Research Output

2018

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils

Carrión, V. J., Cordovez, V., Tyc, O., Etalo, D. W., de Bruijn, I., de Jager, V. C. L., Medema, M. H., Eberl, L. & Raaijmakers, J. M., 2018, In : ISME Journal. 12, p. 2307–2321

Research output: Contribution to journalArticleAcademicpeer-review

25 Citations (Scopus)

LuxR homolog-linked biosynthetic gene clusters in Proteobacteria

Brotherton, C. A., Medema, M. H. & Greenberg, E. P., 26 Jun 2018, In : mSystems. 3, 3, e00208-17.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

Mining bacterial genomes to reveal secret synergy

Alanjary, M. & Medema, M. H., 28 Dec 2018, In : The Journal of biological chemistry. 293, 52, p. 19996-19997

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes

Moran, P. A., Pascoal, S., Cezard, T., Risse, J. E., Ritchie, M. G. & Bailey, N. W., Oct 2018, In : Molecular Ecology. 27, 19, p. 3905-3924

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Predicting variant deleteriousness in non-human species: Applying the CADD approach in mouse

Groß, C., de Ridder, D. & Reinders, M., 12 Oct 2018, In : BMC Bioinformatics. 19, 1, 373.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Profiling of MicroRNAs in the biofluids of livestock species

Ioannidis, J., Risse, J. & Donadeu, F. X., 13 Feb 2018, Methods in Molecular Biology. Ying, S. Y. (ed.). Humana Press Inc., p. 65-77 13 p. (Methods in Molecular Biology; vol. 1733).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Propagating annotations of molecular networks using in silico fragmentation

da Silva, R. R., Wang, M., Nothias, L. F., van der Hooft, J. J. J., Caraballo-Rodríguez, A. M., Fox, E., Balunas, M. J., Klassen, J. L., Lopes, N. P. & Dorrestein, P. C., 18 Apr 2018, In : PLoS Computational Biology. 14, 4, e1006089.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
45 Citations (Scopus)

Road MAPs to engineer host microbiomes

Oyserman, B. O., Medema, M. H. & Raaijmakers, J. M., 1 Jun 2018, In : Current Opinion in Microbiology. 43, p. 46-54

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
23 Citations (Scopus)

Stripping away the soil: Plant growth promoting microbiology opportunities in aquaponics

Bartelme, R. P., Oyserman, B. O., Blom, J. E., Sepulveda-Villet, O. J. & Newton, R. J., 22 Jan 2018, In : Frontiers in Microbiology. 9, JAN, 8.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

Structure and function of the global topsoil microbiome

Bahram, M., Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., Bengtsson-Palme, J., Anslan, S., Coelho, L. P., Harend, H., Huerta-Cepas, J., Medema, M. H., Maltz, M. R., Mundra, S., Olsson, P. A., Pent, M., Põlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L. & 1 others, Bork, P., 1 Aug 2018, In : Nature. 560, 7717, p. 233-237

Research output: Contribution to journalLetterAcademicpeer-review

211 Citations (Scopus)

Transcription factor mediated control of anthocyanin biosynthesis in vegetative tissues

Outchkourov, N. S., Karlova, R. B., Hölscher, M., Schrama, X., Blilou, I., Jongedijk, E. J., Diez Simon, C., van Dijk, A. D. J., Bosch, H. J., Hall, R. D. & Beekwilder, M. J., Feb 2018, In : Plant Physiology. 176, 2, p. 1862-1878

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
13 Citations (Scopus)

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Motazedi, E., de Ridder, D., Finkers, R., Baldwin, S., Thomson, S., Monaghan, K. & Maliepaard, C., 15 Nov 2018, In : Bioinformatics. 34, 22, p. 3864-3872

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control

Leeggangers, H. A. C. F., Rosilio-Brami, T., Nadal Bigas, J., Rubin, N., van Dijk, A. D. J., Nunez de Caceres Gonzalez, F. F., Saadon-Shitrit, S., Nijveen, H., Hilhorst, H. W. M., Immink, G. H. & Zaccai, M., Jan 2018, In : Plant and Cell Physiology. 59, 1, p. 90-106

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)

Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose

van der Hooft, J. J. J., Alghefari, W., Watson, E., Everest, P., Morton, F. R., Burgess, K. E. V. & Smith, D. G. E., Nov 2018, In : Metabolomics. 14, 11, 144.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)
2017

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)

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
573 Citations (Scopus)

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)

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

Construction of a high-density genetic map from RNA-Seq data for an Arabidopsis bay-0 × shahdara ril population

Serin, E. A. R., Snoek, L. B., Nijveen, H., Willems, L. A. J., Jiménez-Gómez, J. M., Hilhorst, H. W. M. & Ligterink, W., 5 Dec 2017, In : Frontiers in Genetics. 8, DEC, 201.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Coping with living in the soil: The genome of the parthenogenetic springtail Folsomia candida

Faddeeva-Vakhrusheva, A., Kraaijeveld, K., Derks, M. F. L., Anvar, S. Y., Agamennone, V., Suring, W., Kampfraath, A. A., Ellers, J., Le Ngoc, G., van Gestel, C. A. M., Mariën, J., Smit, S., van Straalen, N. M. & Roelofs, D., 2017, In : BMC Genomics. 18, 14 p., 493.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
43 Citations (Scopus)
Open Access
19 Citations (Scopus)
Open Access

Dysregulated signaling, proliferation and apoptosis impact on the pathogenesis of TCRγδ+ T cell large granular lymphocyte leukemia

Kallemeijn, M. J., de Ridder, D., Schilperoord-Vermeulen, J., van der Klift, M. Y., Sandberg, Y., van Dongen, J. J. M. & Langerak, A. W., 2017, In : PLoS ONE. 12, 4, e0175670.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Enhancing faba bean (Vicia faba L.) genome resources

Cooper, J. W., Wilson, M. H., Derks, M. F. L., Smit, S., Kunert, K. J., Cullis, C. & Foyer, C. H., 2017, In : Journal of Experimental Botany. 68, 8, p. 1941-1953

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
12 Citations (Scopus)

Genetic basis of metabolome variation in Arabidopsis

Serin, E. A. R., Willems, L. A. J., Nijveen, H., Snoek, L. B., Hilhorst, H. W. M. & Ligterink, W., 10 Apr 2017.

Research output: Contribution to conferencePosterAcademic

Open Access

Genetic variation in the effect of seed maturation environment on seed performance

Serin, E. A. R., Willems, L. A. J., Nijveen, H., Snoek, L. B., Hilhorst, H. W. M. & Ligterink, W., 2017.

Research output: Contribution to conferencePosterAcademic

Open Access

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

Ceniceros, A., Dijkhuizen, L., Petrusma, M. & Medema, M. H., 2017, In : BMC Genomics. 18, 1, 593.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)
Open Access
5 Citations (Scopus)

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens

Cheng, X., Etalo, D. W., van de Mortel, J. E., Dekkers, E., Nguyen, L., Medema, M. H. & Raaijmakers, J. M., Nov 2017, In : Environmental Microbiology. 19, 11, p. 4638-4656

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

Genomics of adaptation depends on the rate of environmental change in experimental yeast populations

Gorter, F. A., Derks, M. F. L., van den Heuvel, J., Aarts, M. G. M., Zwaan, B. J., de Ridder, D. & de Visser, J. A. G. M., 2017, In : Molecular Biology and Evolution. 34, 10, p. 2613-2626

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Mining prokaryotes for antimicrobial compounds: From diversity to function

Tracanna, V., de Jong, A., Medema, M. H. & Kuipers, O. P., 2017, In : FEMS Microbiology Reviews. 41, 3, p. 417-429

Research output: Contribution to journalArticleAcademicpeer-review

33 Citations (Scopus)

Molecular regulation of temperature-dependent floral induction in Tulipa gesneriana

Leeggangers, M., Nijveen, H., Bigas, J. N., Hilhorst, H. W. M. & Immink, R. G. H., 2017, In : Plant Physiology. 173, 3, p. 1904-1919

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)

NCBI-compliant genome submissions: tips and tricks to save time and money

Pirovano, W., Boetzer, M., Derks, M. F. L. & Smit, S., 2017, In : Briefings in Bioinformatics. 18, 2, p. 179-182

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

van Velzen, R., Holmer, R., Bu, F., Rutten, L. J. J., van Zeijl, A. L., Liu, W., Santuari, L., Cao, Q., Sharma, T., Shen, D., Purwana Roswanjaya, Y., Wardhani, T., Seifi Kalhor, M., Jansen, J., van den Hoogen, D. J., Gungor, B., Hartog, M. V., Hontelez, J., Verver, J. W. G., Yang, W. C. & 11 others, Schijlen, E. G. W. M., Repin, R., Schilthuizen, M., Schranz, M. E., Heidstra, R., Miyata, K., Fedorova, E., Kohlen, W., Bisseling, A. H. J., Smit, S. & Geurts, R., 28 Jul 2017, BioRxiv, 88 p.

Research output: Working paperAcademic

PlantiSMASH: Automated identification, annotation and expression analysis of plant biosynthetic gene clusters

Kautsar, S. A., Suarez Duran, H. G., Blin, K., Osbourn, A. & Medema, M. H., 2017, In : Nucleic acids research. 45, W1, p. W55-W63

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
49 Citations (Scopus)

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria

Chevrette, M. G., Aicheler, F., Kohlbacher, O., Currie, C. R. & Medema, M. H., 19 Jun 2017, In : Bioinformatics. 33, 20, p. 3202-3210

Research output: Contribution to journalArticleAcademicpeer-review

24 Citations (Scopus)

Sequence-based analysis of protein degradation rates

Correa Marrero, M., van Dijk, A-J. & de Ridder, D., 2017, In : Proteins : Structure, Function, and Bioinformatics. 85, 9, p. 1593-1601

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Gritsenko, A. A., Weingarten-Gabbay, S., Elias-Kirma, S., Nir, R., de Ridder, D. & Segal, E., 18 Sep 2017, In : PLoS Computational Biology. 13, 9, 23 p., e1005734.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Sex prepares the plant pathogenic fungus Botrytis cinerea for host invasion

Rodenburg, Y. A., Bin Terhem, R. & van Kan, J. A. L., 5 Feb 2017, Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. Genetics Society of America, p. 141-141

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

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

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., Apr 2017.

Research output: Contribution to conferencePoster

The long reads ahead: De novo genome assembly using the MinION

de Lannoy, C., de Ridder, D. & Risse, J., 2017, In : F1000Research. 6, 1083.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
24 Citations (Scopus)

Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution

Huang, A. C., Kautsar, S. A., Hong, Y. J., Medema, M. H., Bond, A. D., Tantillo, D. J. & Osbourn, A., 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 29, p. E6005-E6014

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
46 Citations (Scopus)
2016

AraQTL – Arabidopsis eQTL analysis platform

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

Research output: Contribution to conferencePosterAcademic

Characterization of secreted modifying enzymes from the late blight pathogen Phytophthora infestans

Schoina, C., Bouwmeester, K., Seidl, M. F., Rodenburg, Y. A., Meijer, H. J. G. & Govers, F., 2016.

Research output: Contribution to conferenceAbstractAcademic

Open Access

Comparative genomics of Beauveria bassiana: Uncovering signatures of virulence against mosquitoes

Valero-Jiménez, C. A., Faino, L., Spring in 'T Veld, D., Smit, S., Zwaan, B. J. & van Kan, J. A. L., 2016, In : BMC Genomics. 17, 986.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products

Li, Y. F., Tsai, K. J. S., Harvey, C. J. B. & Medema, M. H., 2016, In : Fungal Genetics and Biology. 89, p. 18-28

Research output: Contribution to journalArticleAcademicpeer-review

43 Citations (Scopus)

Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways

Medema, M. H. & Osbourn, A., 2016, In : Natural Product Reports. 33, 8, p. 951-962

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
34 Citations (Scopus)