DTU Tenure Track Researcher in Computational Kinetic Modelling - DTU Biosustain

We are hiring a researcher to lead research into kinetic modelling of enzyme catalysed reaction networks. The goal of the project is to develop next generation methods for estimation of kinetic parameters from multi-omics experiments and to implement them in user-friendly software that can be used for metabolic engineering.
We are hiring a researcher to lead research into kinetic modelling of enzyme catalysed reaction networks. The goal of the project is to develop next generation methods for estimation of kinetic parameters from multi-omics experiments and to implement them in user-friendly software that can be used for metabolic engineering. This will involve creating a curated, interoperable knowledge base containing relevant kinetic information and experimental datasets, developing new numerical methods integrating novel steady state solvers with Markov Chain Monte Carlo algorithms, developing new statistical models that improve on the state of the art in representing information from quantitative omics experiments, and devising new ways of extracting actionable insights from these models’ outputs.

Responsibilities and qualifications
Kinetic models describe the fluxes though biochemical reactions in terms of parameterised equations derived from consideration of their physical properties. Although equations that accurately describe most enzyme mechanisms have been known for many years, and despite many attempts, there are relatively few accurate kinetic models of important biochemical pathways, due to the difficulty of estimating in vivo kinetic parameters. Fortunately, progress in computational statistics and quantitative biochemical analytics have made this problem more feasible, as shown by several recent papers that demonstrate data-based pathway-scale kinetic modelling. In this role you will seek to build on this progress and develop a general computational kinetic modelling framework that will become widely adopted in metabolic engineering.

There are four intersecting subprojects:

• Develop a curated knowledge base. This will include data pertaining to important and relevant kinetic and thermodynamic parameter values, pathway topologies, experimental datasets and the results of previous statistical kinetic models.
• Develop a steady state aware MCMC algorithm. Data-based kinetic modelling is bottlenecked by the need to numerically solve a costly steady state problem millions of times during MCMC sampling. This bottleneck can be widened by developing a stateful MCMC algorithm that remembers the results of previous steady state solutions.
• Develop new statistical models of the results of quantitative multi-omics experiments. You will develop compositional models of 13C labelling experiments and bias-aware models of quantitative mass spectrometer results.
• Develop new ways to use the results of data-based kinetic models in metabolic engineering. Kinetic models should be integrated with experimental design using Bayesian optimisation.

As part of this project you will work with nearby colleagues, teach and supervise BSc and MSc student projects, be co-supervisor for PhD students and contribute to the teaching of courses. DTU employs two working languages: Danish and English. You are expected to be fluent in at least one of these languages, and in time are expected to master both.

Essential qualifications:

• Strong background in collaborative open source software development, demonstrated by a track record of project contributions
• Expertise in general scientific programming, including manipulation of tabular and structured data, ETL operations, workflow management, automation
• Expertise in gradient-based MCMC algorithms
• Expertise in numerical methods for equation solving with gradients
• Expertise in kinetic modelling of enzyme catalysed reaction networks
• Knowledge of biochemical thermodynamics
• Experience with quantitative multi-omics experiments
• Experience applying Bayesian optimisation in the context of fermentation experiments

As formal qualification you must hold a PhD degree (or equivalent).

You will be assessed against the responsibilities and qualifications stated above and the following general criteria:

• Research experience
• Experience and quality of teaching
• Research vision and potential
• International impact and experience
• Societal impact
• Innovativeness, including commercialization and collaboration with industry
• Leadership, collaboration, and interdisciplinary skills
• Communication skills

Salary and terms of employment
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

The position is part of DTU’s Tenure Track program. Read more about the program and the recruitment process here.

Start date is Jan 1st, 2025 or earlier.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Scientific Director Lars Keld Nielsen, [email protected] or Researcher Stefano Donati, [email protected]

You can read more about DTU Biosustain at https://www.biosustain.dtu.dk/

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark.

Application procedure
Your complete online application must be submitted no later than 15 October 2024 (23:59 Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• Application (cover letter)
• Vision for teaching and research for the tenure track period
• CV including employment history, list of publications, H-index and ORCID (see http://orcid.org/)
• Teaching portfolio including documentation of teaching experience
• Academic Diplomas (MSc/PhD)

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)
Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.

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