PhD student

Laboratory of Bioinformatics and Protein Engineering

Description of the project:
The title of the project is: "A coarse-grained method for RNA 3D structure modeling, with emphasis on non-canonical base pairing". This will be further development of SimRNA. SimRNA is successful, already implemented and published method for RNA folding simulations and 3D structure prediction. (just google "SimRNA"). The main goal will be development towards better recapitulation of non-canonical base pairing, also improving overall prediction ability. The project also includes studies of folding RNA with restraints. Selected candidate will work together with PI (Michał Boniecki) (optionally with other lab members) on further development of SimRNA as well as investigate folding of RNA molecules. Typical tasks are (optionally, only some of them will be done by selected candidate):

•    development (programming) and testing of SimRNA and also other scripts or programs
•    running/setting up simulations, making structure predictions (of RNA molecules)
•    studies of folding with restraints
•    processing results, making statistics
•    deriving statistical potentials (also preparing/filtering data sets of experimentally solved structures PDB)
•    optimization of parameters (at various levels/stages)
•    development of web server that runs SimRNA (in web server mode)
•    preparing conference materials (seminars, posters ...)
•    sharing of knowledge and experience
The project will be executed in prof. Janusz Bujnicki lab (, Principle Investigator of the project will be dr Michał Boniecki.

Candidates with skills listed below will be preferred:
•    MSc in science or engineering (physics, chemistry, computer science, bioinformatics, biology or related)
•    understanding of basic concepts of dealing with / programming geometry 3D
•    programming/designing in languages: C/C++ (python will be an advantage)
•    understanding or/and experience in deriving statistical potentials (machine learning issues)
•    understanding or/and experience in optimization issues (in practice)
•    understanding of issues of folding of biomolecules (especially RNA)
•    understanding or/and Django framework
•    English, fluent spoken and written
•    creativity and dedication towards work and learning
•    good interpersonal skills, sharing knowledge and experience

We are an interdisciplinary team ( that combines basic science (to solve the mysteries of nature) and applied science (to make the discoveries practically useful). In our laboratory, software developers meet with experimental biologists, and high-throughput data analysis combines with sophisticated studies of individual biomacromolecules. We develop new computational methods, new tools for biotechnology, and molecules that will hopefully become drugs against diseases.

Our current research goals are based on a wild ambition: to understand the structure of all RNA molecules that exist, and design molecules that do not exist yet.
We are hosted by IIMCB (, the top-ranked (A+) Polish research institute in biology. The institute provides cutting-edge equipment and facilities, in particular for bioinformatics/
Scholarship agreement, 3000 PLN per month netto

How to apply:
Please send your CV and motivation letter (preferably as one PDF) to This email address is being protected from spambots. You need JavaScript enabled to view it. (please do not send files bigger than 5 MB). Application should include a short statement of research interests, a brief description of scientific achievements (if applicable), and, if possible, contact information for one or two  references.
Questions about the position can be send to This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.

Applications will be collected until 17 of November 2017.

In case no suitable candidates are found, we will continue collecting applications.

Please include in your application the following statement: “In accordance with the personal data protection act from the 29th of August 1997, I hereby agree to process and to store my personal data by the Institution for recruitment purposes”.

The recruitment procedure fulfills the National Science Centre’s regulations on granting the scholarships to young scientists.