Postdoctoral studies in bioinformatics, focusing on molecular sub-phenotyping of obstructive lung diseases including post-COVID and COPD (scholarship)

Do you want to contribute to top quality medical research?

We have an opening for 1-2 post-doctoral researcher in bioinformatics to join a multidisciplinary systems medicine team investigating the molecular mechanisms of obstructive lung diseases, particularly preterm birth related lung disease (PRLD), post-COVID related chronic lung disease, and COPD in never-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.

Duties

In this position, you will play a leading role in our the data analysis segments of our multi-omics studies to investigate various sub-phenotypes of obstructive lung disease. 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. The opportunity to develop Digital Twin projects are also open to candidates with interest in this area. 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.

A main focus of the position will be on our  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 longitudinal home monitoring, home spirometry, as well as sampling from the lung. 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.

Entry requirements

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.

Postdoctoral scholarships may be established for foreign researchers who pursue their postdoctoral research in Sweden. Persons who are resident in Sweden and/or have carried out all or part of their academic education at KI or some other educational institution in Sweden cannot be considered for scholarships from KI. The purpose of scholarships for postdoctoral qualification is to promote internationalization and contribute to research qualification after a doctorate or equivalent.

A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four year period following the receipt of a doctoral degree or equivalent.

To be eligible for a postdoctoral scholarship, the person must have obtained a doctorate or a foreign degree deemed to be equivalent to a doctorate. Applicants who have not completed a doctorate at the end of the application period may also apply, provided that all requirements for a completed degree are met before the (intended) start date of the post doctoral education.

Expertise in the above highlighted research fields, as well as demonstrated collaborative skills will be the primary basis for the assessment.

The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish doctorate or higher.

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. Here, we conduct innovative medical research and provide the largest range of biomedical 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. Students and employees have free access to our modern gym facilities with trained staff on site.

Research environment

The post-doctoral researchers will be part of the Pulmonomics research group (www.pulmonomics.net), led by Associate professor Åsa Wheelock . The Pulmonomics group is a multidisciplinary research group, located at the Center for Molecular Medicine (CMM). As part of both the Division of Immunology and Respiratory Medicine, Dept of Medicine Solna and the Karolinska University hospital Dept of Allergy and Respiratory Medicine, we are well positioned to perform truly translational work. 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 of proteomics, multivariate modeling and data integration. Candidates with an interest in Innovation are encouraged to pursue this avenue through our link to the business incubator Uppsala Innovation Center.  

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 https://www.linkedin.com/in/asa-wheelock/

Type of scholarship

The amount is tax free and it is set for twelve months at a time, paid out on a six months basis. In exceptional cases, shorter periods may be acceptable.

Application process

An application must contain the following documents in English: Cover Letter, Curriculum vitae including full publication list and short description of Research Visions & Experience (Max 2 pages) along with contact information of 3 references.

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

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