PhD Position in AI-Guided Degradomics and Protease Systems Biology - DTU Bioengineering

Are you motivated by the potential of proteomics and AI to uncover hidden biology? Do you want to map the dark extracellular matrix proteome and degradome and reveal novel mechanisms of tissue repair? Join a collaborative PhD project at DTU Bioengineering focused on AI-guided degradomics and protease systems biology.

About the position
Extracellular proteases are critical regulators of extracellular matrix (ECM) remodelling during wound healing. Yet, many proteolytic processes remain uncharacterized due to the complexity of the ECM and limitations in current detection strategies. Advances in mass spectrometry and machine learning now allow us to unravel this “dark proteome.” This position aims to use state-of-the-art AI-guided proteomics and systems biology approaches to map protease activity in pathological and regenerative wound healing scenarios.

The PhD project is part of the Marie Skłodowska-Curie Action Doctoral Network REMOD-HEALING, which aims to target extracellular matrix remodelling in cutaneous wounds to promote better healing. Using state-of-the-art mass spectrometry and machine learning, this project will unravel proteolytic networks that drive pathological and regenerative wound healing. Under the supervision of Asst. Prof. Konstantinos Kalogeropoulos and Assoc. Prof. Erwin Schoof, the PhD candidate will join the Protease Systems Biology group embedded in the Cell Diversity Lab at DTU Bioengineering — a vibrant, multidisciplinary team working at the interface of proteomics, computational biology, and translational research.

Responsibilities and qualifications
You must be well organized, structured, self-driven, and enjoy interacting and collaborating with colleagues, including PhD students and postdocs. You are also expected to take part in the supervision of BSc and MSc students.

In The Project You Will:

• Perform longitudinal proteomic and degradomic analyses of wound healing models and clinical samples.
• Identify proteolytic cleavage sites and post-translational modifications using high-resolution mass spectrometry and AI-based de novo peptide sequencing.
• Develop and apply machine learning models to predict protease activity and substrate specificity, integrating protein language models and structural data.
• Build systems biology frameworks to characterize time-resolved protease network activity during tissue repair.
• Validate identified biomarkers through targeted proteomics assays.
• Publish results in high-impact journals and present findings at scientific conferences.
• Engage in interdisciplinary training to build expertise in both computational and experimental approaches.

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 in a relevant field, such as bioinformatics, biochemistry, molecular biology, biotechnology, or a related discipline. Applicants should not have resided or carried out their main activity (work, studies, etc.) in the country of the host institution for more than 12 months in the 36 months prior to their recruitment date. 

You Must Have:

• A Master’s degree (or equivalent) in Bioinformatics, Biochemistry, Biotechnology, Chemical Engineering, or a closely related field.
• Expertise in either computational biology (e.g., bioinformatics, machine learning) or experimental proteomics, with a strong willingness to learn the complementary skill set.
• Experience in collaborative research environments.
• Excellent communication and teamwork skills.
• A proactive attitude towards learning and applying new skills.

It would further be beneficial if you have some of the following skills:

• Hands-on experience with proteomics workflows and mass spectrometry-based data analysis.
• Basic knowledge of protein biochemistry and enzymology.
• Familiarity with machine learning frameworks (e.g., PyTorch, TensorFlow) and protein language models.
• Experience with programming (Python preferred) for bioinformatics or data science applications.
• Exposure to degradomics methods or post-translational modification analysis.
• Strong analytical skills and demonstrated ability to work effectively in a collaborative, interdisciplinary research environment.

About the REMOD-HEALING Doctoral Network
The Marie Sklodowska-Curie Action Doctoral Network (MSCA-DN) REMOD-HEALING: “Targeting Extracellular Matrix Remodelling in Cutaneous Wounds to Promote Better Healing” Call for applications for 12 Doctoral (PhD) Training Positions in biochemistry, structural biology, proteomics, novel detection and screening methods and pre-clinical models for wound healing and regenerative medicine applications. You can soon read more about the call, and all positions offered on the REMOD-HEALING website (remod-healing.eu).                                                        

REMOD-HEALING is a research network of leading European and Latin American scientists from academia and industry, who want to tackle the burden of pathological wounds by exploiting therapeutic targets and biomarkers associated with extracellular matrix remodelling in cutaneous wounds. Through its research and training activities, the REMOD-HEALING project will contribute to scientific advancement and innovation in wound healing and regenerative medicine through a coordinated, interdisciplinary effort, ultimately leading to societal and economic benefits. 

Participating in REMOD-HEALING offers doctoral candidates many unique opportunities, including: 

• A 36-month project as Marie Skłodowska Curie trainee in one of the participating institutions with the objective of receiving a doctoral degree (PhD). 
• State-of-the art, exciting research in an international consortium with highly integrated research projects. 
• Expert training in basic and applied research, along with a thorough understanding of the process involved in transitioning from basic to pre-clinical research.
• Research training periods in another consortium member's lab lasting from a few weeks up to three months, performed in a different EU country than the country where most of the project will take place. 
• Training in both academic and industrial research environments.
• Application Process 
• REMOD-HEALING will select Doctoral Candidates in a two-step recruitment process. 

The selection procedure will be open, transparent, and merit-based, fully aligned with the Code of Conduct for the Recruitment of Researchers. The selection will be based on the quality of applications and gender balance will also be considered. The closing date for applications is 30th November 2025.

Applicants are advised to familiarize themselves thoroughly with the projects, for which they apply and be ready to answer questions on their chosen topics. The designated project supervisor(s) will review all applications as soon as possible after the application deadline with respect to the candidates’ suitability. As soon as a decision is made, we will notify candidates. If candidates are still eligible after the pre-selection, they will be informed about the possible next step(s) in the selection procedure, including a 6-minute recorded presentation describing why you applied for the project, and how your skills and experience relate to it. The most promising candidates will then be invited to an online interview with members of the REMOD-HEALING Consortium selection committee.

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. Our group is a leader in degradomics, computational proteomics, and protease systems biology, developing advanced technologies to investigate protease activity and regulation. We work with both clinical and preclinical model samples to decipher proteolytic mechanisms underlying wound healing and inflammation.

Salary and appointment terms
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 period of employment is 3 years.

You can read more about career paths at DTU here.

Further Information

Further information may be obtained from Asst. Prof. Konstantinos Kalogeropoulos (konka@dtu.dk).

You can read more about DTU Bioengineering at www.bioengineering.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. 

• Application procedure 
• Your complete online application must be submitted no later than 30 November 2025 (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:

• A letter of motivation which explains the interest in the position and emphasizes the candidate’s strengths regarding the project and its requirements (cover letter, max 2 pages)
• Curriculum vitae (max 2 pages)
• Grade transcripts and MSc diploma (in English) including official description of grading scale
• Two letters of recommendation from relevant and appropriate referees or the names and contact details of two Referees (as former Supervisors/PIs).

You may apply prior to ob­tai­ning your master's degree but cannot begin before having received it. If the degree has not been awarded by the application closing date, the candidate should submit a declaration signed by their supervisor or University official stating that the degree will be obtained by the time of PhD enrolment. 

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. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

The Department of Biotechnology and Biomedicine (DTU Bioengineering) is an international leader in the areas of biotechnology and biomedicine. Our engineering approach to all aspects of biotechnology and biomedicine positions us as a valuable player with unique competences in a growing bio-based economy and with health systems transforming towards personalized medicine. We have a clear focus on the needs in life science- and biotech industries and point towards innovation, new businesses, and scientific services for the benefit of society. The department has extensive collaborations with national and international research units and industry. DTU Bioengineering has approx. 400 employees, of which 2/3 are scientific staff. The department is located at DTU Lyngby Campus.

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.