Research Associate / Senior Research Associate in AI for DNA/RNA Nanotechnology

Salary:

Research Associate: £33,966 to £44,263 per annum

Senior Research Associate: £45,585 to £52,815 per annum

Newcastle University is a great place to work, with excellent benefits. We have a generous holiday package; plus the opportunity to buy more, great pension schemes and a number of health and wellbeing initiatives to support you.

Closing Date: 20 October 2023

The Role

This exciting research opening is looking for computational specialist to work as part of a highly interdisciplinary team lead by Prof. N. Krasnogor. The successful applicant will join the Interdisciplinary Computing and Complex Biosystems research group ICOS.

The post holder will have responsibility for carrying out world-leading research on the application of computational design, modelling, optimisation and/or AI tools in DNA/RNA nanotechnology systems that could be applied to Nucleic Acid Therapeutics and/or DNA data storage.

A successful candidate will bring her/his expertise in either (or all of) AI (e.g. deep neural networks), CAD, computational modelling and/or optimisation (e.g. evolutionary multi-objective optimisation) to systems built from DNA or RNA molecules. Examples of such systems include those that use DNA/RNA strand displacement, DNA/RNA origami, DNA/RNA aptamers or DNA/RNA based data storage systems. 

The post holder will use existing tools such as, e.g., oxDNA, cadnano, cando, tiamat, Vienna Package, etc, and tools built in our own lab to accelerate the Design->Build->Test->Learn cycle in experimental nanotechnology. 

The successful candidate will be expected to both capture experimental data and develop its own novel algorithms and methods to design and model DNA and RNA systems that operate within in vitro, cell-extract, cell-free arrangements as well as in vivo environments.

The successful candidate will work embedded with experimentalist and have access to state-of-the-art computational and bio-nano-technology laboratories to test, debug and improve its computational tools on real-world experimental data.

Candidates must be able to spend time away from Newcastle visiting collaborators' labs abroad and attending business meetings outside Newcastle, including international conferences and project meetings.

This position is available on a full time, fixed term basis, to start immediately and is tenable for 12 months with a potential extension depending on performance until the official project end date.

To apply, please complete an online application and upload a plain text copy of your CV and covering letter only. The covering letter should clearly indicate two key publications, a link to your Github/Bitbucket/GitLab (or equivalent) profile and a brief statement of what you expect to accomplish by joining our team. In your cover letter, you should also evidence how you meet or exceed the essential requirements for the role. Please note, any other ‘Additional Document’ you upload may not be received by the reviewing panel. 

For any informal enquiries please contact Prof. Natalio Krasnogor, Professor of Computing Science and Synthetic Biology via email: Natalio.Krasnogor@newcastle.ac.uk using as subject: “Research Associate or Senior Research Associate in AI for DNA/RNA Nanotechnology”
 
Key Accountabilities

The role will require regular liaison with the other investigators in the project (specifically) and the research group (more generally) to aid in designing experiments to refine the computational tools, organising workloads and data analysis and interpretation. Provide assistance to, and training of, academic, technical and research staff and students on specific computational techniques and in the use of specialised computing equipment when necessary. To keep excellent records of all computational experiments, procedures, protocols, workflows and outcomes, enabling reuse, interpretation with team members and delivery of project milestones.

• Design of DNA/RNA strand displacement, origami, aptamers multi-scaled systems with target functionalities (e.g. data storage, unconventional gene regulation, theranostics, etc)
• Development of multi-scale models of DNA/RNA strand displacement systems, DNA/RNA origami and DNA/RNA aptamers of multi-scaled systems with target functionalities 
• Optimisation of multi-scale DNA/RNA strand displacement systems, DNA/RNA origami and DNA/RNA aptamers to achieve target functionalities.
• Development of Artificial Intelligence tools to support points 1, 2 & 3 above. 
• Contribute to the design of wet-lab experiments to validate, debug and improve all the software created.
• Improve the algorithms and tools used or developed in 1,2 & 3 above based on experimental data from in vitro systems, cell-extract and cell-free systems as well as in vivo systems.
• Following and establishing good software engineering practices within the project and across the research group's projects (e.g. via use of version control system).
• Contribution to writing scientific papers
• Oral presentations at meetings, workshops and conferences
• Contributing to grant writing 
• Contributing to the public communication of the project’s science 

The Person (Essential)

Knowledge, Skills and Experience 

Essential RA

• Demonstrable experience in computational modelling, optimisation or AI in complex settings
• Publication of work in peer-reviewed conferences and journals
• Expert in Python, Java, Ruby, or C/ C++ programming.
• Competence in Linux / OS X programming environments
• Demonstrable experience in using Github, Bitbucket or similar to host open source code

Desirable RA

• Experience in the computational design, modelling, optimisation or AI for DNA/RNA experimental systems (e.g strand displacement, origami, aptamers, data storage)
• Demonstrable experience with molecular computation, e.g. DNA computing, or molecular fabrication, e.g. DNA or RNA origami techniques, DNA or RNA programmable self-assembly (e.g. Winfree's tiles), etc
• Demonstrable experience following good software engineering practices
• Demonstrable experience working with experimentalists on the above techniques
• Demonstrable experience in synthetic biology or nanotechnology
• Presentation of work at scientific meetings

Essential SRA

• Demonstrable experience in computational modelling, optimisation or AI for DNA/RNA experimental systems (e.g strand displacement, origami, aptamers, data storage)
• Publication of work in peer-reviewed conferences and journals
• Expert in Python, Java, Ruby, or C/ C++ programming
• Competence in Linux / OS X programming environments
• Demonstrable experience in using Github, Bitbucket or similar to host open source codeA previous postdoc or research position in a closely related area
• Strong track record in journal publications which evidence work of international significance

Desirable SRA

• Demonstrable experience with molecular computation, e.g. DNA computing, or molecular fabrication, e.g. DNA or RNA origami techniques, DNA or RNA programmable self-assembly (e.g. Winfree's tiles), etc
• Demonstrable experience following good software engineering practices
• Demonstrable experience working with experimentalists on the above techniques
• Demonstrable experience in synthetic biology or nanotechnology
• Presentation of work at scientific meetings
• Experience contributing to grant writing
• Experience of supervising undergraduate and postgraduate student projects
• Experience in the utilisation and development of social media for public dissemination

Attributes and Behaviour

Essential for RA

• An ability to communicate effectively via oral and written media (e.g. technical reports, papers, presentations)
• Capacity for original thought and independent work
• Enthusiastic, hardworking and goal-setter
• Ability to interact with people from different disciplines
• Punctual and generally dependable in working to deadlines

Essential for SRA

• An ability to communicate effectively via oral and written media (e.g. technical reports, papers, presentations).
• Capacity for original thought and independent work.
• Enthusiastic, hardworking and goal-setter.
• Ability to interact with people from different disciplines.
• Ability to supervise student projects.
• Punctual and generally dependable in working to deadlines.
• Communication skills with the public.
• The ability to work autonomously and lead by example 

Qualifications

Essential for RA

• A PhD degree in a suitable field. 

Essential for SRA

• A PhD degree in a suitable field. 
• Evidence of Continued Professional Development (CPD)
   

Newcastle University is a global University where everyone is treated with dignity and respect.  As a University of Sanctuary, we aim to provide a welcoming place of safety for all, offering opportunities to people fleeing violence and persecution.

We are committed to being a fully inclusive university which actively recruits, supports and retains colleagues from all sectors of society.  We value diversity as well as celebrate, support and thrive on the contributions of all of our employees and the communities they represent.  We are proud to be an equal opportunities employer and encourage applications from individuals who can complement our existing teams, we believe that success is built on having teams whose backgrounds and experiences reflect the diversity of our university and student population.

At Newcastle University we hold a silver Athena Swan award in recognition of our good employment practices for the advancement of gender equality.  We also hold a Race Equality Charter Bronze award in recognition of our work towards tackling race inequality in higher education REC.

In addition, we are a member of the Euraxess initiative supporting researchers in Europe. 

Requisition ID: 26064