Staff Researcher in Cardiovascular Disease Bioinformatics

Do you want to contribute to improving human health?

Please join Dr. Björkegren´s team of world-leading bioinformaticians working across the globe in Mount Sinai Hospital in New York to Karolinska Institutet in Sweden and Tartu University Hospital in Estonian. Our main source of systems genetics analyses is the cardiovascular disease (CVD) STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study - a high-dimensional, multi-tissue genetics-of-gene/protein-expression database of >1500 patients with and without CVDs. We study the network biology within and across organs to individual cells to better understand the complex etiologies of CVDs.

Your mission

You will take on the main responsibility of STARNET data within Björkegren´s lab at Karolinska Institutet and in collaborations within the EU and elsewhere. You will not require to develop new bioinformatic tools but to use state-of-the-art methodologies for QC, normalization, correlation and differential expression analyses, protein and gene expression quantitative trait loci (QTLs), co-expression network analysis like WGCNA, directed network analysis using probabilistic and machine learning (e.g., GENIE3) analyses as well as other deep and machine learning methods for data mining and statistical pattern recognition. Examples of integrative analyses, with for instance GWAS, are colocalization, mendelian randomization and transcriptome-wide analyses (TWAS such as SMR, MetaXcan and Coloc). Other roles will include data protection, sharing and cloud storage using established cloud systems such as Amazon Cloud. You are also expected to help draft manuscripts and grants with emphasis on data illustrations and visualization.

Your profile

We are looking for an experienced person with extensive bioinformatical knowledge in the field of systems genetics - integrating DNA and RNA sequencing with proteomics and clinical information from one or more datasets (e.g., GWAS). The applicant should have substantial proficiency working in a Linux environment, as well as possess expertise in the coding languages of Python and R. Experience of working with a computing server is required.

The candidate should have been trained in computer science, bioinformatics, or computational biology during her/his Ph.D. studies. The candidate should fully master (requirement) Python (Python Data Stack tools such as NymPY, SciPY, Pandas, scikit), be proficient in R, and have solid Unix/Linux experience and statistical knowledge. Experience working with high-performance computing is an advantage. The candidate should have experience in genome-wide NGS data analysis, particularly in working with bulk-RNAseq, scRNAseq and scATACseq from FASTQ to analyze data with 10x and other formats such as SmartSeq2. Other merits include the ability to formalize biological questions into computational models to drive projects forward and provide advice on the experimental design before data generation. The candidate should be self-motivated, have good communication skills, and have a proven ability to interact effectively and work productively in an interdisciplinary team. Fluency in English is a requirement.

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. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. Karolinska Institutet is also a state university, which entitles you to several good benefits through our collective agreement. And you get to practice freely in our modern wellness facilities, where trained staff are on site.

Location: Flemingsberg

Department of Medicine (MedH) conducts graduate and post-graduate education, as well as research, within a wide range of the medical field, covering all internal medicine specialties, infectious diseases and dermatology. The department consists of seven units with a total of nearly 60 research groups. Our ambition is to be the leading department for medical research and education.

Choose to work at KI – Ten reasons why

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)

Welcome to apply at the latest 2023-08-31.

Want to make a difference? Join us and contribute to better health for all