Stichting Dienst Landbouwkundig Onderzoek

The largest plant research institute in The Netherlands, conducting multidisciplinary research in the fields of breeding, agronomy, genomics, bioinformatics and plant-environment interactions. Together with plant-research related chairs from Wageningen University it forms the Plant Sciences Group, which is part of Wageningen University and Research Centre (WUR). From early 2009, the Plant Sciences Group is housed in a central building with state-of-the-art facilities and equipment. St.DLO, PPO/PRI plays an important role in many national and international genomics initiatives, including the Centre for BioSystems Genomics (CBSG), the Netherlands Bioinformatics Centre (NBC), the Netherlands Proteomics Centre (NPC) and the Netherlands Metabolomics Centre (NMC) in which functional genomics and bioinformatics research programs have been established with a key aim to identify complex genetic and biochemical mechanisms underlying quality traits.

Roeland van Ham is leading the bioinformatics group at St.DLO, PPO/PRI since 2003. The group develops standardized and generic systems for the management, analysis and integration of plant omics data, in support of the technology platforms of the Wageningen Genomics Facility (sequencing, proteomics and metabolomics). The research interest of the group is broadly in plant bioinformatics with a strong focus on genome analysis. The group plays a leading role in the international initiatives to sequence the genomes of the Solanaceous crops tomato and potato. The main technology expertise includes genome assembly, annotation and comparative analysis, database development and management, webservice and workflow management technology, mass spectrometry data analysis, machine learning, protein structure modelling and analysis, network construction and modelling.

Selected Publications:
Kourmpetis Y.A., van Dijk, A.D.J., Bink, M.C., van Ham, R.C.H.J., ter Braak, C.J.F. (2009) Bayesian markov random field analysis for protein function prediction based on network data. PLoS ONE 5 (2), art. no. e9293.
Visser, R.G.F. et al. (14 coauthors) (2009) Sequencing the potato genome: Outline and first results to come from the elucidation of the sequence of the world’s third most important food crop. American Journal of Potato Research DOI 10.1007/s12230-009-9097-8.
Mueller, L.A. et al. (139 coauthors) (2009) A snapshot of the emerging tomato genome sequence. The Plant Genome 2:78-92.
Kuzniar, A., van Ham, R.C.H.J., Pongor, S., Leunissen, J.A.M. (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends in Genetics 24:539-551.
Fiers, M.W.E.J., van de Burgt, A., Datema, E., de Groot, J.C.W., van Ham, R.C.H.J. (2008) High throughput bioinformatics with the Cyrille2 pipeline system. BMC Bioinformatics 9, 96.

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