Ph.D. Student Position software development, bioinformatics, molecular simulations and modeling

Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology (IIMCB), Warsaw, headed by Prof. Janusz M. Bujnicki , offers a position for a Ph.D. student interested in software development, bioinformatics, molecular simulations and modeling, motivated to develop a career in an interdisciplinary and international team.

Deadline for applications is April 22th, 2019. Preferred job starting date: no later than June 1st, 2019.

Project description: 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, which is now one of the best methods for 3D RNA structure prediction and simulations, in the field. 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.

Required for this position:
• M.Sc. (or equivalent) in computer science, physics, molecular biology, chemistry or related area (defended before the start of the work on the project)
• Basic knowledge in the fields of physics, mathematics, computer science
• Understanding the basic concepts of physics, including interaction, dynamics, thermodynamics
• Understanding issues of 3D geometry, derivation of statistical potentials, running simulations, working in Linux
• Eligibility for PhD studies in Poland
• Documented experience in programming/designing in C/C++ and/or Python
• 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, who are familiar with our work (e.g., our publications and our software) and who can convincingly explain why their expertise is a good fit for our requirements.

We offer:
• Full-time Ph.D. scholarship PhD fellowship 3000 PLN/month
• Position with 100% focus on research (no teaching obligations)
• Participation in courses, scientific training, support from peers, and academic mentoring
• Scientific mentoring, including the supervision of an individual Thesis Advisory Committee
• Technical, administrative, and organizational support from professional English-speaking personnel
• Benefits including reduced-rate for an individual medical care package and membership in MultiSport programme

The funding of the Ph.D. project is provided by a grant entitled “A coarse-grained method for RNA 3D structure modeling, with emphasis on non-canonical base pairing", carried out as the OPUS 2016/23/B/ST6/03433 grant of the Polish National Science Center (NCN).

The team: Our group http://genesilico.pl is highly interdisciplinary and international. We are driven by curiosity to answer fundamental questions in bio-sciences and to make new molecules that are practically useful. We combine various approaches for studying the structures and mechanisms of action of biological macromolecules, in particular RNA, as well as macromolecular complexes involving nucleic acids, proteins, and small molecules. We use computational methods and knowledge-based design to engineer molecules with new structures and functions. Our key strength is the integration of various types of heterogeneous data, and the combination of theoretical and experimental approaches.
The experimentalists in the group use biochemical and biophysical approaches to elucidate the structures and functions of our target molecules, while our theoreticians develop innovative computational tools. We make our software available publicly, often as web servers. We collaborate to gather, process, and analyze the data, make new predictions and discoveries, and to develop new solutions that address important scientific problems.

Ph.D. studies: Our Ph.D. students are enrolled in Ph.D. schools on the campus, in particular at the collaborating institutes of the Polish Academy of Sciences. Ph.D. students have an opportunity to participate in a hands-on training program, covering theoretical and practical aspects of molecular biology, biochemistry, biophysics of proteins and nucleic acids, structural biology, and bioinformatics. Students-programmers are trained in software development. Ph.D. studies involve a full-time research
project in one or more of the areas mentioned above, combined with training in soft skills (e.g., presenting scientific results, writing publications and grant applications, managing projects).

How to apply:
• Apply now to Ten adres pocztowy jest chroniony przed spamowaniem. Aby go zobaczyć, konieczne jest włączenie w przeglądarce obsługi JavaScript.
• In the subject include "PhD-SimRNA-devel" and your first and last name.
• Your application must be submitted in English and should contain: 1) a CV, 2) a cover letter including a short description of your key achievements and explicit responses to the following questions:
What are your scientific interests and how do they relate to requirements of the position offered?
What are your key strengths? What do you know about our laboratory and why do you want to work with us? 3) contacts to at least two potential referees, including your M.Sc. supervisor
• Please include the following statement in your application: “I hereby agree to the processing of my personal data, included in the application documents by the International Institute of Molecular and Cell Biology in Warsaw, 4 Księcia Trojdena Street, 02-109 Warsaw, for the purpose of carrying out the current recruitment process.” Your personal data will be processed for the purpose of the recruitment procedure by the International Institute of Molecular and Cell Biology in Warsaw.
Full information is available under the link https://www.iimcb.gov.pl/pl/information-clause
• The competition may be extended or repeated until a suitable candidate who fulfills all requirements is found

The Ph.D. 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.) and to the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research strategy https://www.iimcb.gov.pl/en/institute/hr-excellence

We would like to inform that the competition for PhD student position in the project entitled „A coarse-grained method for RNA 3D structure modeling, with emphasis on non-canonical base pairing" has been resolved, the selected candidate is Seyed Naeim Moafinejad.