Doctoral student in theoretical physics with a focus on computational biology - Hiring in process/Finished, not possible to apply

PhD position for developing computational modelling in systems biology along with machine learning methods with applications in precision medicine. 

Work duties

The PhD candidate will work on interdisciplinary projects aiming to develop machine learning models for medical decision support along with systems biology frameworks for controlling cell fate decisions. The work will be conducted in close collaboration with several experimental partners.

The systems biology projects will involve single cell RNA-seq data analysis along with the development and application of computational models for gene regulatory networks that control cell fate decisions.The aim is to make model predictions that lead to improved cell reprogramming to various types of brain cells and induced pluripotent stem cells.The computational models are multi-level and multi-scale and include different levels of cell regulation both in individual cells and in cell populations.

The PhD candidate will also work on interdisciplinary project where machine learning and hyperspectral imaging are combined for obtaining personalized skin tumor classification and delineation. The aim is to achieve in vivo, automatic, accurate predictions of 3D tumor borders.  The candidate will develop machine learning techniques including deep models and active contours algorithms combined with image segmentation algorithms to predict the actual size and type of the tumor from different types of imaging data.

The research will be carried out within Computational Biology and Biological Physics (CBBP) and the supervisor will be Victor Olariu Ahnell.

The main duties of doctoral students are to devote themselves to their research studies which includes participating in research projects and third cycle courses. The work duties will also involve teaching and other departmental duties (no more than 20%).

Admission requirements

A person meets the general admission requirements for third-cycle courses and study programmes if the applicant:

• has been awarded a second-cycle qualification, or
• has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second cycle, or
• has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

A person meets the specific admission requirements for third cycle studies in computational science if the applicant has:

• completed an education at basic level in physics, biomedical subjects, chemistry, mathematics, control engineering or computer science, and in addition at least 60 higher education credits at advanced level in bioinformatics, computational biology, computer programming or closely related fields, i.e., a total of at least four years of higher education (240 higher education credits).

Additional requirements:

• Very good oral and written proficiency in English.
• Excellent programming skills.

Assessment criteria

Selection for third-cycle studies is based on the student’s potential to profit from such studies. The assessment of potential is made primarily on the basis of academic results from the first and second cycle. Special attention is paid to the following:

1. Great interest in systems biology and good knowledge of algorithm development and programming is required. Previous experience in collaborating with experimental groups, single cell RNA-seq data analysis and development of computational models based on experimental data is an advantage.
2. Experience in developing machine learning methods along with experience in classification applications is also an advantage.
3. The candidate should have experience in successfully working independently and in a team.
4. The candidate should have excellent written and oral communication skills.
5. Capability of developing computational models from scratch.
6. Basic cell biology knowledge.
7. Experience from interdisciplinary research is an advantage. Capability to communicate both with wet lab researchers and surgeons is important.

Consideration will also be given to good collaborative skills, drive and independence, and how the applicant, through his or her experience and skills, is deemed to have the abilities necessary for successfully completing the third cycle programme.

Terms of employment
Only those admitted to third cycle studies may be appointed to a doctoral studentship. Doctoral studentships are regulated in the Higher Education Ordinance (1993:100), chapter 5, 1-7 §§.

Instructions on how to apply

Applications shall be written in English and include a cover letter stating the reasons why you are interested in the position and in what way the research project corresponds to your interests and educational background. The application must also contain a CV, degree certificate or equivalent, and other documents you wish to be considered (grade transcripts, contact information for your references, letters of recommendation, etc.).