Projects per year
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Active
Mechanisms of root microbiome recruitment under drought stress in Solanaceae
van der Wielen, N. (PhD candidate), Testerink, C. (Promotor) & Karlova, R. (Co-promotor)
1/01/25 → …
Project: PhD
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Developing an efficient, dynamic and versatile pangenome representation to handle large-scale, complex genomic data across diverse taxonomic levels
Flege, P. (PhD candidate), de Ridder, D. (Promotor) & Smit, S. (Co-promotor)
1/12/24 → …
Project: PhD
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Mitigation of negative temperature effects on curd induction and quality in cauliflower
Syma, D. (PhD candidate), Bonnema, G. (Promotor), Immink, R. (Co-promotor) & Smit, S. (Co-promotor)
1/09/24 → …
Project: PhD
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FIBERME
Boneschansker, M. (PhD candidate), Kleerebezem, M. (Promotor), Medema, M. (Promotor), Boekhorst, J. (Co-promotor) & Probst, D. (Co-promotor)
1/09/24 → …
Project: PhD
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Genome responses to stress in crop species
Nieuwenhuis, R. (PhD candidate), de Ridder, D. (Promotor), Fiers, M. (Co-promotor), Nijveen, H. (Co-promotor) & Peters, S. (Co-promotor)
1/06/24 → …
Project: PhD
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Modelling orphan protein evolution using machine learning approaches based on sequence and structure.
Chen, C. (PhD candidate), de Ridder, D. (Promotor) & Kupczok, A. (Co-promotor)
15/01/24 → …
Project: PhD
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Integration of computational mass spectrometry and risk-based datamining in food safety analysis
Dietrich, J. (PhD candidate), de Ridder, D. (Promotor), Mol, H. (Co-promotor) & van der Hooft, J. (Co-promotor)
15/10/23 → …
Project: PhD
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Substructure-driven linking of Genes and Metabolites to accelerate Natural Products Discovery - novel bioactive metabolites
Torres Ortega, R. (PhD candidate), Medema, M. (Promotor), de Ridder, D. (Promotor) & van der Hooft, J. (Co-promotor)
1/10/23 → …
Project: PhD
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Tapping the potential of plant specialized metabolic diversity through integrative omics
del Pup, E. (PhD candidate), Medema, M. (Promotor), de Ridder, D. (Promotor) & van der Hooft, J. (Co-promotor)
1/09/23 → …
Project: PhD
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Identifying and visualising shared building blocks of biosynthetic gene clusters
Lien, A. (PhD candidate), Medema, M. (Promotor), de Ridder, D. (Promotor) & van der Hooft, J. (Co-promotor)
15/08/23 → …
Project: PhD
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Explore the evolution and diversity of Rosa species through genomics
Yang, Z. (PI) & Smit, S. (Project Leader)
1/07/23 → 1/07/25
Project: PostDoc
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Machine-Learning based prediction of meiotic recombination
Peñuela Aristizabal, M. (PI), van Dijk, A.-J. (Project Leader), Bai, Y. (CoI), Bouwmeester, K. (CoI) & Auxier, B. (CoI)
1/07/23 → 30/06/25
Project: PostDoc
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Plant-XR
Noordijk, B. (PhD candidate), de Ridder, D. (Promotor) & van Dijk, A.-J. (Co-promotor)
1/05/23 → …
Project: PhD
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Urinary Tract Infections Revisited: Microbial Eco-evolutionary Drivers and Regulators.
Koetsier, R. (PhD candidate), Medema, M. (Promotor), de Ridder, D. (Promotor) & van der Hooft, J. (Co-promotor)
1/04/23 → …
Project: PhD
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Virus diversity and genome evolution in natural plant ecosystems (V-GENE)
Karapliafis, D. (PhD candidate), de Ridder, D. (Promotor) & Kupczok, A. (Co-promotor)
1/02/23 → …
Project: PhD
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Tapping the potential of plant specialized metabolic diversity through integrative omics
Wolters, F. (PhD candidate), Medema, M. (Promotor), Schranz, E. (Promotor), Bouwmeester, K. (Co-promotor) & van der Hooft, J. (Co-promotor)
15/01/23 → …
Project: PhD
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Inferring spatiotemporal-transcriptome-based gene regulatory networks
Gao, Y. (PhD candidate), de Ridder, D. (Promotor) & van Dijk, A.-J. (Promotor)
1/01/23 → …
Project: PhD
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Characterization of Hirschfeldia incana genes contributing to the high photosynthetic light use efficiency at high irradiance.
Bengoa Luoni, S. (PI), Aarts, M. (Project Leader), Harbinson, J. (CoPI) & de Ridder, D. (CoPI)
1/08/22 → 1/08/25
Project: PostDoc
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Efficient engineering of non-native enzyme properties using representational learning
van der Flier, F. (PhD candidate), de Ridder, D. (Promotor) & van Dijk, A.-J. (Co-promotor)
1/06/22 → …
Project: PhD
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Exploring genome evolution and differentiation of agronomical traits in Solanaceae: A pangenome approach
Papastolopoulou, C. (PhD candidate), de Ridder, D. (Promotor), Peters, S. (Co-promotor) & Smit, S. (Co-promotor)
1/06/22 → …
Project: PhD
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Deciphering plant-microbiome communication for sustainable crop production
Li, Y. (PhD candidate), Medema, M. (Promotor), Mommer, L. (Promotor) & Raaijmakers, J. (Promotor)
1/12/21 → …
Project: PhD
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Meta'omic analysis of sponge microbiota.
Hrab, P. (PhD candidate), Medema, M. (Promotor), Sipkema, D. (Promotor), de Ridder, D. (Promotor) & Schorn, M. (Other)
1/12/21 → …
Project: PhD
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DECIPHER
Meijer, D. (PhD candidate), Medema, M. (Promotor), de Ridder, D. (Promotor) & van der Hooft, J. (Co-promotor)
15/10/21 → …
Project: PhD
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Pangenome mining for quarantine organisms
Pardeshi, L. (PhD candidate), de Ridder, D. (Promotor), Smit, S. (Co-promotor) & van der Lee, T. (Co-promotor)
1/10/21 → …
Project: PhD
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Spec2Bed: Innovative Metabolite Grouping to Learn structure and Function from Metabolomics Profiles
de Jonge, N. (PhD candidate), de Ridder, D. (Promotor) & van der Hooft, J. (Co-promotor)
15/09/21 → …
Project: PhD
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Identification of the microbial consortia and mechanisms of soil suppressiveness to Fusarium culmorum
Jing, J. (PhD candidate), Medema, M. (Promotor) & Raaijmakers, J. (Promotor)
1/09/21 → …
Project: PhD
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Constructing and optimizing the synthetic microbial community using evolutionary principles for mitigating ammonia and greenhouse gases generated by swine fecal microbiota
Liu, J. (PhD candidate), de Ridder, D. (Promotor) & Kupczok, A. (Co-promotor)
1/09/21 → …
Project: PhD
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An integrative analysis of variation in Lactuca.
van Workum, D.-J. M. (PhD candidate), de Ridder, D. (Promotor), Schranz, E. (Co-promotor) & Smit, S. (Co-promotor)
1/11/20 → …
Project: PhD
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Unwiring beneficial functions and regulatory networks in the plant endosphere
Pronk, L. (PhD candidate), Medema, M. (Promotor), de Ridder, D. (Promotor) & Kupczok, A. (Co-promotor)
15/09/20 → …
Project: PhD
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Integration of different " - omics" datasets in Brassicaceae
Lin, K. (PhD candidate), Visser, R. (Promotor) & Bonnema, G. (Co-promotor)
2/01/10 → …
Project: PhD
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Finished
Integrative genome/metabolome mining for marine natural products
Zdouc, M. (PI), Medema, M. (PI) & van der Hooft, J. (PI)
1/02/22 → 1/02/24
Project: PostDoc
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LetttuceKnow, Project 1.1 “Lactuca diversity and evolution”
Feng, T. (PI), Schranz, E. (Project Leader) & Smit, S. (CoI)
1/02/22 → 1/02/22
Project: PostDoc
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A computational framework to interpret the chemical language of the microbiome
Reitz, Z. (PI) & Medema, M. (PI)
1/03/21 → 30/08/22
Project: PostDoc
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Population genomics and phylogenetic studies on Fusarium using a pangenomic approach
Yang, M. (PhD candidate), de Ridder, D. (Promotor), van der Lee, T. (Co-promotor) & Smit, S. (Other)
1/11/19 → 9/09/24
Project: PhD
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Finding genes for traits using system genetics
Hartanto, M. (PhD candidate), de Ridder, D. (Promotor) & Nijveen, H. (Co-promotor)
15/01/19 → 12/12/23
Project: PhD
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Integrative bioinformatics for linking genomics to phenomics (a Netherlands-Pakistan collaboration)
Farooq, M. (PhD candidate), de Ridder, D. (Promotor), Nijveen, H. (Co-promotor) & van Dijk, A.-J. (Co-promotor)
26/11/18 → 20/09/23
Project: PhD
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Pangenomic applications for plants and pathogens
Jonkheer, E. (PhD candidate), de Ridder, D. (Promotor), Smit, S. (Co-promotor) & van der Lee, T. (Co-promotor)
15/09/18 → 17/09/24
Project: PhD
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In pursuit of next-generation lipopeptide antibiotics
Terlouw, B. (PhD candidate), Medema, M. (Promotor) & de Ridder, D. (Promotor)
1/07/18 → 26/09/23
Project: PhD
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Meiotic Recombination in Crops
Fuentes, R. (PhD candidate), de Ridder, D. (Promotor), Peters, S. (Co-promotor) & van Dijk, A.-J. (Co-promotor)
15/05/18 → 28/08/23
Project: PhD
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Integrated omics analysis for small molecule-mediated host-microbiome inteeractions (iOMEGA - integrated omics for metabolomics and genomics annotation)
van der Hooft, J. (PI), de Ridder, D. (Project Leader) & Medema, M. (CoI)
5/05/18 → 30/04/21
Project: PostDoc
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Single-molecule protein sequencing
de Lannoy, C. (PhD candidate) & de Ridder, D. (Promotor)
2/10/17 → 8/11/22
Project: PhD
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Novel approaches to combine large-scale metabolomics and genomics data
van der Hooft, J. (PI), Medema, M. (Project Leader) & Dorrestein, P. C. (Project Leader)
15/09/17 → 14/09/19
Project: PostDoc
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Novel approaches to combine large-scale metabolomics and genomics data
van der Hooft, J. (PI) & Medema, M. (CoI)
15/09/17 → 15/09/19
Project: PostDoc
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Novel enzymes for fragrance and flavour
Durairaj, J. (PhD candidate), de Ridder, D. (Promotor) & van Dijk, A.-J. (Co-promotor)
1/08/17 → 15/09/21
Project: PhD
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Algorithms for biosynthetic pathway discovery and analysis in the human microbiome
Pascal Andreu, V. (PhD candidate), de Ridder, D. (Promotor) & Medema, M. (Co-promotor)
2/01/17 → 13/09/21
Project: PhD
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Exploiting copy number variation for rapid improvement of abiotic stress tolerance in crops
Wijfjes, R. (PhD candidate), de Ridder, D. (Promotor) & Smit, S. (Co-promotor)
15/09/16 → 13/12/21
Project: PhD
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A Computational Framework for the Discovery and Engineering of Biosynthetic Pathways
Kautsar, S. (PhD candidate), de Ridder, D. (Promotor) & Medema, M. (Co-promotor)
1/09/16 → 25/05/21
Project: PhD
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Harnessing the soil microbiome for improved stress tolerance in crop plants
Tracanna, V. (PhD candidate), de Ridder, D. (Promotor) & Medema, M. (Co-promotor)
15/06/16 → 21/02/22
Project: PhD
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Next-generation optical mapping for high-throughput genotyping
Akdel, M. (PhD candidate) & de Ridder, D. (Promotor)
17/05/16 → 7/06/22
Project: PhD