Three Open PhD positions

Bioinformatics (3 years)

PhD in bioinformatics, focusing on orphan genes in bacteria

The Department of Computational Biology at the Faculty of Biology at Adam Mickiewicz University (Poland, Poznan) has a position for a PhD student to work on computational methods for identification of bacterial orphan genes, which may serve as potential drug targets.


Identification and functional annotation of taxonomically-restricted genes in bacteria. The characterized sequences may, among others, serve as molecular markers for metagenomic projects and become a potent candidate for new pharmacological therapies.

  • MSc degree in Biology/Bioinformatics or related discipline (e.g. biotechnology, computer science)
  • molecular biology background
  • knowledge of gene evolution mechanisms
  • programming skills (e.g. Python / Perl / Ruby) [optional: C/C++]
  • fluent written and verbal communication skills in English
  • independent thinking, intellectual curiosity, high motivation and team spirit are skills that are more than welcome

September/October 2018


4500 PLN (~1000 EUR)


Your application file should contain a motivation letter, your marks and degrees during your Bachelor and Master studies with ranking, CV and publication list (if applicable), a summary of your previous research experience, and addresses of 1-2 referees.

Contact: Professor Wojciech Karlowski, Director of the Department of Computational Biology AMU (


20 June 2018


2 PhD positions in bioinformatics, focusing on bacterial RNA regulators


Drug-resistant bacteria are major challenge for modern medicine. Classical approaches for development of novel antibiotics are insufficient, since bacteria adopt very quickly to gain resistance. Promising novel group of targets in antimicrobial treatment are regulatory RNAs, such as riboswitches. Riboswitches are common regulators in bacterial genome, which modulate gene expression on transcriptional or translational level by structural rearrangements in 5’UTR of mRNA, induced by binding of small metabolites. They are composed of two major functional domains – expression platform and aptamer, which binds ligand. Since single family of riboswitches binding the same ligand can control multiple mRNAs acting on different metabolic pathways, applying proper analog of natural ligand can target multiple genes. Such treatment require more complex rearrangements in bacterial genome to gain resistance.

The main goal of the project is identification of RNA regulatory networks, which could be potential targets for novel antimicrobial compounds. Project will focus on methicillin-resistant Staphylococcus aureus (MRSA). In order to identify novel RNA regulators, computational methods for synergistic analysis of high throughput transcriptomic data derived from multiple high throughput experimental approaches will be developed. The multidimensional analysis of experimental data will be applied to identify: i) riboswitches acting by transcription modulation, ii) riboswitches acting by translation modulation, iii) non-coding regulatory RNAs and their targets, iv) other novel regulatory RNA mechanisms.

The realization of the project will enable for the first time high throughput identification of multiple RNA regulators, including translational riboswitches, uORFs and others. Obtained results will enable identification and characterization of novel RNA-dependent regulatory mechanisms related to infection and drug resistance of bacteria, facilitating further development of antimicrobial compounds against multidrug resistant Staphylococcus aureus.

Both PhD students will be working on computational analysis of high throughput sequencing data obtained from experimental part of the project. First PhD project will focus on investigation of the role of RNA secondary structure in regulation of gene expression. Second will address the characterization of RNA-dependent changes in bacterial gene expression. In both cases, it will require the development of novel bioinformatic tools and methods as well as their employment for data analysis and interpretation. We will provide the support of experts in different fields of bioinformatics and RNA biology. Successful candidates will have the opportunity of broad scientific development by attending scientific conferences, obtaining scientific support

More information:

dr Marek Żywicki, (, phone: +48 61 829 5842)

  • MSc degree in Bioinformatics, Molecular Biology or related discipline (e.g. biotechnology, computer science)
  • strong background in molecular biology
  • good knowledge of RNA-based regulatory mechanisms
  • practical programming skills (e.g. Python / Perl / Ruby) [optional: C/C++]
  • fluent written and verbal communication skills in English
  • strong motivation for career in science

October 2018


scholarship of 3500 PLN/month


Initial application should be send by email to dr Marek Żywicki ( Letter should contain:

  1. scientific CV with description of scientific achievements and activities
  2. motivation letter, including description of scientific interest and expertise
  3. contact to at least one scientific referee (e.g. former supervisor)
  4. copy of MSc diploma, or planned date of MsC defense in case of last year students
  5. signed agreement (can be provided also as a scan) for personal data processing in a form:

    According to the Data Protection Act (Dz. U. UE L 119/1 of 4 may 2016) I hereby give consent for my personal data included in the job offer to be processed for the purpose of the recruitment. (Zgodnie z art. 6 ust.1 lit a ogólnego rozporządzenia o ochronie danych osobowych z dnia 27 kwietnia 2016r. (Dz. U. UE L 119/1 z dnia 4 maja 2016r.) wyrażam zgodę na przetwarzania moich danych osobowych zawartych w mojej ofercie pracy dla potrzeb aktualnej rekrutacji).

Selected candidates will be invited for an interview


30 June 2018