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  3. 1 PhD and 1 postdoc position on computational methods to explore and predict natural product biosynthetic diversity

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1 PhD and 1 postdoc position on computational methods to explore and predict natural product biosynthetic diversity

The Medema research group develops innovative computational approaches to identify novel natural product biosynthetic pathways and connect them to specific molecules and (frequently microbiome-associated) phenotypes. This includes drug discovery as well as identification of the ...

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Arbeidsvoorwaarden

Standplaats:
Bornsesteeg, Wageningen, Gelderland
Dienstverband:
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
38 - 38 uur
Opleidingsniveau:
WO

Functieomschrijving

The Medema research group develops innovative computational approaches to identify novel natural product biosynthetic pathways and connect them to specific molecules and (frequently microbiome-associated) phenotypes. This includes drug discovery as well as identification of the molecular basis of interactions between microbes (and their hosts). In this project, you will develop novel algorithms to chart the evolution and biosynthetic diversity of microbial specialized metabolites, and to predict their chemical structures and functions based on sequence information of the enzyme-coding genes involved in their production. Both positions are part of international consortia that aim to leverage this diversity to engineer new high-value products, in particular novel antibiotics and biosurfactants.

Key publications:

  1. Medema MH & Fischbach MA (2015) Computational approaches to natural product discovery. Nature Chemical Biology 11: 639-648.
  2. Chevrette MG, Aicheler F, Kohlbacher O, Currie CR, Medema MH (2017) SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveals biosynthetic diversity across Actinobacteria. Bioinformatics 33(20): 3202-3210.
  3. Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL Jr, Ghequire MG, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, Mot R, Moore BS, Medema MH#, Dorrestein PC# (2016) Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nature Microbiology 2: 16197.

Functie-eisen

We are looking for ambitious, enthusiastic team players and result-driven scientists with:

  • an excellent academic record (MSc or PhD) in bioinformatics, computational biology, microbiology, (bio)chemistry or biotechnology;
  • proven proficiency in programming (in, e.g., Python);
  • affinity with both genome analysis and metabolism / chemistry;
  • intermediate to strong statistical and mathematical skills;
  • expertise in machine learning is a plus;
  • excellent oral and written communication skills in English;

Conditions

We offer the research environment of a young and dynamic group with a strong international profile; a state-of-the-art computational infrastructure; close national and international collaboration with other PhD students and researchers; and the possibility to further develop your scientific education with courses, training and conferences. There will also be opportunities to be involved in teaching at workshops or courses.

Both positions are full-time (38 hours/week).
The PhD position will initially be for 1 year, after which a go/no-go decision will be taken on extension with another three years. The gross salary for the PhD student in the first year is € 2222,- per month rising to € 2840,- in the fourth year for a full-time appointment.
The postdoc position is for 2 years. The gross salary for this position will be according to the VSNU collective labour agreement, starting from € 2984,- up until € 3475,- per month, depending on prior experience.

Additional information

For more information about this position, please contact dr. Marnix Medema (marnix.medema@wur.nl, tel. +31 317 480 706). For information on the selection procedure, please consult mrs. Dorien Wissink (dorien.wissink@wur.nl). Applications can only be submitted online, at www.wageningenur.nl/en/Jobs/Vacancies.htm; please do not mail material directly to the persons above.

You can apply up to and including February 22, 2018.

Bedrijfsomschrijving

Wageningen UR has a global reputation for its ground-breaking research and innovative education in the fields of food and health, sustainable agrosystems, the rural environment, and societal development - all of which make an essential contribution to the quality of life, i.e. the supply of safe and healthy food and drink, on the one hand, and the chance to live, work and play in a balanced ecosystem with a large variety of plants and animals on the other. Within Wageningen UR, the Plant Sciences Group (PSG) brings together science education and scientific, strategic and applied research in the fields of biology, of plants in relation to their environment, of plant-related organisms and of plant production. This project will be carried out at the Bioinformatics Group within PSG. This rapidly expanding research group focuses on fundamental and applied bioinformatics research in the life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of -omics data. The group has a strong track record in genome analysis, algorithm development and tool construction. There are many national and international collaborations with researchers studying microbial and plant metabolism, biotechnology and genomics.