Research Output

2016

Computational strategies for genome-based natural product discovery and engineering in fungi

van der Lee, T. A. J. & Medema, M. H., 2016, In : Fungal Genetics and Biology. 89, p. 29-36

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
28 Citations (Scopus)

CyLineUp: A Cytoscape app for visualizing data in network small multiples

Nijveen, H., Dias Costa, M., Slijkhuis, T., Ligterink, W., Hilhorst, H. W. M. & de Ridder, D., 2016, In : F1000 Research. 5, 635.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Detection of deleterious genomic variation in domesticated animals

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 19 Apr 2016.

Research output: Contribution to conferencePoster

Open Access

Editorial: Synthetic biology and bioinformatics

Medema, M. H. & Zhao, H., 2016, In : Natural Product Reports. 33, 8, p. 913-914

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Effects of parental temperature and nitrate on seed performance are reflected by partly overlapping genetic and metabolic pathways

He, H., Willems, L. A. J., Batushansky, A., Fait, A., Hanson, J., Nijveen, H., Hilhorst, H. W. M. & Bentsink, L., 2016, In : Plant and Cell Physiology. 57, 3, p. 473-487

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
20 Citations (Scopus)

Elucidating and mining the Tulipa and Lilium transcriptomes

Moreno-Pachon, N. M., Leeggangers, M., Nijveen, H., Severing, E., Hilhorst, H. & Immink, R. G. H., 2016, In : Plant Molecular Biology. 92, 3, p. 249-261

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Fire usage and ancient hominin detoxification genes: Protective ancestral variants dominate while additional derived risk variants appear in modern humans

Aarts, J. M. M. J. G., Alink, G. M., Scherjon, F., MacDonald, K., Smith, A. C., Nijveen, H. & Roebroeks, W., 2016, In : PLoS ONE. 11, 9, e0161102.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta

Faddeeva-Vakhrusheva, A., Derks, M. F. L., Anvar, S. Y., Agamennone, V., Suring, W., Smit, S., van Straalen, N. M. & Roelofs, D., 12 Jul 2016, In : Genome Biology and Evolution. 8, 7, p. 2106-2117

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
31 Citations (Scopus)

GeneNetwork: framework for web-based genetics

Sloan, Z., Arends, D., Broman, K. W., Centeno, A., Furlotte, N., Nijveen, H., Yan, L., Zhou, X., Williams, R. W. & Prins, P., 29 May 2016, In : The Journal of Open Source Software. 1, 2, 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Genetic control of environmental maternal effects on seed quality in Arabidopsis

Serin, E. A. R., Snoek, L. B., Nijveen, H., Hilhorst, H. W. M. & Ligterink, W., Jun 2016, p. 14-14.

Research output: Contribution to conferenceAbstractAcademic

Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan

Smit, S., Derks, M. F. L., Bervoets, S., Fahal, A., van Leeuwen, W., van Belkum, A. & van de Sande, W. W. J., 26 May 2016, In : Genome Announcements. 4, 3, e00418-16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

Ferreira de Carvalho, J., Oplaat, C., Pappas, N., Derks, M., de Ridder, D. & Verhoeven, K. J. F., 2016, In : BMC Genomics. 17, 203.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

Nguyen, D. D., Melnik, A. V., Koyama, N., Lu, X., Schorn, M., Fang, J., Aguinaldo, K., Lincecum, T. L., Ghequire, M. G. K., Carrion, V. J., Cheng, T. L., Duggan, B. M., Malone, J. G., Mauchline, T. H., Sanchez, L. M., Marm Kilpatrick, A., Raaijmakers, J. M., De Mot, R., Moore, B. S., Medema, M. H. & 1 others, Dorrestein, P. C., 31 Oct 2016, In : Nature Microbiology. 2, 16197.

Research output: Contribution to journalArticleAcademicpeer-review

59 Citations (Scopus)

Introducing AraQTL – An Arabidopsis eQTL workbench

Nijveen, H. & Snoek, L. B., 2016.

Research output: Contribution to conferenceAbstractAcademic

Learning from co-expression networks: Possibilities and challenges

Serin, E. A. R., Nijveen, H., Hilhorst, H. W. M. & Ligterink, W., 8 Apr 2016, In : Frontiers in Plant Science. 7, 444.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
99 Citations (Scopus)

Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66

Wu, C., Medema, M. H., Läkamp, R. M., Zhang, L., Dorrestein, P. C., Choi, Y. H. & van Wezel, G. P., 2016, In : Acs Chemical Biology. 11, 2, p. 478-490

Research output: Contribution to journalArticleAcademicpeer-review

15 Citations (Scopus)

Metabolic network construction of the Phytophthora infestans – tomato pathosystem

Rodenburg, Y. A., Seidl, M. F., de Ridder, D. & Govers, F., 1 Aug 2016, p. 11.

Research output: Contribution to conferenceAbstractAcademic

PanTools: representation, storage and exploration of pan-genomic data

Sheikhizadeh Anari, S., Schranz, M. E., Akdel, M., de Ridder, D. & Smit, S., 2016, In : Bioinformatics. 32, 17, p. i487-i493

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

Predicting Impact of Variation in Livestock

Gross, C., Reinders, M., de Ridder, D., Derks, M. F. L., Bosse, M., Megens, H. J. W. C. & Groenen, M., 19 Apr 2016.

Research output: Contribution to conferencePoster

Predicting the impact of genetic variation in livestock

Gross, C., Reinders, M., de Ridder, D., Derks, M. F. L., Bosse, M., Megens, H. J. W. C. & Groenen, M., 3 Sep 2016.

Research output: Contribution to conferencePoster

Open Access

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

van Dijk, A-J., Lähdesmäki, H., de Ridder, D. & Rousu, J., 2016, In : BMC Bioinformatics. 17, suppl. 16

Research output: Contribution to journalEditorialAcademic

Open Access
3 Citations (Scopus)

Standardization for natural product synthetic biology

Zhao, H. & Medema, M. H., 2016, In : Natural Product Reports. 33, 8, p. 920-924

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

Blin, K., Medema, M. H., Kottmann, R., Lee, S. Y. & Weber, T., 2016, In : Nucleic acids research. 45, D1, p. D555-D559

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
107 Citations (Scopus)

The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots

Santuari, L., Sanchez-Perez, G. F., Luijten, M., Rutjens, B., Terpstra, I., Berke, L., Gorte, M., Prasad, K., Bao, D., Timmermans-Hereijgers, J. L. P. M., Maeo, K., Nakamura, K., Shimotohno, A., Pencik, A., Novak, O., Ljung, K., Van Heesch, S., De Bruijn, E., Cuppen, E., Willemsen, V. & 6 others, Mähönen, A. P., Lukowitz, W., Snel, B., De Ridder, D., Scheres, B. & Heidstra, R., 2016, In : The Plant Cell. 28, 12, p. 2937-2951

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
46 Citations (Scopus)

You say tomato, I say potato: high-quality genome assembly of the sister-group species Solanum etuberosum provides insights into genome and trait evolution

Berke, L., Grandont, L., Aflitos, S. A., Bachem, C. W. B., Becker, F. F. M., Bouwmeester, K., van de Geest, H. C., Govers, F., de Jong, H., Peters, S. A., Sanchez Perez, G. F., Schijlen, E. G. W. M., van den Berg, R. & Schranz, M. E., 2016, p. 28-29.

Research output: Contribution to conferenceAbstractAcademic

Open Access
2015

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 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)

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)

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)

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
1167 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)

Bacillus thuringiensis-based Products for Insect Pest Control

de Maagd, R. A., 2015, Principles of Plant-Microbe Interactions : Microbes for Sustainable Agriculture. Lugtenberg, B. (ed.). Springer, p. 185-192 185 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Citations (Scopus)

Chromosomal copy number variation in Saccharomyces pastorianus is evidence for extensive genome dynamics in industrial lager brewing strains

van den Broek, M., Bolat, I., Nijkamp, J. F., Ramos, E., Luttik, M. A. H., Koopman, F., Geertman, J. M., de Ridder, D., Pronk, J. T. & Daran, J. M., 2015, In : Applied and Environmental Microbiology. 81, 18, p. 6253-6267

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
33 Citations (Scopus)

Circulating human CD27-IgA+ memory B cells recognize bacteria with polyreactive Igs

Berkowska, M. A., Schickel, J. N., Grosserichter-Wagener, C., De Ridder, D., Ng, Y. S., Van Dongen, J. J. M., Meffre, E. & Van Zelm, M. C., 2015, In : The Journal of Immunology. 195, 4, p. 1417-1426

Research output: Contribution to journalArticleAcademicpeer-review

42 Citations (Scopus)

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

Aflitos, S. A., Severing, E. I., Sanchez Perez, G. F., Peters, S. A., de Jong, H. & de Ridder, D., 2015, In : BMC Bioinformatics. 16, 1, 10 p., 352.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Comparative genomics of virulence towards malaria mosquitoes in Beauveria bassiana

Valero Jimenez, C. A., Spring in 'T Veld, D., Smit, S., Koenraadt, C. J. M., Zwaan, B. J. & van Kan, J. A. L., 2015, Book of Abstracts 28th Fungal Genetics Conference. p. 162

Research output: Chapter in Book/Report/Conference proceedingAbstract

Computational approaches to natural product discovery

Medema, M. H. & Fischbach, M. A., 2015, In : Nature Chemical Biology. 11, 9, p. 639-648

Research output: Contribution to journalArticleAcademicpeer-review

178 Citations (Scopus)

Dick de Ridder over de bioloog die steeds meer een datawetenschapper wordt

de Ridder, D., 2015

Research output: Non-textual formDigital or Visual ProductsOther research output

Open Access

Genomic mutational analysis of the impact of the classical strain improvement program on ß–lactam producing Penicillium chrysogenum

Salo, O. V., Ries, M., Medema, M. H., Lankhorst, P. P., Vreeken, R. J., Bovenberg, R. A. L. & Driessen, A. J. M., 2015, In : BMC Genomics. 16, 15 p., 937.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
26 Citations (Scopus)

High-throughput comparative genomics for plant breeding and its application in the tomato clade

Aflitos, S. A., 2015, Wageningen: Wageningen University. 198 p.

Research output: Thesisinternal PhD, WU

Open Access

Insight into Neutral and Disease-Associated Human Genetic Variants through Interpretable Predictors

van den Berg, B. A., Reinders, M. J. T., de Ridder, D. & de Beer, T. A. P., 2015, In : PLoS ONE. 10, 3, 17 p., e0120729.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Introgression Browser: High throughput whole-genome SNP visualization

Aflitos, S. A., Sanchez Perez, G. F., de Ridder, D., Fransz, P., Schranz, M. E., de Jong, J. H. S. G. M. & Peters, S. A., 2015, In : The Plant Journal. 82, 1, p. 174-182

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Making the difference: integrating structural variation detection tools

Lin, K., Smit, S., Bonnema, A. B., Sanchez Perez, G. F. & de Ridder, D., 2015, In : Briefings in Bioinformatics. 16, 5, p. 852-864

Research output: Contribution to journalArticleAcademicpeer-review

23 Citations (Scopus)

Minimum Information about a Biosynthetic Gene cluster

Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., De Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D. J., Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule, A., Hadjithomas, M. & 134 others, Haines, A. S., Helfrich, E. J. N., Hillwig, M. L., Ishida, K., Jones, A. C., Jones, C. S., Jungmann, K., Kegler, C., Kim, H. U., Kötter, P., Krug, D., Masschelein, J., Melnik, A. V., Mantovani, S. M., Monroe, E. A., Moore, M., Moss, N., Nützmann, H. W., Pan, G., Pati, A., Petras, D., Reen, F. J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N. J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A. K., Balibar, C. J., Balskus, E. P., Barona-Gómez, F., Bechthold, A., Bode, H. B., Borriss, R., Brady, S. F., Brakhage, A. A., Caffrey, P., Cheng, Y. Q., Clardy, J., Cox, R. J., De Mot, R., Donadio, S., Donia, M. S., Van Der Donk, W. A., Dorrestein, P. C., Doyle, S., Driessen, A. J. M., Ehling-Schulz, M., Entian, K. D., Fischbach, M. A., Gerwick, L., Gerwick, W. H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S. E., Ju, J., Katz, L., Kaysser, L., Klassen, J. L., Keller, N. P., Kormanec, J., Kuipers, O. P., Kuzuyama, T., Kyrpides, N. C., Kwon, H. J., Lautru, S., Lavigne, R., Lee, C. Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D. A., Moore, B. S., Moreira, L. M., Müller, R., Neilan, B. A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M. S., Ostash, B., Payne, S. M., Pernodet, J. L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J. M., Salas, J. A., Schmitt, E. K., Scott, B., Seipke, R. F., Shen, B., Sherman, D. H., Sivonen, K., Smanski, M. J., Sosio, M., Stegmann, E., Süssmuth, R. D., Tahlan, K., Thomas, C. M., Tang, Y., Truman, A. W., Viaud, M., Walton, J. D., Walsh, C. T., Weber, T., Van Wezel, G. P., Wilkinson, B., Willey, J. M., Wohlleben, W., Wright, G. D., Ziemert, N., Zhang, C., Zotchev, S. B., Breitling, R., Takano, E. & Glöckner, F. O., 18 Aug 2015, In : Nature Chemical Biology. 11, 9, p. 625-631 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
327 Citations (Scopus)

Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection

Brand, H. K., Ahout, I. M. L., de Ridder, D., van Diepen, A., Li, Y., Zaalberg, M., Andeweg, A., Roeleveld, N., de Groot, R. & Warris, A., 2015, In : PLoS ONE. 10, 7, 14 p., e0131927.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
20 Citations (Scopus)
Open Access

Relevance of Bt toxin interaction studies for environmental risk assessment of genetically modified crops

De Schrijver, A., De Clercq, P., de Maagd, R. A. & van Frankenhuyzen, K., 2015, In : Plant Biotechnology Journal. 13, 9, p. 1221-1223

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

Thompson, O. A., Snoek, L. B., Nijveen, H., Sterken, M. G., Volkers, R. J. M., Brenchley, R., van 't Hof, A., Bevers, R. P. J., Cossins, A. R., Yanai, I., Hajnal, A., Schmid, T., Perkins, J. D., Spencer, D., Kruglyak, L., Andersen, E. C., Moerman, D. G., Hillier, L. W., Kammenga, J. E. & Waterston, R. H., 2015, In : Genetics. 200, 3, p. 975-989

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
44 Citations (Scopus)