If you are curious and proactive scientist with expertise and interest in computational biology and data science, and you are looking to make a difference working on projects that will have impact on world level challenges, this PhD position is for you! The project is supervised by Alberto Santos Delgado at the Technical University of Denmark part (DTU) and co-supervised by Prof. Julios Saez-Rodriguez at the European Bioinformatics Institute (EBI) as part of ProtAIomics, a Horizon Europe MSCA Doctoral Network (https://www.protaiomics.eu/ ). In this project, we will design a federated knowledge graph framework that facilitates the querying, consolidation, analysis, and interpretation of distributed proteomics-focused clinical knowledge graphs. To achieve this, we will employ machine learning techniques to develop local graph representation models, which will be aggregated globally to enhance their predictive power and translational relevance, all while maintaining strict data privacy standards.
As part of the ProtAIomics MSCA Doctoral Network, you will collaborate with top proteomics research scientist and participate in multiple trainings and summer schools. At DTU you will work in an international, motivating, flexible, supportive, and friendly environment at a leading research and education institution in Europe.
About the Multi-omics Network Analytics Group
The Multi-omics Network Analytics (https://multiomics-analytics-group.github.io/
) aims to getting a holistic view of biological systems and their context to understand their complexity and provide new insights and applications that can benefit human and environmental health. We focus on Multimodal Data, processing and analyzing diverse types such as mass spectrometry (proteomics, metabolomics) and metaomics (metagenomics, metatranscriptomics, metaproteomics), tackling complex biological problems.
A key component is integrating and interpreting multi-omics data using graphs and developing machine learning tools. We apply these technologies to explore and understand complex biological problems spanning human and environmental health.
Further, we’re strong advocates of open science, adhering to open principles for our generated data, training, and software, aiming to reduce inequality and promote accessibility by democratizing data science.
Research and Development Opportunities
You will get the opportunity to learn and apply the latest machine learning algorithms/data science methods for clinical proteomics data. Further, during the enrollment process, you will define together with your supervisors (main and co-supervisor) additional relevant courses from the domains covered in the project (30 ECTS points of relevant PhD courses as required in Danish PhD programs). These courses will ensure that you become a bilingual scientist with deep knowledge in data science as well as biology, proteomics, computation, etc. We anticipate that by working with us, you will foster some of the following skills:
Development and application of state-of-the-art machine learning and deep learning on clinical problems
Responsibilities and qualifications
As a PhD student embarking on a three-year journey in proteomics-focused data science and machine learning, you will learn leadership, project management, mentoring, and scientific communication. Here's a snapshot of the key responsibilities you will hold:
Requirements:
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. Furthermore, the PhD salary will be based on the Marie S. Curie compensation scheme conditions and according to the grant agreement. The period of employment is 3 years. Based on seniority the candidate will receive a minimum of DKK 29.701,83 (base salary) and 1551,00 (PhD supplement). In addition, DTU will also pay pension consisting of 18,07%. Finally, it is possible to apply for family allowance
You can read more about career paths at DTU here http://www.dtu.dk/english/about/job-and-career/working-at-dtu/career-paths.
Further information
If you have any questions, you are very welcome to contact Alberto Santos at albsad@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)
through the DTU system. Additionally, to be eligible, you must also submit your application via the ProtAIomics portal https://www.protaiomics.eu/call-for-applicants/
, following the application instructions provided.
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:
You may apply prior to obtaining your master's degree but cannot begin before having received it.
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.
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.