PhD Position Predicting Compatibility of Network-dependent Enzymes

Do you want to combine AI-based tools and lab work to improve the design of engineered pathways?

Many enzymes rely on intracellular protein networks to acquire essential cofactors or modifications. Due to the evolutionary diversification of such protein networks between species, it is not uncommon for network-dependent enzymes to show limited or no activity when expressed within cells of a foreign species. It is currently not possible to predict whether a given enzyme will show activity when expressed in a foreign species, and this presents a major limitation in bioengineering. For instance, biosynthesis of many valuable molecules, such as biofuels, relies on network-dependent enzymes.

In this PhD project, you will combine bioinformatics with experimental work to gain better understanding of the principles that render an enzyme functional or non-functional within a specific biological background. You will get to work with state-of-the-art AI tools for protein structure prediction, explore 3D structures and dynamical behaviour of proteins, build machine learning models, and verify your predictions in the wet lab.

This project is a collaboration between Sostaric and Bokinsky labs. For more information, you can visit group websites: https://nikolinasostaric.github.io/ and https://sites.google.com/site/bokinskylab/

We are looking for a candidate who:

• Holds (or is approaching the completion of) a Master’s degree in Bioinformatics, Molecular biology, Bioengineering, or a related field.
• Has excellent spoken and written English skills.
• Has an affinity for both computational and experimental research (i.e., both bioinformatics/computational biology and molecular biology/biochemistry).
  Has a critical and creative mindset.
• Can work independently and thrives in international, multidisciplinary, collaborative environment.
• Experience with computer programming (Python, R, or another language) and machine learning will be considered a plus.

Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis. For more details please check the Graduate Schools Admission Requirements .

Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1,5 year contract with an official go/no go progress assessment within 15 months. Followed by an additional contract for the remaining 2,5 years assuming everything goes well and performance requirements are met.

Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2770 per month in the first year to € 3539 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance, and a monthly work costs contribution. Flexible work schedules can be arranged. 

For international applicants, TU Delft has the Coming to Delft Service . This service provides information for new international employees to help you prepare the relocation and to settle in the Netherlands. The Coming to Delft Service offers a Dual Career Programme  for partners and they organise events to expand your (social) network.

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context.

At TU Delft we embrace diversity as one of our core values  and we actively engage  to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration.

Challenge. Change. Impact!

With more than 1,100 employees, including 150 pioneering principal investigators, as well as a population of about 3,600 passionate students, the Faculty of Applied Sciences is an inspiring scientific ecosystem. Focusing on key enabling technologies, such as quantum- and nanotechnology, photonics, biotechnology, synthetic biology and materials for energy storage and conversion, our faculty aims to provide solutions to important problems of the 21st century. To that end, we educate innovative students in broad Bachelor’s and specialist Master’s programmes with a strong research component. Our scientists conduct ground-breaking fundamental and applied research in the fields of Life and Health Science & Technology, Nanoscience, Chemical Engineering, Radiation Science & Technology, and Engineering Physics. We are also training the next generation of high school teachers.

Click here  to go to the website of the Faculty of Applied Sciences.

For more information regarding this vacancy, you’re welcome to contact Nikolina Sostaric ([email protected] ). 

Are you interested in this vacancy? Please apply no later than 3 March 2024 via the application button and upload:

• Curriculum vitae.
• Motivation letter, detailing why you wish to pursue a PhD and why you are suited for this position.
• Transcripts of BSc and MSc courses.

Please note:

• A pre-employment screening can be part of the selection procedure.
• You can apply online. We will not process applications sent by email and/or post.
• Please do not contact us for unsolicited services.