Postdoctoral fellow in bioinformatics and systems biology - Hiring in process/Finished, not possible to apply

The Department of Medical Sciences is a large clinical institution with more than 250 employees and over 900 additional coworkers connected via the Uppsala University Hospital. The Department of Medical Sciences has a broad research profile with strong research groups in a number of different areas. The research carried out at the department is performed in close connection with the clinical activities at the Uppsala University Hospital, which includes both basic studies on the causes of a variety of illnesses and the development and evaluation of improved diagnostics and new treatment methods. More information about the Department of Medical Sciences can be found at www.medsci.uu.se

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Bioinformatic systems biology based on “Big data” will be key for enabling precision medicine, where diagnostics and therapeutics are individually tailored based on genetics, environment and lifestyle. In the current project, bioinformatics and systems biology will be employed at the level of an international cohort project, as well as state-of-the-art interventional sleep & circadian studies, that are centered on neurocognitive and metabolic diseases.

The position is for two years and will be conducted at the Department of Medical Sciences

One aim of the project is to utilize systems biology to advance precision medicine (diagnostics, biomarkers and therapeutics) in the area of neurocognitive diseases (such as Alzheimer's disease) and sleep disorders.

Based on an international multi-site cohort, this aim of the project will focus on providing novel insight into diseases that afflict the brain, focusing on sleep and neurodegenerative diseases – some of the great health challenges of our time. For example, EEG-based sleep data, blood-based biomarkers and actigraphy data (for analysis of physical activity and circadian rhythms) will be analyzed with assistance from a newly developed artificial intelligence platform, to discover novel biomarkers and tailored therapeutics.

In parallel, we will use clinical intervention studies to uncover how sleep and lifestyle factors interact with common public health diseases that affect cognition and metabolism, such as type 2 diabetes. Here, one of the goals will also be to discover new biomarkers, such as blood-based or intestinal biomarkers that may modulate therapeutic responses.

You will join a driven team focused on high-quality and impactful research in sleep and circadian rhythms. The team is part of Uppsala University’s strong research network in sleep and circadian rhythms. This encompasses groups on the clinical side, who treat patients with sleep and circadian disorders, as well as several groups that carry out state-of-the-art interventional sleep and circadian rhythm trials. As such, you will be able to gain broad expertise in these research areas, while also having the opportunity to acquire wet lab experience and extensive networking with our international partners. You will also have opportunities for first-author positions on manuscripts, collaborative research efforts, and for presentations at national and international conferences.

Duties

• Bioinformatic analyses comprising integration of several data types, so-called systems biological analyses (such as blood-based biomarkers, EEG data), to find new biomarkers and disease mechanisms that are specific to different types of sleep, neurocognitive and metabolic disorders.
• Analysis of activity data (actigraphy) and EEG data to analyze sleep and parameters of the circadian rhythm, and how this relates to disease mechanisms and neurocognitive parameters (such as memory assessments) in neurocognitive and metabolic disorders.
• Analysis of participant data such as metabolomics and metagenomics data, derived from cohort studies and interventional sleep & circadian trials.
• Collaboration with the partner groups within an EU-Horizon project, for analyses at facilities at Uppsala University and our partners. This comprises broad profiling (e.g. multiplexed) panels, as well as targeted metabolic, cardiovascular and neurodegeneration biomarkers.

Requirements

• Doctoral degree in bioinformatics or system biology, or a foreign degree that is judged to correspond to a doctoral degree in bioinformatics or system biology.
• The degree must be completed no later than at the time when the employment decision is made. In particular those who have graduated no more than three years ago will be considered. When calculating the timeframe of three years, the starting point is the last application date. If there are special reasons, the degree may have been received earlier. Special reasons refer to leave due to illness, parental leave, positions of trust within trade unions, etc.
• Experience, supported by scientific publications, in bioinformatics and/or integration of several data types (such as transcriptome data, metabolomics and metagenomics of the intestinal flora), with supporting work and visualization in relevant scripting environments (such as R and Python).
• Experience, with the support of scientific publications, of working with the above types of human data, preferably with a focus on public health diseases such as sleep disorders, obesity, type 2 diabetes and neurodegenerative diseases.

Desirable / meritorious in other respects

Experience in bioinformatically relevant database queries (such as KEGG). Multi-omics integration, genome-scale metabolic models, experience in relevant bioinformatics pipelines and relevant bioinformatic quality control tools (such as PCA, PLSDA, t-SNE). Experience in relevant visualization environments (ggplot2, illustrator), programming in other languages (including script languages), experience of research collaborations and relevant project organization. Wet lab work, such as with ELISA methods, qPCR and western blotting.

About the employment
The employment is a temporary position of two (2) years according to central collective agreement. Scope of employment 100 %. Starting date as agreed. Placement: Uppsala.

For further information about the position, please contact: Jonathan Cedernaes, jonathan.cedernaes@medsci.uu.se

Please submit your application by October 14 2022, UFV-PA 2022/3421.

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