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PostDoc: Application of our Integrated Proteogenomics Approach* to identify missed protein coding ORFs in prokaryotic genome sequences of various pathogens and key model organisms

     
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Duration

The contract duration is initially for 12 months; options for an extension.
Occupation rate100%
Start1st of September 2018 (or by agreement).

Proteogenomics refers to the identification of as of yet unannotated protein-coding genes (CDS) in genomes using tandem mass spectrometry data. This highly visible area of research benefits from the exponential increase of completely sequenced prokaryotic genomes, which represent an optimal basis for accurate genome annotation. We have recently developed a publicly available solution for this problem (*Omasits, Varadarajan et al., Genome Res, 2017, 12:2083-2095). We now aim to make our solution more broadly available, and apply it in selected collaboration projects, e.g. with Prof. Dr. Ruedi Aebersold (ETHZ) and Prof. Dr. S. Gagneux (Swiss TPH) and several collaborators from the German Priority Programme “Small Proteins in Prokaryotes, an Unexplored World” (SPP 2002, ?url=http%3A%2F%2Fwww.spp2002.uni-kiel.de%2Fwordpress%2F&module=jobs&id=905746" target="_blank" rel="nofollow">www.spp2002.uni-kiel.de/wordpress/).

The project will entail the generation of integrated proteogenomics databases (iPtgxDBs) for a number of relevant prokaryotic organisms, to search existing proteomics data to identify as of yet unannotated CDSs, to explore their conservation and functional relevance using bioinformatics tools and in close interaction with experimental groups. For several datasets, analysis of closely related strains will be possible, allowing to identify protein variants relevant for disease progression, virulence or other key functional aspects. The project will provide outstanding opportunities to analyze large datasets and push the proteogenomics field forward. In addition, the successful candidate will be able to assess integration of Transposon mutagenesis data (Tnseq) and proteogenomics data and their impact on finding essential genes and improving genome annotations.

A PostDoc position is available for a highly motivated scientist with a broad background in proteomics and bioinformatics data analysis. The successful candidate will join the research group “Molecular Diagnostics, Genomics and Bioinformatics” at the Competence Division “Method Development and Analytics” of Agroscope in Wädenswil. She/he will largely benefit from being an associated member of the SIB Swiss Institute of Bioinformatics.

Description

  • Carry out a proteogenomics research project in collaboration with Profs. Ruedi Aebersold (ETHZ) and Sebastién Gagneux (Swiss Tropical and Public Health Institute) on a very large proteomics dataset of Mycobacterium tuberculosis
  • Carry out proteogenomics research projects with several collaborators from the German SPP2002, that study a number of important model organisms, and to selected prokaryotic organisms of particular interest (biocontrol agents, pathogens, founder strains of gene knockout collections, model organisms, microbiome isolates, etc.)
  • Work on data integration of proteogenomics and Transposon mutagenesis (Tnseq) datasets
  • Perform a Meta-analysis of existing proteogenomics projects
  • Sustain and extend the functionality of our existing pipeline(s) for integrated proteogenomics analysis ?url=https%3A%2F%2Fiptgxdb.expasy.org%2F&module=jobs&id=905746" target="_blank" rel="nofollow">https://iptgxdb.expasy.org/
  • Prepare scientific reports; present results in scientific publications and at conferences

Requirements

  • Highly motivated scientist with a PhD Degree preferentially in Proteome Informatics, Bioinformatics or Computational Biology
  • Strong experience in data analysis of proteomics (shotgun, DDA, DIA) and functional genomics data (genome assembly, comparative genomics, RNA-Seq based transcriptomics data)
  • Knowledge in targeted proteomics data analysis and data independent acquisition (DIA) is an asset
  • Solid programming experience (Python, Linux scripting/bash, R); plus a record of scientific publishing
  • Excellent team spirit and good communication skills 2/2
  • A good standard of written and spoken English; basic knowledge of German (or commitment to learn it)

We offer

Agroscope is an innovative research institute for agriculture and nutrition. It is part of the federal administration and attached to the Federal Department of Economic Affairs, Education and Research EAER. It has research stations at a number of sites around Switzerland, and closely interacts with numerous other research institutes.

The successful candidate will interact with colleagues at the ETH Zurich, at the Swiss Bioinformatics Institute and at Agroscope. We offer an interesting research topic in a dynamic and dedicated research team with a strong publication record, competent supervision, and outstanding computational research infrastructure. If desired, the candidate could learn to perform de novo genome assembly using NGS data from various technologies (Illumina, PacBio, Oxford Nanopore) and subsequent genome annotation for selected prokaryotes.

Salary Category: According to the standards of the Swiss National Science Foundation

Address

Please send your complete application in one pdf file, including CV, motivation, academic transcripts and the addresses of 2-3 referees to christian.ahrensagroscope.admin.ch.

Closing date for applications: We plan to fill the position as soon as possible (or until position is filled).

For further information, please feel free to contact Dr. Christian H. Ahrens, Team Leader Genomics and Bioinformatics, & Group Leader at the SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/ahrens-christian/).
Email address: christian.ahrensagroscope.admin.ch.
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Web https://www.sib.swiss/ahrens-christian/
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