Jan-Peter (Jp) Nap

dr.ir.

    1983 …2020

    Research output per year

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    2020

    Farm-scale bio-power-to-methane: Comparative analyses of economic and environmental feasibility

    Bekkering, J., Zwart, K., Martinus, G., Langerak, J., Tideman, J., van der Meij, T., Alberts, K., van Steenis, M. & Nap, J. P., 10 Mar 2020, In : International Journal of Energy Research. 44, 3, p. 2264-2277 14 p.

    Research output: Contribution to journalArticleAcademicpeer-review

    2018

    pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

    Warris, S., Timal, N. R. N., Kempenaar, M., Poortinga, A. M., van de Geest, H., Varbanescu, A. L. & Nap, J. P., 1 Jan 2018, In : PLoS ONE. 13, 1, e0190279.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    4 Citations (Scopus)
    2017

    Similarities between plant traits based on their connection to underlying gene functions

    Nap, J. P., Sanchez-Perez, G. F. & van Dijk, A-J., 2017, In : PLoS ONE. 12, 8, e0182097.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    2016

    Compact tomato seedlings and plants upon overexpression of a tomato chromatin remodelling ATPase gene

    Folta, A., Bargsten, J. W., Bisseling, T., Nap, J. P. H. & Mlynarova, L., 2016, In : Plant Biotechnology Journal. 14, 2, p. 581-591

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    3 Citations (Scopus)
    2015

    Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS

    Warris, S., Yalcin, F., Jackson, K. J. & Nap, J. P. H., 2015, In : PLoS ONE. 10, 4, 13 p., e0122524.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    8 Citations (Scopus)

    Reduced seed germination in Arabidopsis over-expressing SWI/SNF2 ATPase genes

    Leeggangers, H. A. C. F., Folta, A., Muras, A., Nap, J. P. H. & Mlynarova, L., 2015, In : Physiologia Plantarum. 153, 2, p. 318-326

    Research output: Contribution to journalArticleAcademicpeer-review

    6 Citations (Scopus)

    Towards recommendations for metadata and data handling in plant phenotyping

    Krajewski, P., Chen, D., Cwiek, H., van Dijk, A. D. J., Fiorani, F., Kersey, P., Klukas, C., Lange, M., Markiewicz, A., Nap, J. P. H., van Oeveren, J., Pommier, P., Scholz, U., van Schriek, M., Usadel, B. & Weise, S., 2015, In : Journal of Experimental Botany. 66, 18, p. 5417-5427

    Research output: Contribution to journalArticleAcademicpeer-review

    71 Citations (Scopus)
    2014

    Biological process annotation of proteins across the plant kingdom

    Bargsten, J. W., Severing, E. I., Nap, J. P. H., Sanchez Perez, G. F. & van Dijk, A. D. J., 2014, In : Current Plant Biology. 1, p. 73-82

    Research output: Contribution to journalArticleAcademicpeer-review

    6 Citations (Scopus)

    Over-expression of Arabidopsis AtCHR23 chromatin remodeling ATPase results in increased variability of growth and gene expression

    Folta, A., Severing, E. I., Krauskopf, J., van de Geest, H. C., Verver, J., Nap, J. P. H. & Mlynarova, L., 2014, In : BMC Plant Biology. 14, 18 p., 76.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    13 Citations (Scopus)

    Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

    Bargsten, J. W., Nap, J. P. H., Sanchez Perez, G. F. & van Dijk, A. D. J., 2014, In : BMC Plant Biology. 14, 330.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    18 Citations (Scopus)
    2013

    Snf2 Family Gene Distribution in Higher Plant Genomes Reveals DRD1 Expansion and Diversification in the Tomato Genome

    Bargsten, J. W., Folta, A., Mlynárová, L. & Nap, J. P. H., 2013, In : PLoS ONE. 8, 11, 11 p., e81147.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    7 Citations (Scopus)
    2011

    Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

    Goodwin, S. B., Ben M'Barek, S., Dhillon, B., Wittenberg, A. H. J., Crane, C. F., Hane, J. K., Foster, A. J., van der Lee, T. A. J., Grimwood, J., Aerts, A., Antoniw, J., Bailey, A., Bluhm, B., Bowler, J., Bristow, J., van der Burgt, A., Canto-Canché, B., Churchill, A. C. L., Conde-Ferràez, L., Cools, H. J. & 37 others, Coutinho, P. M., Csukai, M., Dehal, P., de Wit, P. J. G. M., Donzelli, B., van de Geest, H. C., van Ham, R. C. H. J., Hammond-Kosack, K. E., Henrissat, B., Kilian, A., Kobayashi, A. K., Koopmann, E., Kourmpetis, Y., Kuzniar, A., Lindquist, E., Lombard, V., Maliepaard, C. A., Martins, N., Mehrabi, A., Nap, J. P. H., Ponomarenko, A., Rudd, J. J., Salamov, A., Schmutz, J., Schouten, H. J., Shapiro, H., Stergiopoulos, I., Torriani, S. F. F., Tu, H., de Vries, R. P., Waalwijk, C., Ware, S. B., Wiebenga, A., Zwiers, L. H., Oliver, R. P., Grigoriev, I. V. & Kema, G. H. J., 2011, In : Plos Genetics. 7, 6, 17 p., e1002070.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    322 Citations (Scopus)
    2009

    In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

    van der Burgt, A., Fiers, M. W. E. J., Nap, J. P. H. & van Ham, R. C. H. J., 2009, In : BMC Genomics. 10, 24 p., 204.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    29 Citations (Scopus)
    2007

    A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat

    Alberts, R., Terpstra, P., Hardonk, M., Bystrykh, L. V., de Haan, G., Breitling, R., Nap, J. P. H. & Jansen, R. C., 2007, In : BMC Bioinformatics. 8, 10 p., 132.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    11 Citations (Scopus)

    Intragenic vectors for gene transfer without foreign DNA

    Conner, A. J., Barrell, P. J., Baldwin, S. J., Lokerse, A. S., Cooper, P. A., Erasmuson, A. K., Nap, J. P. H. & Jacobs, J. M. E., 2007, In : Euphytica. 154, 3, p. 341-353

    Research output: Contribution to journalArticleAcademicpeer-review

    41 Citations (Scopus)

    Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains

    Ren, X. Y., Stiekema, W. J. & Nap, J. P. H., 2007, In : Plant Molecular Biology. 65, 1-2, p. 205-217

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    23 Citations (Scopus)

    The (epi)genetics of human synovial sarcoma

    de Bruijn, D. R. H., Nap, J. P. H. & Kessel, A. G., 2007, In : Genes Chromosomes and Cancer. 46, 2, p. 107-117

    Research output: Contribution to journalArticleAcademicpeer-review

    31 Citations (Scopus)

    The SWI/SNF chromatin-remodeling gene AtCHR12 mediates temporary growth arrest in Arabidopsis thaliana upon perceiving environmental stress

    Mlynarova, L., Nap, J. P. H. & Bisseling, T., 2007, In : The Plant Journal. 51, 5, p. 874-885

    Research output: Contribution to journalArticleAcademicpeer-review

    77 Citations (Scopus)
    2006

    Directed microspore-specific recombination of transgenic alleles to prevent pollen-mediated transmission of transgenes

    Mlynarova, L., Conner, A. J. & Nap, J. P. H., 2006, In : Plant Biotechnology Journal. 4, 4, p. 445-452

    Research output: Contribution to journalArticleAcademicpeer-review

    71 Citations (Scopus)

    DNAVis: interactive visualization of comparative genome annotations

    Fiers, M. W. E. J., van de Wetering, H., Peeters, T. H. J. M., van Wijk, J. J. & Nap, J. P. H., 2006, In : Bioinformatics. 22, 3, p. 354-355

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    6 Citations (Scopus)

    In plants, highly expressed genes are least compact

    Ren, X. Y., Vorst, O. F. J., Fiers, M. W. E. J., Stiekema, W. J. & Nap, J. P. H., 2006, In : Trends in Genetics. 22, 10, p. 528-532

    Research output: Contribution to journalArticleAcademicpeer-review

    95 Citations (Scopus)

    Transgenic plants that make non-transgenic pollen

    Mlynarova, L. & Nap, J. P. H., 2006, In : ISB News Report. 3 p.

    Research output: Contribution to journalArticleProfessional

    Open Access
    2005

    Local coexpression domains of two to four genes in the genome of Arabidopsis

    Ren, X. Y., Fiers, M. W. E. J., Stiekema, W. J. & Nap, J. P. H., 2005, In : Plant Physiology. 138, 2, p. 923-934

    Research output: Contribution to journalArticleAcademicpeer-review

    43 Citations (Scopus)

    Tentacles of in vitro-grown round-leaf sundew (Drosera rotundifolia L.) show induction of chitinase activity upon mimicking the presence of prey

    Matusikova, I., Salaj, J., Moravcikova, J., Mlynarova, L., Nap, J. P. H. & Libantova, J., 2005, In : Planta. 222, 6, p. 1020-1027

    Research output: Contribution to journalArticleAcademicpeer-review

    39 Citations (Scopus)
    2004

    Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

    Fiers, M. W. E. J., Kleter, G. A., Nijland, H., Peijnenburg, A. A. C. M., Nap, J. P. H. & van Ham, R. C. H. J., 2004, In : BMC Bioinformatics. 5, 6 p., 133.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    88 Citations (Scopus)

    Regulating gene expression: surprises still in store

    Jansen, R. C. & Nap, J. P. H., 2004, In : Trends in Genetics. 20, 5, p. 223-225

    Research output: Contribution to journalArticleAcademicpeer-review

    21 Citations (Scopus)

    The insectivorous sundew (Drosera rotundifolia, L.) might be a novel source of PR genes for biotechnology

    Matusikova, I., Libantova, J., Moravcikova, J., Mlynarova, L. & Nap, J. P. H., 2004, In : Biologia. 59, 6, p. 719-725

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    6 Citations (Scopus)
    2003

    A self-excising Cre recombinase allows efficient recombination of multiple ectopic heterospecific lox sites in transgenic tobacco

    Mlynarova, L. & Nap, J. P. H., 2003, In : Transgenic Research. 12, 1, p. 45-57

    Research output: Contribution to journalArticleAcademicpeer-review

    29 Citations (Scopus)

    De kleren van de keizer. Heeft de biotech-discussie in Nederland wat om het lijf gehad?

    Nap, J. P. H., 2003, In : Spil. 2003, p. 191-192

    Research output: Contribution to journalArticleProfessional

    Genetic transformation of Slovak cultivar of potato (Solanum tuberosum L.): efficiency and the behavior of the transgene

    Moravcikova, J., Libantova, J., Matusikova, I., Libiakova, G., Nap, J. P. H. & Mlynarova, L., 2003, In : Biologia. 58, 6, p. 1075-1080

    Research output: Contribution to journalArticleAcademicpeer-review

    5 Citations (Scopus)

    Seed-expressed fluorescent proteins as versatile tools for easy (co)transformation and high-throughput funtional genomics in Arabidopsis

    Stuitje, A. R., Verbree, E. C., van der Linden, K. H., Mietkiewska, E. M., Nap, J. P. H. & Kneppers, T. J. A., 2003, In : Plant Biotechnology Journal. 1, 4, p. 301-309

    Research output: Contribution to journalArticleAcademicpeer-review

    The presence of a chromatin boundary appears to shield a transgene in tobacco from RNA silencing

    Mlynarova, L., Hricova, A., Loonen, A. & Nap, J. P. H., 2003, In : The Plant Cell. 15, p. 2203-2217

    Research output: Contribution to journalArticleAcademicpeer-review

    31 Citations (Scopus)

    The release of genetically modified crops into the environment - Part I. Overview of current status and regulations

    Nap, J. P. H., Metz, P. L. J., Escaler, M. & Conner, A. J., 2003, In : The Plant Journal. 33, 1, p. 1-18

    Research output: Contribution to journalArticleAcademicpeer-review

    177 Citations (Scopus)

    The release of genetically modified crops into the environment - Part II. Overview of ecological risk assessment

    Conner, A. J., Glare, T. R. & Nap, J. P. H., 2003, In : The Plant Journal. 33, 1, p. 19-46

    Research output: Contribution to journalArticleAcademicpeer-review

    360 Citations (Scopus)
    2002

    Errors in genomics and proteomics

    Jansen, R. C., Nap, J. P. H. & Mlynárová, L., 2002, In : Nature Biotechnology. 20, p. 19

    Research output: Contribution to journalArticleAcademicpeer-review

    27 Citations (Scopus)

    The potato Lhca3.St.1 promoter confers high and stable transgene expression in chrysanthemum, in contrast to CaMV-based promoters

    Annadana, S., Mlynárová, L., Udayakumar, M., de Jong, J. & Nap, J. P. H., 2002, In : Molecular Breeding. 8, p. 335-344

    Research output: Contribution to journalArticleAcademicpeer-review

    25 Citations (Scopus)

    The promiscuity of heterospecific lox sites increases dramatically in the presence of palindromic DNA

    Mlynárová, L., Libantová, J., Vrba, L. & Nap, J. P. H., 2002, In : Gene. 296, p. 129-137

    Research output: Contribution to journalArticleAcademicpeer-review

    18 Citations (Scopus)
    2001

    Genetical genomics: the added value from segregation

    Jansen, R. C. & Nap, J. P. H., 2001, In : Trends in Genetics. 17, p. 388-391

    Research output: Contribution to journalArticleAcademicpeer-review

    759 Citations (Scopus)

    Molecular markers associated with leptinine production are located on chromosome 1 in Solanum chacoense

    Hutvagner, G., Banfalvi, Z., Milankovics, I., Silhavy, D., Polgar, Z., Horvath, S., Wolters, P. & Nap, J. P. H., 2001, In : Theoretical and Applied Genetics. 102, p. 1065-1071

    Research output: Contribution to journalArticleAcademicpeer-review

    19 Citations (Scopus)

    The effect of MAR elements on variation in spatial and temporal regulation of transgene expression

    van Leeuwen, W., Mlynárová, L., Nap, J. P. H., van der Plas, L. H. W. & van der Krol, A. R., 2001, In : Plant Molecular Biology. 47, p. 543-554

    Research output: Contribution to journalArticleAcademicpeer-review

    21 Citations (Scopus)
    2000

    Detailed characterization of the posttranscriptional gene-silencing-related small RNA in a GUS gene-silenced tobacco

    Hutvágner, G., Mlynarova, L. & Nap, J. P. H., 2000, In : RNA-A Publication of the RNA Society. 6, 10, p. 1445-1454

    Research output: Contribution to journalArticleAcademicpeer-review

    51 Citations (Scopus)
    1999
    Open Access

    Een banaan in je aardappel

    Nap, J. P. H., 1999, In : Eindhovens Dagblad. 30 Maart

    Research output: Contribution to journalArticlePopular

    Gentechniek heeft ook voordelen

    Stiekema, W. J., de Maagd, R., Jongsma, M., Bosch, D. & Nap, J. P. H., 1999, In : Trouw. 21-04-1999

    Research output: Contribution to journalArticlePopular

    Gentechnologie niet anders dan veredeling

    Nap, J. P. H., 1999, In : De Gelderlander.

    Research output: Contribution to journalArticlePopular

    1998

    A transgene-centered approach to the biosafety of transgenic phosphinothricin-tolerant plants

    Metz, P. L. J., Stiekema, W. J. & Nap, J. P. H., 1998, In : Molecular Breeding. 4, p. 335-341

    Research output: Contribution to journalArticleAcademicpeer-review

    12 Citations (Scopus)

    Biosafety of E. coli ß-glucuronidase (GUS) in plants

    Gilissen, L. J. W. J., Metz, P. L. J., Stiekema, W. J. & Nap, J. P. H., 1998, In : Transgenic Research. 7, 3, p. 157-163

    Research output: Contribution to journalArticleAcademicpeer-review

    42 Citations (Scopus)

    Evaluation of diallel analysis using ß-glucuronidase activity from transgenes in Nicotiana tabacum

    Conner, A. J., Keizer, L. C. P., Mlynarova, L., Stiekema, W. J. & Nap, J. P. H., 1998, In : Euphytica. 102, p. 161-168

    Research output: Contribution to journalArticleAcademicpeer-review

    6 Citations (Scopus)