PhD Scholarship in Deep Generative Models for Single-Cell Sequencing Analysis - DTU Compute

Are you passionate about cutting-edge deep learning, generative models and bioinformatics? This fully funded PhD position offers a unique opportunity to work at the forefront these fields, directly contributing to advancements in single-cell sequencing analysis. You will gain access to world-class research environments, cutting-edge deep learning techniques, and collaborate with leading experts. This is an excellent opportunity to develop your career as a scientist while breaking new ground in applying AI to unlock critical insights into human health and disease.

The position is based at DTU Compute and is supervised by Jes Frellsen, with co-supervision by Kristoffer Vitting-Seerup from DTU Health Tech.

Responsibilities and qualifications
The PhD position focuses on developing deep generative models to advance the analysis of single-cell RNA sequencing data. The goal is to apply advanced techniques, including latent variable models, transformers, and foundational models, to uncover new insights into cell-type specific variations and isoform-level details that play crucial roles in diseases such as Alzheimer’s and ulcerative colitis. You will collaborate closely with experts in generative modeling and bioinformatics and be part of a dynamic, interdisciplinary research environment.

Your primary tasks will include:

• Developing and implementing deep generative models, including latent variable models, transformer-based architectures, and foundational models for single-cell RNA sequencing data.
• Conducting research to enhance the understanding of single-cell expression profiles
• Collaborating with interdisciplinary teams in computational biology and bioinformatics
• Publishing research findings in leading scientific journals and conferences
• Presenting project updates and findings at national and international events

The ideal candidate should have a strong background in machine learning, particularly deep generative models, and experience in handling large biological datasets. A master’s degree in computer science, bioinformatics, computational biology, or a related field is required. Proficiency in programming (Python preferred) and experience with deep learning frameworks such as PyTorch, TensorFlow, or Jax are essential. Excellent command of the English language, both written and spoken, is also required.

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. 

Assessment
The assessment of the applicants will be made by Jes Frellsen (DTU Compute) and Kristoffer Vitting-Seerup (DTU Health Tech). 

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 1st of January 2025 (or according to mutual agreement). 

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Associate Professor Jes Frellsen (DTU Compute, jefr@dtu.dk) and Associate Professor Kristoffer Vitting-Seerup (DTU Health Tech, krivi@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 9 November 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)
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Curriculum vitae (including GPA for both BSc and MSc)
• Two letters of recommendation (mandatory)
• An example of a technical text you have written in English (e.g., your MSc thesis, a course project, a consulting report or a scientific article)

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.

DTU Compute
DTU Compute is a unique and internationally recognized academic department with 385 employees and 11 research sections spanning the science disciplines mathematics, statistics, computer science, and engineering. We conduct research, teaching and innovation of high international standard – producing new knowledge and technology-based solutions to societal challenges. We have a long-term involvement in applied and interdisciplinary research, big data and data science, artificial intelligence (AI), internet of things (IoT), smart and secure societies, smart manufacturing, and life science. At DTU Compute we believe in a diverse workplace with a flexible work-life balance.

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.