Three Open PhD positions

Bioinformatics (3 years)

PhD position in bioinformatics, focusing on bacterial RNA regulators

PROJECT DESCRIPTION

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.

The PhD project will focus on investigation of the role of RNA secondary structure in regulation of gene expression by computational analysis of high throughput sequencing data obtained from experimental part of the project. In the course of the project PhD student will develop novel bioinformatic tools and methods, as well as use them for data analysis and interpretation. Successful candidates will have the opportunity of broad scientific development by attending scientific conferences, internships and obtaining scientific support of experts in different fields of bioinformatics and RNA biology.

More information:

dr Marek Żywicki, (Marek.Zywicki@amu.edu.pl, phone: +48 61 829 5842)

QUALIFICATIONS:
  • 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
STARTING DATE

October/November 2018

SALARY

scholarship of 3500 PLN/month

HOW TO APPLY

Initial application should be send by email to dr Marek Żywicki (Marek.Zywicki@amu.edu.pl). 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

DEADLINE FOR APPLICATION

No deadline, continuous application


PhD position in bioinformatics, focusing on regulation of ribosomes by small RNAs

PROJECT DESCRIPTION

Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information encrypted in the DNA to create the proteins in all cells. All ribosomes are composed of ribosomal RNA and ribosomal proteins. Although their function during protein biosynthesis is evolutionary conserved (is performed in the same way in all organisms), the components of the ribosome differ between organisms, developmental stages or under different environmental changes within one organism. It has been therefore suggested that such reason for heterogeneity of the ribosomes most probably provides means to prepare the translational program of stressed cells for recovery, because proper ribosome functioning is crucial to the health of the cell. Recently, we have described a novel class of ncRNAs, namely ribosome-associated noncoding RNAs (rancRNAs), which directly bind and regulate the ribosome function in yeast Saccharomyces cerevisiae. It was the first report presenting the possibility of regulation of ribosome function by direct interactions with small noncoding RNAs as a response to stress conditions.

The main aim of the project is to explore in details the heterogeneity of Saccharomyces cerevisiae ribosomes caused by differential environmental conditions as well as to characterize ribosome-associated noncoding RNAs (rancRNAs) interacting with different subpopulations of heterogeneous ribosomes. This goal will be reached by employment of already established and development of novel methods to computational analysis of data obtained from high throughput transcriptomics and proteomics. The results of the project will reveal a new levels of control of gene expression, regulating ribosome heterogeneity during stress in eukaryotic species.

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, (Marek.Zywicki@amu.edu.pl, phone: +48 61 829 5842)

QUALIFICATIONS:
  • MSc degree in Bioinformatics, Molecular Biology or related discipline (e.g. biotechnology, computer science)
  • strong background in molecular biology
  • experience in NGS data analysis will be beneficial
  • 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
STARTING DATE

October/November 2018

SALARY

scholarship of 3500 PLN/month

HOW TO APPLY

Initial application should be send by email to dr Marek Żywicki (Marek.Zywicki@amu.edu.pl). 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

DEADLINE FOR APPLICATION

No deadline, continuous application