Bioinformatician, Cardiovascular Research - Hiring in process/Finished, not possible to apply

The Department of Clinical Sciences, Malmö, Cardiovascular Research - Translational Studies, is looking for a bioinformatician. The employment is full time and for two years. Start date as soon as possible or by arrangement.

Work duties

Applicants are invited to apply for a position as bioinformatician at the Prof Isabel Goncalves' research group. The group consists of 10 people (including nurses, biomedical scientists, fellows, postdocs and PhD students) and is a part of the LUDC where there is a growing bioinformatics unit. Due to the growing amount of data generated by the Goncalves' group this bioinfomatician would work only with that group but would be welcome to interact with the existing unit for change of ideas and further development.

The applicant is expected to have excellent communication skills (spoken and written), an interest in collaborating with other researchers and to contribute to the common goals of the group and of the centre.

Prof Goncalves created the world-unique project entlitled Carotid Plaque Imaging Project (CPIP) in late 2005. This project benefits of a unique situation where equipment and expertise are gathered in the Lund University, Clinical Research Center, Malmö and a large patient population is taken care of at the Skånes University Hospital. It enclose currently one of the largest human atherosclerotic plaque biobank in the world and is unique because of the extensive characterisation of the samples (snap-frozen plaques, serum and blood-derived living cells, standardised ultrasound images, extensive patient evaluation and follow-up). Inclusion is on going and more than 1200 patients have been included and followed up with interviews and national registries. This biobank extensively generates transcriptomic, genetic and epigenetic profiles, lipidomics, metabolomics, extracellular matrix-omics, proteomic, single cell transcriptomics isolated from human plaques, spatial transcriptomics from plaques beyond circulating lipidomics, metabolomics. An important part of the work that the candidate will perform will include quality control (QC), processing, and analysis of these data. We expect the applicants to have extensive experience with implementing and developing pipelines for the analyses of large datasets, including microarray, NGS and single-cell technologies.

The bioinformatics field is broad and developing at an impressive pace. Thus, the candidate is expected to independently follow the development, work on improving existing pipelines and present alternative solutions on how to best utilize available data and resources, including visualizations and machine learning applications for our large material of human data.

Qualifications

Requirements

- PhD in Bioinformatics, Mathematical Statistics, Computer Science or another quantitative discipline
- Experience in data analysis and data mining to identify trends and produce meaningful data visualizations
- Proficiency in R and either Python (Pandas and NumPy stack) or a lower level  programming language (C++, Java, etc.)
- Extensive experience with analysing RNA-seq data, knowledge of modern RNA-seq related methodology: Star, Kallisto, DESeq2 etc.
- Experience in one of the following core areas: Chip-SEQ, WGBS, WGS or Exome-seq
- Knowledge of modern bioinformatics tools such as Snakemake, Nextflow, etc.
- Solid understanding of data analysis and machine learning principles
- Proficiency in working in a Linux environment
- Proficiency in oral and written English

Requests

- Experience with single-cell sequencing would be advantageous
- Experience with version control systems such as git or mercurial. Source code availability in public repositories would be advantageous.

We will also pay attention to personal attributes, favoring individuals that are flexible, social and used to collaborative work, taking initiatives and working in a well-documented way. Experience of working in an international environment will be considered as a plus.