PhD student in functional breast cancer genomics - Hiring in process/Finished, not possible to apply

The Functional breast cancer genomics research group
The technology for high-throughput sequencing has revolutionised cancer research and facilitated the identification of a large number of oncogenes and tumour suppressors. In the clinic, high-throughput sequencing is used for example in genetic testing for hereditary cancers and to identify treatment-predictive mutations. In the Functional breast cancer genomics group, we study how genetic variation and mutations control the expression of genes and proteins. We also investigate their effects on breast cancer risk and tumour biology.

At the Division of Oncology in Medicon Village several research groups study different tumour types and the research has for many years been at the forefront of cancer genomics. An active research environment with seminars, journal clubs, courses, and poster evenings is created together with the co-localised Division of Translational Cancer Genomics and Lund University Cancer Centre.

The research group, which is located in Medicon Village in Lund, is now looking for a PhD student for research education within the project "Functional synonymous variants and variants in splicing regulatory regions in breast cancer". It is a four-year, full-time position. Suggested starting date is July 1, 2023, or upon agreement.

Within the department we aim to maintain a good working environment based on mutual respect and consideration. We constantly strive to improve the conditions for work, development and participation for all employees.

Work assignments
The purpose of the project is to understand how specific types of genetic variants, which so far have not been extensively studied, impact breast cancer risk and tumour biology through effects on the transcriptome and proteome of cancer cells. This includes variants that affect mRNA splicing and synonymous variants in both familial and sporadic breast cancer.

We are looking for a well-organised and ambitious PhD student with good knowledge of bioinformatics and programming. The main task will be to conduct research studies within the subject of breast cancer. The project involves bioinformatic analyses of high-throughput sequencing data using existing and custom-made software, including analyses of genetic variation, mutations, and alternative splicing. Statistical analyses will be a substantial part of the work. Scientific writing and reading of current scientific literature are also included. The PhD student is furthermore expected to participate and present their research in research group meetings, seminars, and at international scientific conferences. Teaching may also be included in the tasks.

Qualifications
Applicants should fulfil the basic eligibility requirements for the Faculty of Medicine (https://www.medicine.lu.se/research-and-research-studies/postgraduate-research-studies/prospective-phd-students/entry-requirements) with a degree in a relevant subject for the project.

Requirements for the position:

• Undergraduate degree in bioinformatics or similar.
• Good knowledge and practical experience of programming in Python, R, and bash.
• The successful applicant should also have an excellent command of English – both oral and written.

Meriting:

• Undergraduate degree or university-level courses in mathematics and/or statistics.
• Experience of working with computer clusters and patient data (sensitive data).
• Experience of RNA and DNA sequencing data analysis.
• Experience of analysis of genetic variation and mutations in sequencing data, especially in cancer.
• Experience of analysis of alternative splicing of mRNA.

Eligibility
Students with basic eligibility for third-cycle studies are those who- have completed a second-cycle degree- have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, or- have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

The employment of doctoral students is regulated in the Swedish Code of Statues 1998: 80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

Type of employment
Limit of tenure, four years according to HF 5 kap 7§.

The Department of Clinical Sciences Lund is one of six departments at the Faculty of Medicine. Clinical Sciences Lund cooperates closely with Skåne University Hospital and the Faculty of Medicine in order to optimize the conditions for preclinical and clinical translational research, research strategies and development, as well as education on both undergraduate and postgraduate levels.