Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

    Records 1 - 2 / 2

    • help
    • print

      Print search results

    • export

      Export search results

    Check title to add to marked list
    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
    Schmidt, Maximilian H.W. ; Vogel, Alexander ; Denton, Alisandra K. ; Istace, Benjamin ; Wormit, Alexandra ; Geest, H.C. van de; Bolger, Marie E. ; Alseekh, Saleh ; Mass, Janina ; Pfaff, Christian ; Schurr, Ulrich ; Chetelat, Roger ; Maumus, Florian ; Aury, Jean-Mary ; Koren, Sergey ; Fernie, Alisdair Robert ; Zamir, Dani ; Bolger, Anthony ; Usadel, Björn - \ 2017
    The Plant Cell 29 (2017)10. - ISSN 1040-4651 - p. 2336 - 2348.
    Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
    Check title to add to marked list

    Show 20 50 100 records per page

     
    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.