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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    Complete genome sequences of two highly divergent Japanese isolates of Plantago asiatica mosaic virus
    Komatsu, Ken ; Yamashita, Kazuo ; Sugawara, Kota ; Verbeek, Martin ; Fujita, Naoko ; Hanada, Kaoru ; Uehara-Ichiki, Tamaki ; Fuji, Shin Ichi - \ 2017
    Archives of Virology 162 (2017)2. - ISSN 0304-8608 - p. 581 - 584.
    Plantago asiatica mosaic virus (PlAMV) is a member of the genus Potexvirus and has an exceptionally wide host range. It causes severe damage to lilies. Here we report on the complete nucleotide sequences of two new Japanese PlAMV isolates, one from the eudicot weed Viola grypoceras (PlAMV-Vi), and the other from the eudicot shrub Nandina domestica Thunb. (PlAMV-NJ). Their genomes contain five open reading frames (ORFs), which is characteristic of potexviruses. Surprisingly, the isolates showed only 76.0–78.0 % sequence identity with each other and with other PlAMV isolates, including isolates from Japanese lily and American nandina. Amino acid alignments of the replicase coding region encoded by ORF1 showed that the regions between the methyltransferase and helicase domains were less conserved than other regions, with several insertions and/or deletions. Phylogenetic analyses of the full-length nucleotide sequences revealed a moderate correlation between phylogenetic clustering and the original host plants of the PlAMV isolates. This study revealed the presence of two highly divergent PlAMV isolates in Japan.
    The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
    Katayama, T. ; Wilkinson, D.W. ; Micklem, G. ; Kawashima, S. ; Yamaguchi, A. ; Nakao, M. ; Yamamoto, T. ; Okamoto, S. ; Oouchida, K. ; Chung, H. ; Aerts, J. ; Afzal, H. ; Antezana, E. ; Arakawa, K. ; Aranda, B. ; Belleau, F. ; Bolleman, J. ; Bonnal, R.J.P. ; Chapman, B. ; Cock, P.J.A. ; Eriksson, T. ; Gordon, P.M.K. ; Goto, N. ; Hayashida, K. ; Horn, H. ; Ishiwata, R. ; Kaminuma, E. ; Kasprzyk, A. ; Kawaji, H. ; Kido, N. ; Kim, Y. ; Kinjo, A.R. ; Konishi, F. ; Kwon, K.H. ; Labarga, A. ; Lamprecht, A. ; Lin, Y. ; Lindenbaum, P. ; McCarthy, L. ; Morita, H. ; Murakami, K. ; Nagao, K. ; Nishida, K. ; Nishimura, K. ; Nishizawa, T. ; Ogishima, S. ; Ono, K. ; Oshita, K. ; Park, K. ; Prins, J.C.P. ; Saito, T. ; Samwald, M. ; Satagopam, V.P. ; Shigemoto, Y. ; Smith, R. ; Splendiani, A. ; Sugawara, H. ; Taylor, J. ; Vos, R.A. ; Withers, D. ; Yamasaki, C. ; Zmasek, C.M. ; Kawamoto, S. ; Okubo, K. ; Asai, K. ; Takagi, T. - \ 2013
    Journal of Biomedical Semantics 4 (2013). - ISSN 2041-1480
    protein-interaction database - systems biology - ontology - bioinformatics - tool - representation - services - language - framework - networks
    Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. source provider, through middleware, to the end-consumer.
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