological features (growth in water, no ergosterol, inhabiting harsh environments, hosting associated bacteria). We will use sequences of fungal genomes and use diverse tools to predict functional categories and characterize these proteins.

One of the aims of this project is to maximize the usage of available protein sequences in the frame of green bioinformatics, reusing the dataset processed in our previous project on low complexity regions currently deposited  will re-annotate the proteins to comprehend the underpinnings of fungal ecology and adaptability. The project will integrate information on the evolution of Mortierellomycota compared to other fungal groups, their characteristic structures, and ecological properties identified in the course of this project.

We will try to answer questions about their genome organization, whether they have two-speed genomes, and to what extent nonvertical processes are shaping their adaptability. We will try to tackle questions such as, why do some gene families proliferate? What happened to the horizontally transferred genes and transposons in the recipient genomes? Are genes encoding unknown protein products expressed at the same level as known genes (in publicly available RNASeq datasets from the same isolates as the proteomes)?

Are the xenologs and transposons randomly distributed in the genomes?

Holding a degree of Master of Science [Magister], Master of Engineering [Magister Inżynier], medical doctor or equivalent in the field of: exact sciences, natural sciences, medical sciences or related disciplines, granted by a Polish or foreign university; a person who does not possess the qualifications described above may take part in the competition, but must obtain the qualifications in question and provide the relevant documents before the start of the programme at the Doctoral School (i.e., 1st March 2026).

Specific Requirements

• working in a Linux environment, basic Bash, scripting in Python (awk, R or other);
• being familiar with protein sequence and structure analyses (eg. structure prediction and docking);
• knowledge of biological databases, algorithms and pipelines;
• experience in working with phylogenetic/ genomic/transcriptomic/systems biology tools will be a bonus;
• being well organized, eager to learn and ready to assimilate literature;
• fluency in spoken and written English

Research Field Biological sciences

• Scholarship amount (net, monthly, PLN): 1st year: 4000; 2nd year: 4000; 3rd year: 4 739,51; 4th year: 4 739,51
• Possibility of renting a room in the Institute's hotel for the first 3 months at a special price (depending on rooms’ availability);
• Possibility to join a medical plan;
• Res…