At the Plant Sciences Group of Wageningen UR we are looking for a PhD student to work on prediction and identification of key determinants of protein-protein interaction specificity. In this project, you will develop novel bioinformatics methods, based on machine learning, to predict which domains and amino acids specify protein-protein interaction potential.
In plants, protein complexes, formed by highly specific protein-protein interactions, regulate transcription patterns underlying major developmental processes. During evolution, genome duplication events have resulted in sets of proteins with relatively similar sequences, but completely different interaction patterns. For example, one of the best studied protein families, the MADS domain transcription factor family, contains over 100 members with very diverse interaction patterns. The expansion of this family enabled the evolution of the flower and contributes to the enormous diversity in flowering plants that we see today. It has been shown that MADS domain proteins form interactions with each other and with transcriptional co-regulators ― such as chromatin remodelling factors ― that determine their function. A key question is how interaction specificity is laid down in the amino-acid sequence, how interaction specificity has evolved, and how this relates to the 3D structure of these transcription factor proteins.
In this project, you will develop novel bioinformatics methods, based on machine learning, to predict which domains and amino acids specify protein-protein interaction potential. Ultimately, this will shed light on the way proteins select their interaction partners and, in particular, how plant MADS domain transcription factors function and how they have evolved. You will be part of a team that includes wet lab scientists from the Immink group with ample experience on plant developmental biology and computational scientists from the Bioinformatics group, experts in machine learning and data integration.
We are looking for an ambitious, enthusiastic team player and result-driven scientist with:
• an excellent academic record (MSc) in bioinformatics or systems biology
• demonstrable expertise in the use of machine learning/pattern recognition/data mining algorithms
• proven proficiency in programming
• affinity with protein structure and protein interactions, transcription regulation and plant development biology
• excellent oral and written communication skills in English
We offer the research environment of two young, dynamic and driven groups with a strong international profile and large numbers of PhD students; a state-of-the art computational infrastructure; close collaboration with other PhD students and researchers in the plant sciences; and the possibility to further develop your scientific education with courses, training, conferences. There will be opportunities to be involved in teaching at workshops or courses.
The position is full-time (38 hours/week), initially for 1 year after which a go/no-go decision will be taken on extension with another three years. The gross salary in the first year is € 2083,- per month rising to € 2664,- in the fourth year for a full-time appointment.
For more information about this position, please contact dr. Aalt-Jan van Dijk (firstname.lastname@example.org, tel. +31 317 480 944), prof. Dick de Ridder (email@example.com, tel. +31 317 484 074) or prof. Richard Immink (firstname.lastname@example.org, tel. +31 317 484 069. For information on the selection procedure, please consult mrs. Dorien Wissink (email@example.com). Applications can only be submitted online, at http://www.wageningenur.nl/en/Jobs/Vacancies.htm; please do not mail material directly to the persons above.
The deadline for application is April 15, 2015.
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 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 position is shared between two groups in the Plant Sciences Group:
- The rapidly expanding Bioinformatics Group focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, we develop and apply novel computational methods for the analysis and integration of –omics data. The group has a strong track record in genomics, algorithm development and tool construction. We maintain collaborations with a large number of researchers in plant sciences, animal sciences and ecology.
- The Immink group investigates the transcriptional regulation of plant developmental processes, such as flowering time control, floral organ development and leaf and floral organ growth, with special interest in the role of protein-protein interactions. We collaborate with national and international plant science and systems biology oriented research groups and implement state-of-the-art –omics tools.