Postdoctoral researcher: Microbiome Bioinformatics

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100%, Zurich, fixed-term

The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global microbial biodiversity as part of the Microbiota Vault initiative’s efforts to preserve our microbial heritage.

Microbial diversity is globally threatened by urbanization and environmental change proceeding at an unprecedented pace. The Microbiota Vault initiative aims to preserve the biodiversity of human-associated and environmental microbiota, while still possible, by constructing an institution for the safe storage and preservation of microbiota samples and collections

Project background

The position is located in the Institute of Food, Nutrition, and Health at ETH Zurich within the Laboratory of Food Systems Biotechnology (Prof. Dr. Nicholas Bokulich). The Bokulich laboratory develops bioinformatics methods and software for microbiome research, including QIIME 2, and applies these tools to study microbiomes at the interfaces of foods and human health.

Job description

The Microbiota Vault initiative is working to catalog and preserve the microbial biodiversity of our planet, starting with human microbiota from diverse human populations. We are looking for a postdoc to join the FSB group and spearhead development of metagenomics tools and standards for the Initiative. She or he will develop and use bioinformatics methods for analysis and integration of microbiome and other omics datasets, including:

  • Develop standardized bioinformatics pipelines for analysis of marker-gene (16S, ITS) and shotgun metagenome datasets
  • Develop standards and protocols for metadata reporting and standard ontologies for the Microbiota Vault initiative
  • Analyze human microbiome data (marker-gene and shotgun metagenome) from diverse sources

You will be comfortable coordinating with a collaborative team of interdisciplinary scientists at the local, national, and global scale, to expand the Microbiota Vault initiative. This position will also involve supervision of doctoral, masters, and bachelors students, so candidates must have excellent leadership and communication skills and an interest in student supervision and education.

Your profile

Key Qualifications
You are a self-motivated scientist with outstanding academic qualifications, superb inter-personal and communication skills, and enthusiasm to engage with a collaborative team of scientists.

  • Doctoral degree in microbiology, computational biology, ecology, statistics, computer science, or other relevant fields
  • Extensive experience working with microbiome (marker gene and metagenome) or other omics data
  • Skilled in biological/statistical data analysis
  • Excellent interpersonal communication, teamwork and organizational skills
  • English language proficiency
  • Strong record of scientific communication (publications and/or open source software projects)
  • Knowledge of metadata standards (e.g., MIMARK, MIXS, ENVO, EMP)
  • Familiarity with microbiome sequence data repositories (e.g., EBI-ERA, SRA, Qiita)
  • Experience working with high-performance computing environments and/or cloud computing environments
  • Demonstrated leadership and teaching abilities

Desired Qualifications

  • Experience working with QIIME 2 and related open-source software
  • Proficient programming skills (Python, R, UNIX/bash scripting)
  • Experience with Git or other software version control systems
  • Experience in integrative analysis of multi-omics datasets (metagenomics, metatranscriptomics, metaproteomics, metabolomics)


ETH Zurich

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