PhD scholarship in computational modelling of protein and nutrient bioavailability of microbial foods

PhD scholarship in computational modelling of protein and nutrient bioavailability of microbial foods - BRIGHT

Are you fascinated by how the food we eat shapes our microbiome and metabolic health? Excited by the prospect of determining how nutritious are microbial foods? Eager to work in a cutting-edge, interdisciplinary research environment tackling major food-system challenges? Then join us as our new PhD Student in computational modelling of protein and nutrient bioavailability of microbial foods

This position sits within BRIGHT’s Microbial Foods mission. You will help developing computational tools to predict the nutritional value of alternative proteins and nutrients. Our goal is to predict how well a protein or microbial food is digested, absorbed and assimilated in humans, so that foodstuffs can be tailored for a nutritious and sustainable diet without compromising taste and texture.

You will build the computational model at the heart of our mission, combining protein language model embeddings with nutritional composition, proteomics and metabolomics data into a multi-modal AI/ML system that predicts digestibility and bioavailability of proteins as well as the bioavailability of micronutrients and food-derived bioactives. The position is fully computational, and you will work with a talented team of scientists generating the in vitro and clinical data that will train and validate your model.

Responsibilities and qualifications

• Review the state-of-the-art in protein bioavailability, covering digestion, absorption and assimilation, with a focus on microbial foods
• Build a multi-modal AI/ML model that predicts protein digestibility and bioavailability, combining protein language model embeddings with nutritional composition data and benchmarking against DIAAS and ileal digestibility datasets
• Create and curate a database of selected microbial foods, for example, Yarrowia lipolytica and Aspergillus spp.
• Model proteolytic digestion and the absorption of peptides and amino acids and small molecules including transporter-mediated uptake
• Test and refine the model against proteomics and metabolomics data for single microbial proteins and whole microbial cells
• Retrain the model with in vitro digestion data and with clinical trial data generated by our experimental partners
• Apply the model to the computational redesign of microbial foods for improved bioavailability, and release it as an open-source tool
• Report your research results in peer-reviewed scientific publications and international conferences
• Collaborate within BRIGHT as well as our local, national and international networks
• Disseminate your results through scientific publications, public engagement and social media
• Teach and supervise MSc and BSc students

• MSc in bioinformatics, computational biology, machine learning, computer science, food science or a related area
• Advanced programming experience in Python
• Experience with machine learning, including deep learning frameworks such as PyTorch
• Excellent English proficiency in written and oral form
• Excellent communication and social skills for working within an interdisciplinary research team
• Strong analytical skills and ability to work independently

• Experience with protein language models or other sequence-based representation learning
• Familiarity with protein digestion, nutrition or food science, including metrics like DIAAS and PDCAAS
• Experience working with proteomics or metabolomics data
• Experience with data curation and building structured databases, and an interest in open-source software development

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment

The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education.

We offer

DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms

The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. Please see DTU’s salary structure for scientific staff: www.inside.dtu.dk/en/human-resources/during-employment/salary/salary-structures.