PhD fellowship in Deep Learning for Microbiome Variation at Novo Nordisk Foundation Center for Protein Research
A PhD position is available in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research. The Center has been established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. The Center comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms.
The Programme for Disease Systems Biology (DSB) consists of three research groups covering many systems level aspects of biology and medicine, including large scale analysis of human variation data and integration of molecular-level and healthcare data.
The Human Proteome Variation group is part of DSB and led by Simon Rasmussen focus on proteome and genome variation, coding variation and deep learning for integration of genomics, proteomics and clinical data.
Responsibilities and tasks
The Ph.D will work in a multidisciplinary project team focusing on integrating and analyzing human variation data. Within recent years, the microbiota has been established to have an important role in human health and is profoundly investigated to discover microbial interventions. To be able to successfully achieve this, we need the knowledge of which biological components are present, how they interact as a dynamic living system and with the human host. We have developed the first deep learning frameworks for unsupervised discovery of microbial organisms and will extend this to domain of microbiome ‘dark-matter’ such as bacteriophages or fungi.
The candidate will focus on developing and applying deep learning methods to identify phages from microbiome data and to catalogue phages across massive datasets of human microbiome and other metagenomes. The complete bacterial and phage information obtained from these tools will be further used to discover hub organisms and microbial consortia from datasets with relevance to human disease.
Principal supervisor is Associate professor Simon Rasmussen, Novo Nordisk Foundation Center for Protein Research; e-mail: email@example.com, Direct Phone: +45 3533 2159.
Start date: 1 September 2019.
Duration: 3 years.
Your key tasks are:
- Carry through an independent research project under supervision.
- Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points.
- Participate in active research environments including a stay at another research team.
- Obtain experience with teaching or other types of dissemination related to your PhD project.
- Teach and disseminate your knowledge.
- Write a PhD thesis on the grounds of your project.
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