Studies in Bioinformatics/Computer science (scholarship, Undergraduate and graduate level education)

We have an opening for 1-2 master students wishing to join a multidisciplinary systems medicine project investigating the clinical and molecular basis for post-acute sequele of COVID-19 (PASC), or post-COVID) with focus on lung involvement. The successful candidate will be joining a large research team of clinicians, experimental scientists, statisticians and bioinformaticians to investigate post-COVID using eHealth tools in combination with molecular phenotyping.

In this research project you will assist in developing a literature integration- and mining tool designed to aid researchers, clinicians, epidemiologists, policy makers, and others in need of daily updates of the latest trends and findings in the COVID field. The project may be expanded to other research areas within the field of obstructive lung diseases.

Entry requirements

bioinformatics, or related field who is interested in gaining some hands-on experience in performing medical research, and potentially interested in performing a doctoral education down the line. We are a multidisciplinary team, and the ability to work in a team, and communicate your work also to non-computer scientists is an essential skill to be effective in your work.

Required experience

• Experience in processing, managing, and integrating biological datasets, especially in scraping and organizing data (both XML and JSON form) from NCBI's APIs with Python scripts.
• Proficiency with Python and data analysis and visualization packages (graph database Neo4j), and databases (SQL, MYSQL, etc)
• Familiarity with Web Development. Good Experience in full-stack web development with Flask and Vue.js (such as Vuex and Vue Router). Proficiency with programming languages such as HTML, CSS, and JavaScript. Have good knowledge of UX design and data visualization with JavaScript.

Preferred experience

• Extensive experience with Git and Linux environments.
• Familiarity with high-performance computing environments and cloud services/management systems (Docker and AWS)
• Good command of bioinformatics, statistics and machine learning

A scholarship on undergraduate and graduate level education aim to provide undergraduate or advanced level students early practical experience of research work to strengthen the link between education and research and encourage future studies at the doctoral level.
The scholarships can either be given for studies within an existing course, or for a shorter period of practice research experience (documented by an individual study plan / research plan) for admitted students at undergraduate or advanced level.

The scholarships may only be awarded to:

• persons admitted (and registered in Ladok) to undergraduate education or advanced level at KI,
• persons admitted (and registered) to basic education, or advanced level at a university with which KI collaborates.

The scholarships may be established for a maximum of 12 months, divided into a maximum of four courses / periods.

The student will be part of the Pulmonomics research group (www.pulmonomics.net ), led by Associate professor Åsa Wheelock at the Respiratory Medicine Unit, Center for Molecular Medicine and Department of Medicine, Solna. Our research interests can be broadly defined as developing a respiratory systems medicine framework for molecular sub-phenotyping of chronic inflammatory diseases of the lung. We focus equal efforts on translational studies of the response to environmental exposures in patient cohorts, and innovation & methodology development in the fields of 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.

The amount is tax free and can be established for a maximum of twelve months.

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

• A complete curriculum vitae
• Cover letter.
• Certificate of registration

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.

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