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

Technical University Of Denmark; Denmark; On-site; DKK 360,000 - 480,000; Full time

Job summary

BRIGHT – The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition at DTU invites applications for a PhD student position in computational modelling of protein and nutrient bioavailability of microbial foods.

The project sits within BRIGHT’s Microbial Foods initiative and aims to build a multi-modal AI/ML system to predict digestibility and bioavailability of proteins and micronutrients.

Qualifications

• 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

Responsibilities

• 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

Skills

Python programming

Machine learning

Deep learning

English proficiency

Interdisciplinary teamwork

Analytical skills

Education

MSc in bioinformatics / computational biology

Tools

PyTorch

Job description

BRIGHT – The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition

Organisation/Company Technical University Of Denmark Department BRIGHT – The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition Research Field Engineering Researcher Profile First Stage Researcher (R1) Positions PhD Positions Application Deadline 30 Nov 2026 - 23:59 (Europe/Copenhagen) Country Denmark Type of Contract Temporary Job Status Full-time Hours Per Week 37 Offer Starting Date 1 Apr 2027 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

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

Responsibilities:

• 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

Qualifications:

• 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

Preferred qualifications but not mandatory:

• 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.

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
The period of employment is 3 years. The position is full time.
The preferred starting date is 1st April 2027 (or sooner according to mutual agreement).

You can read more about career paths at DTU here.

Further information may be obtained from Carlos Acevedo-Rocha: [e-mail]
More information about BRIGHT: https://bright.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 . Furthermore, you have the option of joining our monthly free seminar "PhD relocation to Denmark and startup "Zoom" seminar" for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

BRIGHT Mission 2: Microbial Foods

BRIGHT Mission 2 aims to build an AI-powered framework for the rational design of microbial foods that meet four targets: consumer acceptance, health, sustainability and scalability. The first phase focuses on two fungal chassis, Aspergillus and Yarrowia, characterizing more than 500 prototypes through multi-omics, sensory analysis, life-cycle assessment and safety testing. Predictive models for flavor, texture, nutrition and process scale-up are trained iteratively through active learning. The scientific scope spans strain engineering, adaptive laboratory evolution, solid- and liquid-state fermentation, sensory and consumer research, and pre-clinical and clinical evaluation of safety, bioavailability and cardiometabolic health, in collaboration with national and international partners.

BRIGHT – The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition

The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition (BRIGHT) is a major initiative based at DTU that aims to accelerate the development of biosolutions and strengthen the bio-based economy. BRIGHT serves as a hub for academic and industrial partners working together to unlock the potential of bioproduction. BRIGHT focuses on three main areas: Sustainable materials (Developing bio-based alternatives to fossil-derived materials), Microbial foods (Innovating food production through microbial technologies), and Microorganisms for net-zero agriculture (Creating solutions to reduce greenhouse gas emissions in agriculture). The goal is to develop and scale innovative biosolutions within these areas, ultimately creating sustainable and competitive alternatives to fossil-based products and processes that can make significant contributions to reducing global greenhouse gas emissions.

DTU is one of Europe's leading elite technical universities. Through research and education at an international top level, we create solutions to the major societal challenges of our time and help secure Europe's global leadership in sustainable technological development. Since Hans Christian Ørsted founded DTU almost 200 years ago, our mission has remained the same: We develop and create value through the natural and technical sciences for the benefit of society. DTU has 13,800 students, 1,600 PhD students, and 6,500 employees. We work in an international environment and have an inclusive, stimulating, and informal work culture. DTU has campuses in all parts of Denmark and in Greenland and collaborates with the best universities around the world.

DTU – For the benefit of society since 1829

Number of offers available 1 Company/Institute BRIGHT – The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition, Technical University of Denmark Country Denmark State/Province Copenhagen City Copenhagen Postal Code 2800 Street Søltofts Pl. Building 220 Geofield