Bioinformatician

Published: 2021-02-04

The deadline for applying to this position has passed.

Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 45,000 students, more than 7,000 employees and a turnover of around SEK 7 billion.

The Department of Medical Sciences is a large clinical institution with more than 250 employees and over 300 additional coworkers connected via the Uppsala University Hospital. The Department of Medical Sciences has a broad research profile with strong research groups in a number of different areas. The research carried out at the department is performed in close connection with the clinical activities at the Uppsala University Hospital, which includes both basic studies on the causes of a variety of illnesses and the development and evaluation of improved diagnostics and new treatment methods. More information about the Department of Medical Sciences can be found at www.medsci.uu.se.

The research group Molecular Epidemiology at the Department of Medical Sciences, Uppsala University is led by Professor Tove Fall. The group integrates information from large population studies with modern molecular measurement methods and epidemiological methods to study how chronic diseases such as diabetes and heart disease covary with genetic variation, circulating biomarkers such as proteins or metabolites, or phenotype or organ function that can be estimated using imaging diagnostic methods such as ultrasound or MRI. Different lifestyle traits are also studied in the group. In our research, we leverage power provided by combining data from several different sources, including data registries and cohort studies that include analyses of their DNA, circulating proteins and metabolites. Furthermore, we research the association of intestinal microbiota with non-communicable diseases, and more recently we are investigating transmission of SARS-Cov-2 and the relationship between symptoms of COVID-19 and chronic diseases.

Additional information about the Molecular epidemiology/Fall research group can be found via: https://www.medsci.uu.se/research/molecular-epidemiology/

Project description: SCAPIS - Swedish CArdioPulmonary bioImage Study is a unique Swedish research project within the field of cardiac, vascular and pulmonary disease with 31,100 participants between the ages of 50 and 64 years old. The study is a collaboration among University of Gothenburg, Lund University, Linköping University, Uppsala University, Umeå University, and Karolinska Institutet, that together with university hospitals in the respective locations, recruit and conduct the examinations. The study results in a database where common diseases such as cardiovascular disease and chronic obstructive pulmonary disease (COPD) can be studied. By conducting research within the framework of SCAPIS, it will be possible to better understand disease mechanisms and improve preventive measures and treatment methods.

One of our studies, "Genetic investigation of image-based measurements of cardiovascular and lung disease risk factors in a large Swedish cohort" aims to identify genetic variants associated with imaging-based measurements of cardiovascular disease risk factors. The risk factors are measured with imaging techniques (computed tomography, magnetic resonance imaging (MRI), and ultrasound measurements). By identifying the genetic variation that is linked to early stages of heart and lung disease and their risk factors, we intend to better understand the underlying mechanisms of these diseases.

By extracting DNA from about 31,000 samples and genotyping a large number of single-nucleotide polymorphisms (SNPs) across the genome, we can analyze which variations are linked to the phenotypes (atherosclerosis, fat deposits in muscles and abdominal cavity, liver fat and emphysema) that we are interested in by performing a genome-wide association study.

We will then investigate how these SNPs are linked to other diseases and risk factors measured in SCAPIS and in other studies by re-analyzing publicly available results. In this way, we can better understand the consequences of the risk factors we study, using Mendelian randomization.

We seek a highly motivated, detail-oriented bioinformatician with an interest in epidemiology and genetics. The candidate will during 2021-2022 perform quality control of genotyping data and imputation, data management, and statistical analyses. Tasks in other research projects with different types of data will also be included.

Duties description:

• Be primarily responsible for the bioinformatics challenges of the group
• Manage permissions and folder structures in server systems
• Develop software (Shell scripts, R scripts, etc) connected to bioinformatics tasks in a UNIX/Linux environment
• Handle large complex datasets and computationally intensive programs on remote servers, using a queue management system
• Validate, filter and prepare genetic data for subsequent in-silico analysis
• Carry out imputation of genotype datasets using state-of-the-art software tools
• Keep detailed documentation of performed analysis and data management steps
• Communicate methods and results to the members of the group and other scientists
• Contribute to the manuscripts of the group with the bioinformatics part
• Support the research group with general bioinformatics expertise

Qualifications:

• Master's degree in bioinformatics, scientific programming, epidemiology or another relevant subject area
• Extensive documented experience with bioinformatics, preferably with genetic data
• Work experience in a Linux/UNIX server environment, including scripting languages (Bash, R, or similar)
• Excellent ability to work independently and collaborate in an international group
• Experience of working methodically and structured
• Keen interest in documenting developed tools, methods and results carefully
• Excellent ability to communicate in speech and writing in English

Additional Qualifications:

• PhD in a relevant subject area
• Experience of working with genotype data, including validation of such data
• Hands-on experience in performing imputation of (human) genotypic data
• Practical knowledge in medical statistics and of statistical programming, preferably in R
• Authorship in high-quality peer-reviewed scientific publications
• Experience with epidemiological research
• Programming skills in html and/or Java Script
• Knowledge of one or more of the following software tools: PLINK, SNPTEST, IMPUTE2, MiniMac, SLURM workload management system

Application: The application, preferably written in English, includes:

• Letter of interest describing yourself, your research interests and your motivation to apply for the position of bioinformatician (max 2 pages)
• Curriculum vitae Publication list
• Copy of your Master’s degree certificate, course grades and Master thesis or other relevant publication
• Names and contact information for two reference persons.

Salary: Individual pay.

Starting date: As soon as possible.

Type of employment: Permanent employment with 6 months trial period.

Scope of employment: 100 %.

For further information about the position please contact: Tove Fall, tove.fall@medsci.uu.se

Please submit your application by February 25, 2021, UFV-PA 2021/390.

Please do not send offers of recruitment or advertising services.

Submit your application through Uppsala University's recruitment system.