PhD scholarship in developing novel single-cell proteomics sample preparation techniques - DTU Bioengineering

If you are establishing your career as scientist and are looking for a solid foundation to fulfill your dreams and ambitions in the context of single-cell biology, it is right here in front of you. At DTU Bioengineering, you will break new ground at the absolute forefront of single-cell proteomics by Mass Spectrometry (scp-MS) and other single-cell technologies and use your skills to answer fundamental clinical questions and develop the next generation experimental and computational workflows

Our mission
Our mission in the Cell Diversity Lab  is to unravel fundamental biological concepts  controlling heterogeneity within complex biological systems, especially those of the blood system and cancer. Our aim is to use our leading position in the scp-MS field to identify druggable signalling mechanisms  that will advance therapy and diagnostics for patients suffering from complex diseases. By computationally integrating several experimental approaches such as Mass Spectrometry (MS), Next-Generation Sequencing, FACS sorting and in vivo models, we aim to gain a better understanding of cellular signal processing at the single cell level. The ultimate ambition is to translate the molecular insights derived from a range of modalities (DNA, mRNA and proteins) to in-depth knowledge about how cellular heterogeneity contributes to disease phenotypes and ultimately, development of effective and personalized therapeutic strategies.

The Project
The PhD project, which is fully funded, is part of the department’s major long-term strategy to a combine experimental and computational approaches to establish scp-MS as a routine tool for deciphering cell heterogeneity in complex biological systems. The project is primarily focused on developing novel sample preparation methods, including enrichment of Post-Translational Modifications, for conducting high-throughput scp-MS experiments.

Responsibilities and qualifications
Your primary tasks will be to:

• Use a range of mass spectrometry data acquisition strategies to explore their application in low-input proteomics all the way down to single cells
• Use low-volume liquid handling approaches to develop next-generation scp-MS sample preparation workflows that can be combined with PTM-enrichment 
• Explore novel chromatography approaches to enhance sensitivity for scp-MS

You will also be involved in the:

• Teaching and supervision of BSc and MSc student projects, and co-supervision of fellow PhD students and postdocs
• Writing of manuscripts, dissemination of results at international symposia and networking with collaborators around the world
• General operation of MS instruments and inherent data handling.

Relevant reading: 

https://www.nature.com/articles/s41467-021-23667-y

https://www.sciencedirect.com/science/article/pii/S1535947622000275?via%3Dihub

https://www.nature.com/articles/s41467-023-41602-1

https://www.biorxiv.org/content/10.1101/2024.07.31.605978v1

You hold 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. Relevant subject areas are biochemistry, biomedicine, medicinal chemistry, molecular biology, immunology or related subjects. You should be curious, ambitious, organized, highly motivated and a team player, and are expected to have a strong interest in fundamental scientific discoveries and elevating their translational potential.

You are expected to have:

• Advanced understanding of Mass Spectrometry-based proteomics workflows 
• Track record in single-cell proteomics method development
• Hands-on experience with LC-MS 
• Hands-on experience with mammalian cell culture techniques
• Experience with automated, low volume liquid handling and cell sorting equipment (e.g. CellenOne)
• Fundamental knowledge about FACS and other cell isolation / analysis techniques
• Sufficient level of computational / bioinformatics analysis of proteomics datasets with R and python
• Good communication skills, with an excellent command of English (written and spoken)

Experience with any of the following is desirable, but not essential

• Single-cell molecular approaches such as sc-RNAseq
• Machine learning, Python and R
• Immunology and Cancer biology
• FACS sorting and analysis

Approval and Enrolment  
The scholarship for the PhD degree is subject to academic approval, and you 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 . 

Assessment
The assessment of the applicants will be made by Associate Professor Erwin M. Schoof together with relevant project partners.

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. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

Starting date is January 15th, 2025.

You can read more about career paths at DTU here .

Further information  
Further information may be obtained from Associate Professor Erwin Schoof at DTU Bioengineering.

He can be contacted at [email protected] , or via Twitter/X @erwinschoof 

You can read more about DTU Bioengineering at https://www.bioengineering.dtu.dk/english  and the Cell Diversity Lab at https://www.bioengineering.dtu.dk/research/research-sections/section-for-protein-science-and-biotherapeutics/cell-diversity-lab

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 17 September 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 online", 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
• List of publications (if any)
• Grade transcripts and BSc/MSc diploma including official description of grading scale
• Names and contact details for two professional references

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, race, disability, religion or ethnic background are encouraged to apply.

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 the 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.