Research Output

A bioinformatics approach to marker development

Tang, J., 2008, [S.l.]. 150 p.

Research output: Thesisinternal PhD, WU

Open Access

A blueprint of seed desiccation sensitivity in the genome of Castanospermum australe

Correia Silva Santana Marques, A., Dias Costa, M. C., Chathuri, U., Jonkheer, E., Zhao, T., Schijlen, E. G. W. M., Derks, M. F. L., Nijveen, H., Marcet-Houben, M., Julca, I., Delahaie, J., Schranz, E., Gabaldon, T., Pelletier, S., Leprince, O., Ligterink, W., Buitink, J., Hilhorst, H. W. M. & Farrant, J. M., 10 Jun 2019.

Research output: Working paperAcademic

Open Access

Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings

Borges, G., Ottaviani, J. I., van der Hooft, J. J. J., Schroeter, H. & Crozier, A., Jun 2018, In : Molecular Aspects of Medicine. 61, p. 18-30

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)

Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography-High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics

Wolfender, J. L., Nuzillard, J. M., Van Der Hooft, J. J. J., Renault, J. H. & Bertrand, S., 2 Jan 2019, In : Analytical Chemistry. 91, 1, p. 704-742

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)

Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics

Mihaleva, V. V., Vorst, O. F. J., Maliepaard, C. A., Verhoeven, H. A., de Vos, C. H., Hall, R. D. & van Ham, R. C. H. J., 2008, In : Metabolomics. 4, 2, p. 171-182

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
21 Citations (Scopus)

ACE: accurate correction of errors using K-mer tries

Sheikhizadeh Anari, S. & de Ridder, D., 2015, In : Bioinformatics. 31, 19, p. 3216-3218

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes

van der Hooft, J. J. J., Schorn, M., Dorrestein, P. C. & Medema, M. H., 12 Dec 2018. 1 p.

Research output: Contribution to conferenceAbstractAcademic

Open Access

A comparison of database systems for XML-type data

Risse, J. E. & Leunissen, J. A. M., 2010, In : In Silico Biology. 10, 3-4, p. 193-205

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

A computational framework to explore large-scale biosynthetic diversity

Navarro-Muñoz, J. C., Selem-Mojica, N., Mullowney, M. W., Kautsar, S. A., Tryon, J. H., Parkinson, E. I., De Los Santos, E. L. C., Yeong, M., Cruz-Morales, P., Abubucker, S., Roeters, A., Lokhorst, W., Fernandez-Guerra, A., Cappelini, L. T. D., Goering, A. W., Thomson, R. J., Metcalf, W. W., Kelleher, N. L., Barona-Gomez, F. & Medema, M. H., 25 Nov 2019, In : Nature Chemical Biology. 16, p. 60-68

Research output: Contribution to journalArticleAcademicpeer-review

26 Citations (Scopus)

A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Dias Costa, M. C., Silva Artur, M. A., Maia de Oliveira, J., Jonkheer, E., Derks, M., Nijveen, H., Williams, B., Mundree, S., Jiménez-Gómez, J. M., Hesselink, T., Schijlen, E. G. W. M., Ligterink, W., Oliver, M. J., Farrant, J. M. & Hilhorst, H. W. M., 27 Mar 2017, In : Nature Plants. 3, 10 p., 17038.

Research output: Contribution to journalArticleAcademicpeer-review

49 Citations (Scopus)

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds

Dias Costa, M. C., Righetti, K., Nijveen, H., Yazdanpanah, F., Ligterink, W., Buitink, J. & Hilhorst, H. W. M., 2015, In : Planta. 242, 2, p. 435-449

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
25 Citations (Scopus)

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

Witjes, L., Kooke, R., van der Hooft, J. J. J., de Vos, R. C. H., Keurentjes, J. J. B., Medema, M. H. & Nijveen, H., 2 Apr 2019, In : BMC Research Notes. 12, 1, 194.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis

Bakker, E. H., Achenbach, U., Bakker, J. D., van Vliet, J. M., Peleman, J., Segers, B., van der Heijden, S., van der Linde, P., Graveland, R., Hutten, R. C. B., van Eck, H. J., Coppoolse, E. R., van der Vossen, E. A. G. & Goverse, A., 2004, In : Theoretical and Applied Genetics. 109, 1, p. 146-152

Research output: Contribution to journalArticleAcademicpeer-review

50 Citations (Scopus)

AIL and HDG proteins act antagonistically to control cell proliferation

Horstman, A., Fukuoka, H., Muino Acuna, J. M., Nitsch, L. M. C., Guo, C., Passarinho, P. A., Sanchez Perez, G. F., Immink, R. G. H., Angenent, G. C. & Boutilier, K. A., 2015, In : Development. 142, p. 454-464

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

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)

A multilevel analysis of fruit growth of two tomato cultivars in response to fruit temperature

Okello, R. C., de Visser, P. H. B., Heuvelink, E., Lammers, M., de Maagd, R. A., Struik, P. C. & Marcelis, L. F. M., 2015, In : Physiologia Plantarum. 153, 3, p. 403-418

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits

Snoek, B. L., Volkers, J. M., Nijveen, H., Petersen, C., Dirksen, P., Sterken, M. G., Nakad, R., Riksen, J. A. G., Rosenstiel, P. C., Stastna, J. J., Braekman, B. P., Harvey, S. C., Schulenburg, H. & Kammenga, J. E., 12 Mar 2019, In : BMC Biology. 17, 17 p., 24.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

Kaul, S., Koo, H. L., Jenkins, J., Rizzo, M., Rooney, T., Tallon, L. J., Feldblyum, T., Nierman, W., Benito, M. I., Lin, X. & Stiekema, W. J., 2000, In : Nature. 408, p. 796-815

Research output: Contribution to journalArticleAcademicpeer-review

6267 Citations (Scopus)

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics

Sosio, M., Gaspari, E., Iorio, M., Pessina, S., Medema, M. H., Bernasconi, A., Simone, M., Maffioli, S. I., Ebright, R. H. & Donadio, S., 17 May 2018, In : Cell Chemical Biology. 25, 5, p. 540-549.e4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

An analysis of characterized plant sesquiterpene synthases

Durairaj, J., Di Girolamo, A., Bouwmeester, H. J., de Ridder, D., Beekwilder, J. & van Dijk, A. D. J., Feb 2019, In : Phytochemistry. 158, p. 157-165

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

An ancient R gene from Solanum bulbocastanum confers broad-spectrum resistance to late Phytophthora infestans in cultivated potato and tomato

van der Vossen, E. A. G., Sikkema, A., te Lintel Hekkert, B., Gross, J., Stevens, P., Muskens, M., Wouters, T. C. A. E., Pereira, A. B., Stiekema, W. J. & Allefs, S., 2003, In : The Plant Journal. 36, 6, p. 867-882

Research output: Contribution to journalArticleAcademicpeer-review

288 Citations (Scopus)

An evaluation of the performance of three semantic background knowledge sources in comparative anatomy

van Ophuizen, E. A. A. & Leunissen, J. A. M., 2010, In : Journal of integrative bioinformatics. 7, 3, p. 124

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

A new web-based data mining tool for the identification of candidate genes for human genetic disorders

van Driel, M. A., Cuelenaere, K., Kemmeren, P. P. C. W., Leunissen, J. A. M. & Brunner, H. G., 2003, In : European Journal of Human Genetics. 11, p. 57-63

Research output: Contribution to journalArticleAcademicpeer-review

72 Citations (Scopus)

An integrated genome wide genetic map of sequenced NBS-LRR disease resistance gene homologues (RGH) and resistance loci in potato

Bakker, E. H., Borm, T. J. A., Prins, J. C. P., van der Geest, A. H. M., van der Vossen, E., Uenk, G. E., Sabatino, G. J. H., Arens, M. J. B., Nap, J. P. H., de Boer, J. M., van Eck, H., te Lintel Hekkert, B., van Ham, R. C. H. J., Vossen, J., van der Linden, G., Muskens, M., Allefs, S., Bakker, J. & Goverse, A., 2010, Potato breeding after the completion of the dna sequence of the potato genome, EUCARPIA - EAPR joint meeting, Wageningen, The Netherlands, 27 - 30 June, 2010. Wageningen: Eucarpia, p. 53-53

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

An integrative algorithmic approach towards knowledge discovery by bioinformatics

Alako Tadontsop, F. B., 2008, [S.l.. 124 p.

Research output: Thesisinternal PhD, WU

Open Access

A novel Cry9Aa with increased toxicity for Spodoptera exigua (Hübner)

Naimov, S., Nedyalkova, R., Staykov, N., Weemen-Hendriks, M., Minkov, I. & de Maagd, R. A., 2014, In : Journal of Invertebrate Pathology. 115, p. 99-101

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., Lee, S. Y., Fischbach, M. A., Müller, R., Wohlleben, W., Breitling, R., Takano, E. & Medema, M. H., 2015, In : Nucleic acids research. 43, W1, p. W237-W243

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1166 Citations (Scopus)

AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification

Blin, K., Wolf, T., Chevrette, M. G., Lu, X., Schwalen, C. J., Kautsar, S. A., Suarez Duran, H. G., De Los Santos, E. L. C., Kim, H. U., Nave, M., Dickschat, J. S., Mitchell, D. A., Shelest, E., Breitling, R., Takano, E., Lee, S. Y., Weber, T. & Medema, M. H., 2017, In : Nucleic acids research. 45, W1, p. W36-W41

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
569 Citations (Scopus)

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Blin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S. Y., Medema, M. H. & Weber, T., 2 Jul 2019, In : Nucleic acids research. 47, W1, p. W81-W87

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
341 Citations (Scopus)

A pipeline for high throughput detection and mapping of SNPs from EST databases

Anithakumari, A. M., Tang, J., van Eck, H. J., Visser, R. G. F., Leunissen, J. A. M., Vosman, B. & van der Linden, C. G., 2010, In : Molecular Breeding. 26, 1, p. 65-75

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
37 Citations (Scopus)

Application of bioinformatics in plant breeding

Vassilev, D., Leunissen, J., Atanassov, A., Nenov, A. & Dimov, G., 2005, In : Biotechnology and Biotechnological Equipment. 19, spec. iss., p. 139-152

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

Application of high performance compute technology in bioinformatics

Warris, S., 2019, Wageningen: Wageningen University. 156 p.

Research output: Thesisinternal PhD, WU

Open Access

Applications in computer-assisted biology

Nijveen, H., 2013, Wageningen: Wageningen UR. 106 p.

Research output: Thesisinternal PhD, WU

Open Access

Applied evolution: Phylogeny-based approaches in natural products research

Adamek, M., Alanjary, M. & Ziemert, N., 1 Sep 2019, In : Natural Product Reports. 36, 9, p. 1295-1312 18 p.

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology

Casini, A., Chang, F. Y., Eluere, R., King, A. M., Young, E. M., Dudley, Q. M., Karim, A., Pratt, K., Bristol, C., Forget, A., Ghodasara, A., Warden-Rothman, R., Gan, R., Cristofaro, A., Borujeni, A. E., Ryu, M. H., Li, J., Kwon, Y. C., Wang, H., Tatsis, E. & 7 others, Rodriguez-Lopez, C., O'Connor, S., Medema, M. H., Fischbach, M. A., Jewett, M. C., Voigt, C. & Gordon, D. B., 28 Mar 2018, In : Journal of the American Chemical Society. 140, 12, p. 4302-4316

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)

A Protein Classification Benchmark collection for machine learning

Sonego, P., Pacurar, M., Dhir, S., Kertész-Farkas, A., Kocsor, A., Gáspári, Z., Leunissen, J. A. M. & Pongor, S., 2007, In : Nucleic acids research. 35, p. D232-D236

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
37 Citations (Scopus)

A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network

Valentim, F. L., van Mourik, S., Posé, D., Kim, M. C., Schmid, M., van Ham, R. C. H. J., Busscher, M., Sanchez Perez, G. F., Molenaar, J., Angenent, G. C., Immink, R. G. H. & van Dijk, A. D. J., 2015, In : PLoS ONE. 10, 2, e0116973.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
22 Citations (Scopus)

Arabidopsis BIRD zinc finger proteins jointly stabilize tissue boundaries by confining the cell fate regulator SHORT-ROOT and contributing to fate specification

Long, Y., Smet, W., Cruz-Ramírez, A., Sanchez Perez, G., Scheres, B. & Blilou, I., 2015, In : The Plant Cell. 27, 4, p. 1185-1199

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
58 Citations (Scopus)

AraQTL – Arabidopsis eQTL analysis platform

Nijveen, H., Ligterink, W., de Ridder, D. & Snoek, L. B., Dec 2016.

Research output: Contribution to conferencePosterAcademic

AraQTL - Workbench and Archive for systems genetics in Arabidopsis thaliana

Nijveen, H., Ligterink, W., Keurentjes, J. J. B., Loudet, O., Long, J., Sterken, M. G., Prins, P., Hilhorst, H. W., De Ridder, D., Kammenga, J. E. & Snoek, B. L., 2017, In : The Plant Journal. 89, 6, p. 1225-1235

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

Artificial intelligence in the lab: ask not what your computer can do for you

de Ridder, D., Jan 2019, In : Microbial Biotechnology. 12, 1, p. 38-40

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access
4 Citations (Scopus)

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

Mungan, M. D., Alanjary, M., Blin, K., Weber, T., Medema, M. H. & Ziemert, N., 2 Jul 2020, In : Nucleic acids research. 48, W1, p. W546-W552

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

A snapshot of the emerging tomato genome sequence

Mueller, L. A., Klein Lankhorst, R. M., Tanksley, S. D., Peters, R. M., van Staveren, M. J., Datema, E., Fiers, M. W. E. J., van Ham, R. C. H. J., Szinay, D. & de Jong, J. H. S. G. M., 2009, In : The Plant Genome. 2, 1, p. 78-92

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l.

Ernst, M., Nothias, L. F., van der Hooft, J. J. J., Silva, R. R., Saslis-Lagoudakis, C. H., Grace, O. M., Martinez-Swatson, K., Hassemer, G., Funez, L. A., Simonsen, H. T., Medema, M. H., Staerk, D., Nilsson, N., Lovato, P., Dorrestein, P. C. & Rønsted, N., 2 Jul 2019, In : Frontiers in Plant Science. 10, 846.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow

Kang, K. B., Woo, S., Ernst, M., van der Hooft, J. J. J., Nothias, L. F., da Silva, R. R., Dorrestein, P. C., Sung, S. H. & Lee, M., 1 May 2020, In : Phytochemistry. 173, 112292.

Research output: Contribution to journalArticleAcademicpeer-review

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

Severing, E. I., van Dijk, A. D. J. & van Ham, R. C. H. J., 2011, In : BMC Plant Biology. 11, 10 p., 82.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
27 Citations (Scopus)

Assessing the impact of alternative splicing on the diversity and evolution of the proteome in plants

Severing, E. I., 2011, [S.l.]. 119 p.

Research output: Thesisinternal PhD, WU

Open Access

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: Prospects for research-based educational experiences

Epstein, S. C., Charkoudian, L. K. & Medema, M. H., 11 Jul 2018, In : Standards in Genomic Sciences. 13, 1, 16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
12 Citations (Scopus)

A survey of deleterious variants in highly managed commercial layer lines

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 2017.

Research output: Contribution to conferencePoster

Open Access

A survey of functional genomic variation in domesticated chickens

Derks, M. F. L., Megens, H. J., Bosse, M., Visscher, J., Peeters, K., Bink, M. C. A. M., Vereijken, A., Gross, C., De Ridder, D., Reinders, M. J. T. & Groenen, M. A. M., 16 Apr 2018, In : Genetics Selection Evolution. 50, 1, 17.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)