Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Specific root length as an indicator of environmental change
    Ostonen, I. ; Püttsepp, Ü. ; Biel, C. ; Alberton, O. ; Bakker, M.R. ; Löhmus, K. ; Majdi, H. ; Metcalfe, J.D. ; Olsthoorn, A.F.M. ; Pronk, A.A. ; Vanguelova, E. ; Weih, M. ; Brunner, I. - \ 2007
    Plant Biosystems 141 (2007)3. - ISSN 1126-3504 - p. 426 - 442.
    spruce picea-abies - elevated atmospheric co2 - pine pinus-sylvestris - soil solution chemistry - potential growth-rate - fine-root - norway spruce - l. karst. - nutrient availability - silver birch
    Specific root length (SRL, m g-1) is probably the most frequently measured morphological parameter of fine roots. It is believed to characterize economic aspects of the root system and to be indicative of environmental changes. The main objectives of this paper were to review and summarize the published SRL data for different tree species throughout Europe and to assess SRL under varying environmental conditions. Meta-analysis was used to summarize the response of SRL to the following manipulated environmental conditions: fertilization, irrigation, elevated temperature, elevated CO2, Al-stress, reduced light, heavy metal stress and physical disturbance of soil. SRL was found to be strongly dependent on the fine root classes, i.e. on the ectomycorrhizal short roots (ECM), and on the roots
    A text-mining analysis of the human phenome
    Driel, M.A. van; Bruggeman, J. ; Vriend, G. ; Brunner, H.G. ; Leunissen, J.A.M. - \ 2006
    European Journal of Human Genetics 14 (2006)5. - ISSN 1018-4813 - p. 535 - 542.
    saccharomyces-cerevisiae - protein families - gene ontology - genome - identification - biology - knowledgebase - products - database - disease
    A number of large-scale efforts are underway to define the relationships between genes and proteins in various species. But, few attempts have been made to systematically classify all such relationships at the phenotype level. Also, it is unknown whether such a phenotype map would carry biologically meaningful information. We have used text mining to classify over 5000 human phenotypes contained in the Online Mendelian Inheritance in Man database. We find that similarity between phenotypes reflects biological modules of interacting functionally related genes. These similarities are positively correlated with a number of measures of gene function, including relatedness at the level of protein sequence, protein motifs, functional annotation, and direct protein¿protein interaction. Phenotype grouping reflects the modular nature of human disease genetics. Thus, phenotype mapping may be used to predict candidate genes for diseases as well as functional relations between genes and proteins. Such predictions will further improve if a unified system of phenotype descriptors is developed. The phenotype similarity data are accessible through a web interface at http://www.cmbi.ru.nl/MimMiner/
    GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases
    Driel, M.A. van; Cuelenaere, K. ; Kemmeren, P.P.C.W. ; Leunissen, J.A.M. ; Brunner, H.G. ; Vriend, G. - \ 2005
    Nucleic acids research 33 (2005)SUPP/2. - ISSN 0305-1048 - p. w758 - w761.
    candidate genes - expression database - genome database - disorders - identification - malformations - knowledgebase - map
    The identification of genes underlying human genetic disorders requires the combination of data related to cytogenetic localization, phenotypes and expression patterns, to generate a list of candidate genes. In the field of human genetics, it is normal to perform this combination analysis by hand. We report on GeneSeeker (http://www.cmbi.ru.nl/GeneSeeker/), a web server that gathers and combines data from a series of databases. All database searches are performed via the web interfaces provided with the original databases, guaranteeing that the most recent data are queried, and obviating data warehousing. GeneSeeker makes the same selection of candidate genes as the human geneticists would have performed, and thus reducing the time-consuming process to a few minutes. GeneSeeker is particularly well suited for syndromes in which the disease gene displays altered expression patterns in the affected tissue(s).
    Toekomstige natuur in een ander klimaat
    Vonk, M. ; Leemans, R. - \ 2004
    In: Opgewarmd Nederland / Roos, R., Woudenberg, S., Dorren, G., Brunner, E., Amsterdam : Stichting Natuurmedia & Uitgeverij Jan van Arkel - ISBN 9789080815827 - p. 174 - 181.
    ecosystemen - landgebruik - klimaatverandering - toekomst - ecosystems - land use - climatic change - future
    Hoe ecosystemen zich kunnen aanpassen aan een (snelle) klimaatverandering is moeilijk te zeggen. Scenario's zijn ontwikkeld om het bij benadering te kunnen schatten
    De kalender van de natuur
    Vliet, A.J.H. van - \ 2004
    In: Opgewarmd Nederland laat klimaateffecten zien / Roos, R., Woudenberg, S., Dorren, G., Brunner, E., Amsterdam : Stichting Natuurmedia & Uitgeverij Jan van Arkel - ISBN 9789080815827 - p. 26 - 27.
    A new web-based data mining tool for the identification of candidate genes for human genetic disorders
    Driel, M.A. van; Cuelenaere, K. ; Kemmeren, P.P.C.W. ; Leunissen, J.A.M. ; Brunner, H.G. - \ 2003
    European Journal of Human Genetics 11 (2003). - ISSN 1018-4813 - p. 57 - 63.
    recessive robinow-syndrome - human genome - expression database - noonan-syndrome - adult-syndrome - sequence - mutation - dysplasia - mouse - ror2
    To identify the gene underlying a human genetic disorder can be difficult and time-consuming. Typically, positional data delimit a chromosomal region that contains between 20 and 200 genes. The choice then lies between sequencing large numbers of genes, or setting priorities by combining positional data with available expression and phenotype data, contained in different internet databases. This process of examining positional candidates for possible functional clues may be performed in many different ways, depending on the investigator's knowledge and experience. Here, we report on a new tool called the GeneSeeker, which gathers and combines positional data and expression/phenotypic data in an automated way from nine different web-based databases. This results in a quick overview of interesting candidate genes in the region of interest. The GeneSeeker system is built in a modular fashion allowing for easy addition or removal of databases if required. Databases are searched directly through the web, which obviates the need for data warehousing. In order to evaluate the GeneSeeker tool, we analysed syndromes with known genesis. For each of 10 syndromes the GeneSeeker programme generated a shortlist that contained a significantly reduced number of candidate genes from the critical region, yet still contained the causative gene. On average, a list of 163 genes based on position alone was reduced to a more manageable list of 22 genes based on position and expression or phenotype information. We are currently expanding the tool by adding other databases. The GeneSeeker is available via the web-interface (http://www.cmbi.kun.nl/GeneSeeker/).
    Beoordeling expertiseverslag 'GAB Robins Takkenberg B.V.' inzake gistvorming in potten gemarineerde haring
    Aalberts, C.H.J. ; Brunner, K.K. - \ 2003
    IJmuiden : RIVO (Rapport / Nederlands Instituut voor Visserij Onderzoek C038/03) - 7
    voedselveiligheid - visproducten - voedselbesmetting - microbiële besmetting - voedselkwaliteit - food safety - fish products - food contamination - microbial contamination - food quality
    Op verzoek van 'Ouwehands Rederij en Visverwerking BV" in Katwijk werd door het RIVO een beoordeling uitgevoerd van een expertiseverslag van "GAB Robins Takkenberg BV" in Rotterdam. Het expertiseverslag was opgesteld naar aanleiding van toenemende consumentenklachten over gistvorming in potten gemarineerde haring.
    World-wide high quality fish
    Vis, J.W. van de; Kloosterboer, R.J. ; Morzel, M. ; Brunner, K.K. - \ 2002
    IJmuiden : RIVO (RIVO report C050/02) - 75 p.
    A ß-glucosidase/xylosidase from the phytopathogenic oomycete, Phytophthora infestans
    Brunner, F. ; Wirtz, W. ; Rose, J.K.C. ; Darvill, A.G. ; Govers, F. ; Scheel, D. ; Nürnberger, T. - \ 2002
    Phytochemistry 59 (2002). - ISSN 0031-9422 - p. 689 - 696.
    An overview of soil and sediment treatment research in the Netherlands
    Rulkens, W.H. - \ 2001
    In: Treatment of contaminated soil - Fundamentals, Analysis, Applications / Stegmann, R., Brunner, G., Calmano, W., Matz, G., Berlin : Springer - ISBN 9783540417361 - p. 21 - 34.
    Verslag voorlopig deskundigen-onderzoek Gebr. Hakvoort B.V./Barentz B.V., Central Food Technic B.V
    Brünner, K.K. - \ 1997
    Unknown Publisher (RIVO-DLO Rapport C045/97)
    Kwaliteitsbeoordeling van een partij diepgevroren haring
    Brünner, K. ; Gouda, J.W.M. - \ 1997
    Unknown Publisher (RIVO-DLO Rapport C056/97)
    Horse mackerel (Trachurus trachurus) and flounder (Platichthys flesus) mince for extrusion experiments
    Bon, J. ; Vis, J.W. van de; Smit, A.A.M. ; Brünner, K.K. ; Gouda, J.W.M. - \ 1997
    Unknown Publisher (RIVO-DLO Report C023/97)
    Onderzoek naar het effect van de toepassing van het decontaminatiemiddel 'glyroxyl' bij de verwerking van garnalen
    Brünner, K.K. ; Gouda, J.W.M. - \ 1996
    Unknown Publisher (RIVO-DLO RAPPORT C011/96)
    De houdbaarheid van gekookte mosselen in een gasverpakking
    Lammers, C. ; Brünner, K.K. - \ 1996
    Unknown Publisher (RIVO-DLO Rapport C044/96)
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