Post-doctoral researcher in bioinformatics, focusing on molecular sub-phenotyping of obstructive lung diseases including post-COVID and COPD

  • Contract
  • Sweden

Karolinska Institutet


Do you want to contribute to top quality medical research?

We have an opening for a post-doctoral researcher in bioinformatics to join a multidisciplinary systems medicine team investigating the molecular mechanisms of obstructive lung diseases, particularly long-COVID and COPD in non-smokers. The successful candidate will have a leading role in the analysis of bulk- and single cell RNA-seq data, miRNA seq data from scarce particle samples, multi-omics integration and network medicine.

Your mission

In this position, you will play a leading role in our recently launched study investigating lung involvement in post-COVID patients. As the bioinformatics lead, you will implement computational quality control and analysis pipelines for various types of omics data from clinical samples from the lung, and assist wet lab-oriented post-docs and PhD students in bioinformatics analysis and data visualization of our ongoing research projects on molecular characterization at the mRNA, miRNA, proteome and metabolome level from multiple lung compartments. Our research group has a long standing interest in integration of multi-modal data, in which you will also receive training from a senior colleague. This part of the work is expandible, with support in writing own grants and developing into an independent research group leader if the successful candidate is interested in this type of carrier path.

The main focus of the position will be on our recently launched HemCOV study, investigation clinical and molecular features of post-COVID with lung involvement. At the core of the study is our in-house developed eHealth tool for home monitoring, home spirometry, as well as sampling from the lung. You will be an essential part of the core team in this study, being involved from the start. A large proportion of our research efforts are also dedicated to our unique LUNAPRE cohort (www.clinicaltrials.gov/ct2/show/NCT02923648 ), consisting of very prematurely born individuals with or without bronchopulmonary dysplasia (BPD) in the neonatal period that have been followed since birth. The overall goals of the project involve molecular sub-phenotyping and mechanistic investigations of the obstructive lung disease in this heterogeneous, relatively unknown, and rapidly growing patient group.

The specific research projects can be adapted to the experience and interest of the successful candidate, and may include RNA-seq, miRNA-seq and proteome characterizations of various compartments including single cell- or bulk sorted immune cells and extracellular vesicles from the lung of the patient cohort, as well as from cell culture model systems. The studies are performed in close collaboration with clinicians at the Karolinska University Hospital.The successful candidate is also highly encouraged to pursue and develop his/her own research interests, within the scope of the research interests of the group.

Your profile

We are looking for a highly motivated researcher with experience of designing and deploying data management, quality control, and analysis pipelines for bulk and single-cell RNA-seq data (specifically,  on remote Linux-based computational clusters). The successful candidate will possess a good grasp of statistical analysis and complex data visualization, and knowledge of relevant bioinformatic tools. A Ph.D. in a relevant discipline (bioinformatics, biostatistics, systems medicine or omics-related field with extensive data analysis experience) is a requirement. Previous post-doctoral experience is a merit, as is experience with analysis of longitudinal time-series and fluctuation analysis. The successful candidate must have excellent communication skills in English. Demonstrated excellent communication skills and an ability to interact socially and scientifically with post docs and students in the laboratory and with collaborators in various networks are essential.

To be eligible for employment as a postdoctor a doctoral degree or a foreign degree deemed to be equivalent to a doctoral degree is required. This eligibility requirement must be fulfilled at the latest at the time of the employment decision. It is considered as an advantage if you have completed your doctoral degree within the last three years, if there are special reasons, your degree may have been completed earlier.

What do we offer?

A creative and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world’s leading medical universities. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. At KI, you get to meet researchers working with a wide range of specialisms and methods, giving you ample opportunity to exchange knowledge and experience with the various scientific fields within medicine and health. It is the crossover collaborations, which have pushed KI to where it is today, at the forefront of global research. Several of the people you meet in healthcare are educated at KI. A close relationship with the health care providers is important for creating groundbreaking top quality education and research. Karolinska Institutet is also a state university, which entitles you to several benefits through our collective agreement.

Location

The position is located within the Department of Medicine, Solna . The department consists of eleven divisions and each division consists of several research groups. The position is located within the Pulmonomics group which is a multidisciplinary research group, located at BioClinicum. As part of the Division of Respiratory Medicine, we are in integral part of the Center for Molecular Medicine (CMM), the Department of Medicine Solna as well as the Karolinska University hospital Department of Allergy and Respiratory Medicine. Our research interests can be broadly defined as developing a respiratory systems medicine framework for molecular sub-grouping of chronic inflammatory diseases of the lung. We focus equal efforts on translational studies in patient cohorts, and innovation & methodology development in the fields proteomics, multivariate modeling and data integration. Our translational systems medicine studies encompass profiling at multiple molecular levels (mRNA, miRNA, proteomes, metabolomes and lipid mediators) from multiple lung compartments (airway epithelium, alveolar macrophages, exosomes, and bronchoalveolar exudates) using a range of omics platforms, in combination with extensive clinical phenotyping. The strength of our approaches is the ability to integrate information from multiple molecular levels and anatomical locations both to improve the statistical power of detecting and defining molecularly distinct sub-groups in small patient cohorts, and to improve our understanding of disease mechanisms on a systems level.

Read more at https://staff.ki.se/people/asa-wheelock or www.pulmonomics.net

— [Video about a Karolinska Institutet, how we work towards “a better health for all”] —

Application

An employment application must contain the following documents in English or Swedish:

  • A complete resumé, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
  • A complete list of publications
  • A summary of current work (no more than one page)

The application is to be submitted through the Varbi recruitment system.

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