Research Output 2000 2020

2020

Mass spectrometry searches using MASST

Wang, M., Jarmusch, A. K., Vargas, F., Aksenov, A. A., Gauglitz, J. M., Weldon, K., Petras, D., da Silva, R., Quinn, R., Melnik, A. V., van der Hooft, J. J. J., Caraballo-Rodríguez, A. M., Nothias, L. F., Aceves, C. M., Panitchpakdi, M., Brown, E., Di Ottavio, F., Sikora, N., Elijah, E. O., Labarta-Bajo, L. & 16 others, Gentry, E. C., Shalapour, S., Kyle, K. E., Puckett, S. P., Watrous, J. D., Carpenter, C. S., Bouslimani, A., Ernst, M., Swafford, A. D., Zúñiga, E. I., Balunas, M. J., Klassen, J. L., Loomba, R., Knight, R., Bandeira, N. & Dorrestein, P. C., 1 Jan 2020, In : Nature Biotechnology. 38, p. 23-26 4 p.

Research output: Contribution to journalLetterAcademicpeer-review

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

Kautsar, S. A., Blin, K., Shaw, S., Navarro Munoz, J. C., Terlouw, B., van der Hooft, J. J. J., Van Santen, J. A., Tracanna, V., Suarez Duran, H., Pascal Andreu, V., Selem Mojica, N., Alanjary, M., Robinson, S., Lund, G., Epstein, S. C., Sisto, A. C., Charkoudian, L. K., Collemare, J., Linington, R. G., Weber, T. & 1 others, Medema, M. H., 8 Jan 2020, In : Nucleic acids research. 48, D1, p. D454-D458

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Multigene Family
Microbial Genome
Chemical Databases
Data Mining
Explosions

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages

Gauglitz, J. M., Aceves, C. M., Aksenov, A. A., Aleti, G., Almaliti, J., Bouslimani, A., Brown, E. A., Campeau, A., Caraballo-Rodríguez, A. M., Chaar, R., da Silva, R. R., Demko, A. M., Di Ottavio, F., Elijah, E., Ernst, M., Ferguson, L. P., Holmes, X., Jarmusch, A. K., Jiang, L., Kang, K. B. & 27 others, Koester, I., Kwan, B., Li, J., Li, Y., Melnik, A. V., Molina-Santiago, C., Ni, B., Oom, A. L., Panitchpakdi, M. W., Petras, D., Quinn, R., Sikora, N., Spengler, K., Teke, B., Tripathi, A., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vrbanac, A., Vu, A. Q., Wang, S. C., Weldon, K., Wilson, K., Wozniak, J. M., Yoon, M., Bandeira, N. & Dorrestein, P. C., 1 Jan 2020, In : Food Chemistry. 302, 125290.

Research output: Contribution to journalArticleAcademicpeer-review

Processed foods
Food and Beverages
raw foods
Metabolomics
Beverages
2019

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
Castanospermum australe
desiccation (plant physiology)
genome
seeds
legumes
20 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

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

Multigene Family
Biological Products
Cluster Analysis
Genome
Metabolomics

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
Plant Genes
Metabolomics
Multigene Family
Genes
Metabolites
2 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
life history trait
inbred lines
quantitative trait loci
genotype
life history
3 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

Sesquiterpenes
sesquiterpenoids
terpenoids
Databases
Mutagenesis
75 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
Bacterial Genomes
Multigene Family
Fungal Genome
Halogenated Diphenyl Ethers
Genome

Application of high performance compute technology in bioinformatics

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

Phylogeny
Biological Products
Chemical compounds
Multigene Family
Metabolites
4 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
2 Citations (Scopus)

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, H. C., 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
Euphorbia
metabolites
herbivores
metabolomics
Eurasia
1 Citation (Scopus)

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K. & 92 others, Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., 9 Aug 2019, In : Nature Biotechnology.

Research output: Contribution to journalComment/Letter to the editorAcademic

HTML
Microbiota
1 Citation (Scopus)

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Meleshko, D., Mohimani, H., Tracanna, V., Hajirasouliha, I., Medema, M. H., Korobeynikov, A. & Pevzner, P. A., 1 Aug 2019, In : Genome Research. 29, 8, p. 1352-1362 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Multigene Family
Metagenomics
Genome
Microbial Genome
Firearms
2 Citations (Scopus)

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

Kang, K. B., Ernst, M., van der Hooft, J. J. J., da Silva, R. R., Park, J., Medema, M. H., Sung, S. H. & Dorrestein, P. C., 20 Feb 2019, In : The Plant Journal.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Rhamnaceae
Mass Spectrometry
mass spectrometry
metabolites
phenotype
2 Citations (Scopus)

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters

Del Carratore, F., Zych, K., Cummings, M., Takano, E., Medema, M. H. & Breitling, R., 28 Feb 2019, In : Communications Biology. 2, 83.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbial Genes
Gene Regulatory Networks
Multigene Family
multigene family
Genes
2 Citations (Scopus)

Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines

Alanjary, M., Cano-Prieto, C., Gross, H. & Medema, M. H., 1 Sep 2019, In : Natural Product Reports. 36, 9, p. 1249-1261 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Polyketides
Peptide Synthases
Polyketide Synthases
Peptides
Biosynthesis
8 Citations (Scopus)

Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

Wiegand, S., Jogler, M., Boedeker, C., Pinto, D., Vollmers, J., Rivas-Marín, E., Kohn, T., Peeters, S. H., Heuer, A., Rast, P., Oberbeckmann, S., Bunk, B., Jeske, O., Meyerdierks, A., Storesund, J. E., Kallscheuer, N., Lücker, S., Lage, O. M., Pohl, T., Merkel, B. J. & 17 others, Hornburger, P., Müller, R. W., Brümmer, F., Labrenz, M., Spormann, A. M., Op den Camp, H. J. M., Overmann, J., Amann, R., Jetten, M. S. M., Mascher, T., Medema, M. H., Devos, D. P., Kaster, A. K., Øvreås, L., Rohde, M., Galperin, M. Y. & Jogler, C., 18 Nov 2019, In : Nature Microbiology. 5, p. 126-140

Research output: Contribution to journalArticleAcademicpeer-review

Cell Division
Ecosystem
Genome
Research
Pharmaceutical Preparations
2 Citations (Scopus)

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

Rogers, S., Wei Ong, C., Wandy, J., Ernst, M., Ridder, L. & Van Der Hooft, J. J. J., 29 Jan 2019, In : Faraday Discussions. 218, p. 284-302 24 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
annotations
metabolites
Metabolites
substructures
Mass spectrometry

Designing Eukaryotic Gene Expression Regulation Using Machine Learning

de Jongh, R. P. H., van Dijk, A. D. J., Julsing, M. K., Schaap, P. J. & de Ridder, D., 17 Aug 2019, In : Trends in Biotechnology.

Research output: Contribution to journalArticleAcademicpeer-review

Gene expression regulation
Gene Expression Regulation
Gene expression
Learning systems
Gene Expression

Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae

Liu, Z., Suarez Duran, H., Harnvanichvech, Y., Stephenson, M. J., Schranz, M. E., Nelson, D., Medema, M. H. & Osbourn, A., 26 Nov 2019, In : New Phytologist.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Exercise self-efficacy is weakly related to engagement in physical activity in persons with long-standing spinal cord injury

Kooijmans, H., Post, M., Motazedi, E., Spijkerman, D., Bongers-Janssen, H., Stam, H. & Bussman, H., 24 Mar 2019, In : Disability and Rehabilitation.

Research output: Contribution to journalArticleAcademicpeer-review

Self Efficacy
Spinal Cord Injuries
Regression Analysis
Gardening
Physical Exertion

Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads

Motazedi, E., Maliepaard, C., Finkers, R., Visser, R. & De Ridder, D., 16 Apr 2019, In : Frontiers in Genetics. 10, MAR, 335.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Polyploidy
Haplotypes
Alleles
Genotype
Population

GeneNoteBook, a collaborative notebook for comparative genomics

Holmer, R., van Velzen, R., Geurts, R., Bisseling, T., de Ridder, D. & Smit, S., 15 Nov 2019, In : Bioinformatics (Oxford, England). 35, 22, p. 4779-4781 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Comparative Genomics
Genomics
Genome
Genes
Bioinformatics

Genome analysis of the marine bacterium Labrenzia sp. strain 011, a potential protective agent of mollusks

Moghaddam, J. A., Dávila-Céspedes, A., Alanjary, M., Blom, J., König, G. M. & Schäberle, T. F., 20 Feb 2019, In : Data. 4, 1, 33.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacteria
Genes
Metabolites
Microorganisms
Sediments

Haplotype estimation in polyploids using DNA sequence data

Motazedi, E., 2019, Wageningen: Wageningen University. 153 p.

Research output: Thesisinternal PhD, WU

Open Access

Hecaton: Reliably detecting copy number variation in plant genomes using short read sequencing data

Wijfjes, R. Y., Smit, S. & De Ridder, D., 7 Nov 2019, In : BMC Genomics. 20, 1, 818.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Plant Genome
Lycopersicon esculentum
Workflow
Arabidopsis
Zea mays
1 Citation (Scopus)
Protein-protein Interaction
Contact
Proteins
Protein
Mutation
1 Citation (Scopus)

Induction of desiccation tolerance in desiccation sensitive Citrus limon seeds

Marques, A., Nijveen, H., Somi, C., Ligterink, W. & Hilhorst, H., May 2019, In : Journal of Integrative Plant Biology. 61, 5, p. 624-638

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Citrus limon
Desiccation
Citrus
desiccation (plant physiology)
paclobutrazol

In silico optimization of mass spectrometry fragmentation strategies in metabolomics

Wandy, J., Davies, V., Van Der Hooft, J. J. J., Weidt, S., Daly, R. & Rogers, S., 1 Oct 2019, In : Metabolites. 9, 10, 219.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolomics
Computer Simulation
Mass spectrometers
Mass spectrometry
Mass Spectrometry

Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization

Rodenburg, S. Y. A., Seidl, M. F., Judelson, H. S., Vu, A. L., Govers, F. & de Ridder, D., 9 Jul 2019, In : mBio. 10, 4, e00454-19.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Phytophthora infestans
Lycopersicon esculentum
Infection
Oomycetes
Thiamine
5 Citations (Scopus)

Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools

Ernst, M., Kang, K. B., Caraballo-Rodríguez, A. M., Nothias, L. F., Wandy, J., Chen, C., Wang, M., Rogers, S., Medema, M. H., Dorrestein, P. C. & van der Hooft, J. J. J., 16 Jul 2019, In : Metabolites. 9, 7, 144.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolomics
Metabolome
Computer Simulation
Workflow
Mass Spectrometry
2 Citations (Scopus)

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Carrión, V. J., Perez-Jaramillo, J., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz-Buck, D., Mendes, L. W., van Ijcken, W. F. J., Gomez-Exposito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., van der Oost, J., Paulson, J. N., Mendes, R., van Wezel, G. P., Medema, M. H. & Raaijmakers, J. M., 1 Nov 2019, In : Science. 366, 6465, p. 606-612 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Microbiota
Peptide Synthases
Polyketide Synthases
Flavobacterium
Mycoses
1 Citation (Scopus)

poreTally: run and publish de novo nanopore assembler benchmarks

de Lannoy, C., Risse, J. E. & de Ridder, D., 1 Aug 2019, In : Bioinformatics. 35, 15, p. 2663-2664 2 p.

Research output: Contribution to journalArticleAcademicpeer-review

Nanopores
Nanopore
Benchmarking
Benchmark
Sequencing
12 Citations (Scopus)

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters

Blin, K., Kim, H. U., Medema, M. H. & Weber, T., Jul 2019, In : Briefings in Bioinformatics. 20, 4, p. 1103-1113 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Multigene Family
Metabolites
Genes
Genome
Biological Products
68 Citations (Scopus)

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, T. C., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K. & 92 others, da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., 1 Aug 2019, In : Nature Biotechnology. 37, 8, p. 852-857 6 p.

Research output: Contribution to journalArticleAcademic

4 Citations (Scopus)

Structural variants in 3000 rice genomes

Fuentes, R. R., Chebotarov, D., Duitama, J., Smith, S., De la Hoz, J. F., Mohiyuddin, M., Wing, R. A., McNally, K. L., Tatarinova, T., Grigoriev, A., Mauleon, R. & Alexandrov, N., 1 May 2019, In : Genome Research. 29, 5, p. 870-880 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genome
5' Untranslated Regions
Genome-Wide Association Study
Computational Biology
Genes
1 Citation (Scopus)

Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli

Van Der Hooft, J. J. J., Goldstone, R. J., Harris, S., Burgess, K. E. V. & Smith, D. G. E., 19 Feb 2019, In : Frontiers in Microbiology. 10, FEB, 252.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Probiotics
Escherichia coli
Citrulline
Metabolome
Ornithine
27 Citations (Scopus)

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

Blin, K., Pascal Andreu, V., de Los Santos, E. L. C., Del Carratore, F., Lee, S. Y., Medema, M. H. & Weber, T., 8 Jan 2019, In : Nucleic acids research. 47, D1, p. D625-D630

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbial Genome
Bacterial Genomes
Multigene Family
Genome
Databases

The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

Thines, M., Sharma, R., Rodenburg, Y. A., Gogleva, A., Judelson, H. S., Xia, X., van den Hoogen, D. J., Kitner, M., Klein, J., Neilen, M., de Ridder, D., Seidl, M. F., van den Ackerveken, G., Govers, F., Schornack, S. & Studholme, D. J., 31 Jul 2019, BioRxiv.

Research output: Working paperAcademic

Peronospora
heterozygosity
Oomycetes
promoter regions
genome

The Metabolomics Society—Current State of the Membership and Future Directions

Zanetti, K. A., Hall, R. D., Griffin, J. L., Putri, S., Salek, R. M., Styczynski, M. P., Tugizimana, F. & van der Hooft, J. J. J., 3 May 2019, In : Metabolites. 9, 89.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolomics
Postal Service
Social Media
Surveys and Questionnaires
Direction compound

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

Van Santen, J. A., Jacob, G., Singh, A. L., Aniebok, V., Balunas, M. J., Bunsko, D., Neto, F. C., Castaño-Espriu, L., Chang, C., Clark, T. N., Cleary Little, J. L., Delgadillo, D. A., Dorrestein, P. C., Duncan, K. R., Egan, J. M., Galey, M. M., Haeckl, J., Hua, A., Hughes, A. H., Iskakova, D. & 23 others, Khadilkar, A., Lee, J. H., Lee, S., Legrow, N., Liu, D. Y., Macho, J. M., McCaughey, C. S., Medema, M. H., Neupane, R. P., O'Donnell, T. J., Paula, J. S., Sanchez, L. M., Shaikh, A. F., Soldatou, S., Terlouw, B. R., Tran, T. A., Valentine, M., Van Der Hooft, J. J. J., Vo, D. A., Wang, M., Wilson, D., Zink, K. E. & Linington, R. G., 27 Nov 2019, In : ACS Central Science. 5, 11, p. 1824-1833 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Biological Products
Interoperability
Microorganisms
Data mining
Websites
2018
21 Citations (Scopus)

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

Catechin
Metabolism
Metabolites
Urine
Plasmas
Open Access
7 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
Biosynthetic Pathways
Nucleosides
Genes
Anti-Bacterial Agents
Multigene Family
26 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

Cell-Free System
Streptomyces
Pyrrolnitrin
Enediynes
Streptomyces coelicolor
9 Citations (Scopus)

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
Workflow
Multigene Family
Research
Synthetic Genes
Molecular Sequence Annotation