Polish Bioinformatics Society

PhD student position

in development of methods for RNA 3D structure prediction and simulations

Bujnicki group in IIMCB, Warsaw, Poland

We are looking for a junior scientist, interested in software development, bioinformatics, molecular simulations and modeling, and motivated to develop a career in an interdisciplinary and international team.

Key information about us:

• To have an idea of the working activity of the host group, check the website http://genesilico.pl

• 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 goal is to understand the structure of RNA molecules, and design molecules that do not exist yet. We are also involved in efforts towards commercialization of our results.

• We are one of the most successful RNA modeling teams in the world: see rankings of RNA Puzzles. Our recent focus and biggest successes are in computational and experimental analyses of RNA and protein-RNA complexes. For examples, see: Smietanski et al. Nature Commun 2014, Boniecki et al. Nucleic Acids Res 2015.

• We are hosted by IIMCB (http://iimcb.gov.pl), the top-ranked (A+) Polish research institute in biology, with cutting-edge equipment and facilities, in particular for bioinformatics, experimental molecular and structural biology.
IIMCB also provides support for science commercialization, development of spin-off companies etc.

• IIMCB is an equal opportunity employer and holds 'HR Excellence in Research' logo for the implementation of the provisions of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers.

The project "A coarse-grained method for RNA 3D structure modeling, with emphasis on non-canonical base pairing" (PI: dr. Michal Boniecki) is carried out as the OPUS 2016/23/B/ST6/03433 grant of the Polish National Science Center. The PhD student will be selected from candidates in an open competition, according to the procedure complying the rules for granting scholarships for young scientists in research projects funded by the National Science Centre (NCN Council Resolution No. 96/2016 dated. October 27, 2016 r.)

The goal of the project is to further develop SimRNA, one of the best methods for 3D RNA structure prediction and simulations. We intend to improve the prediction of non-canonical base-pairs, and to improve the overall specificity. Additional tasks include RNA 3D structure prediction with additional restraints and setting up a web server. We provide opportunities for interdisciplinary collaborations within the team, in the institute, as well as with international partners.

Requirements:

• MSc in computer science, physics, chemistry or related area (defended before the start of the work on the project)

• Eligibility for PhD studies in Poland

• Documented experience in programming/designing in C/C++ and/or Python

• Understanding issues of 3D geometry, derivation of statistical potentials, running simulations, working in Linux

• Proactive approach to achieving tasks and objectives, good interpersonal skills, collaborative attitude

• Experience in bioinformatics, molecular modeling etc. is advantageous, but not essential.

• Priority will be given to candidates with expertise most relevant to the project and to the profile of the laboratory.

We offer:

• PhD fellowship 3000 PLN/month

• Appointment starting between April and October 2018, funding guaranteed initially for 3 years, possible extension

• Position with 100% focus on research (no teaching obligations)

• Participation in courses, scientific training, support from peers, and academic mentoring

• Benefits including reduced-rate for an individual medical care package and membership in MultiSport programme

How to apply:

• We will collect applications until April 9th 2018

• Apply now (or ask any questions you may have) to mboni@genesilico.pl

• In the subject include "PhD-SimRNA-devel" and your first and last name.

• Your application must be in English and should contain a CV, a motivation letter (What are your key strengths? Why do you want to work with us? Your scientific dream?) preferably in one pdf file, below 5 MB, a description of your key achievements, and contacts to at least two potential referees, including at least one direct supervisor.

• Please include the following statement in your application: "I hereby give consent for my personal data included in my application to be processed for the purposes of the recruitment process under the Personal Data Protection Act as of 29 August 1997, consolidated text: Journal of Laws 2016, item 922 as amended.”

• Best candidate(s) may be given additional questions and tasks before the final interview.

• The competition may be extended until a suitable candidate who fulfills all requirements is found.