PhD scholarships in single-cell multi-omics - DTU Biosustain

The Novo Nordisk Foundation for Biosustainability (DTU Biosustain) at the Technical University of Denmark is seeking highly motivated PhD candidates with an interest in deep learning and bioinformatics approaches for cutting-edge single-cell technologies with applications in complex diseases. If your areas of interest and competence are genomic big data science and machine learning/deep leaning framework development, and you are looking to gain experience while working on projects that will make an impact on the world, this is your chance. All code that you will develop will have a permissive open-source license (e.g., MIT), hosted on GitHub, and will be promoted at the international level via publications and conferences.  Through this, you will get the opportunity to utilize everything you know and help break new ground at the very forefront of what is possible. 

Computational integration of Single-Cell Genomic, spatial and Metabolic Data: Methods and Applications
Single-cell technologies in genomics and metabolism offer insights into biological systems, aiding in fields like oncology and mycology. However, integrating single-cell genomic, spatial and metabolic data is complex due to the volume, sparsity and diversity of the data. Current methods focus on multi-omics data integration. However, techniques either lose key biological information or are not scalable for large-scale analyses. 

The project aims to develop a computational platform for integrating single-cell genomic, spatial and metabolic data, focusing on:

• Graph Neural Network Development: To merge single-cell data types at the genomic level, creating shared representations and capturing interrelations.
• Integrative Model for Genomic and Metabolic Data: This model considers metabolic states within a multi-omics cellular system, integrating with genome-scale metabolic models for accurate predictions.
• Method Validation: Applying the developed method to real-world scenarios, such as fungal product exploration and cancer progression, to evaluate its effectiveness

The integration of single-cell genomic and metabolic data holds immense potential for accelerating scientific discoveries. In oncology, it could lead to the identification of novel therapeutic targets and a better understanding of cancer heterogeneity. 

Your role will primarily be to perform computational modelling, write scientific publications, as well as take 30 ECTS points of relevant PhD courses as required in Danish PhD programs.

Competencies of the ideal candidate
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.

We also ask that you are motivated by working in an international environment with colleagues and partners from all over the world. Added to this, the CV of the ideal candidate comprises: 

• Experience programming in Python
• Workflow/pipeline development and management
• Prototyping in Jupyter notebooks
• Familiarity in deep learning frameworks like pytorch
• Motivation for large-scale genomic data analysis/joining our lab
• A degree in biology/computer science/data science/computational biology/bioinformatics or related
• Ability to work independently and as part of a team. 
• Ability to successfully work on multiple concurrent projects and meet deadlines.
• Knowledge of genomic problems, data types for humans and complex diseases

You can look forward to being part of a leading research and education institution in Europe where on-going development of skills and knowledge is a part of the foundation. You will have great flexibility, as trust and respect are some of the values we build our results on. You will be supervised professionally/have your strong mentoring attention to ensure your professional training.

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 terms of employment
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 three years.

You can read more about career paths at DTU here .

Further information
If you would like additional information about the position, please contact Shilpa Garg at [email protected] . 

You can read more about DTU Biosustain at www.biosustain.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 
Please submit your online application no later than 30 March 2024 (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 motivating the application (cover letter)
• Curriculum vitae 
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Research statement/plan
• Demonstration of coding/large-scale data analysis skills

Candidates may apply prior to obtaining their master's degree but cannot begin before having received it. 

Applications and enclosures received after the deadline will not be considered.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)
Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods.  Learn more at biosustain.dtu.dk.

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.