Research output per year
Research output per year
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Dive into the research topics where Dick de Ridder is active. These topic labels come from the works of this person. Together they form a unique fingerprint.
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction
Capela, J., Zimmermann-Kogadeeva, M., van Dijk, A. D. J., de Ridder, D., Dias, O. & Rocha, M., 2025, In: BMC Bioinformatics. 26, 21 p., 68.Research output: Contribution to journal › Article › Academic › peer-review
Open Access -
Exploring intra- and intergenomic variation in haplotype-resolved pangenomes
Jonkheer, E. M., de Ridder, D., van der Lee, T. A. J., de Haan, J. R., Berke, L. & Smit, S., 2025, In: Plant Biotechnology Journal. 23, 3, p. 874-886 13 p.Research output: Contribution to journal › Article › Academic › peer-review
Open Access -
A catalogue of recombination coldspots in interspecific tomato hybrids
Fuentes, R. R., Nieuwenhuis, R., Chouaref, J., Hesselink, T., van Dooijeweert, W., van den Broeck, H. C., Schijlen, E., Schouten, H. J., Bai, Y., Fransz, P., Stam, M., de Jong, H., Trivino, S. D., de Ridder, D., van Dijk, A. D. J. & Peters, S. A., 1 Jul 2024, In: Plos Genetics. 20, 22 p., e1011336.Research output: Contribution to journal › Article › Academic › peer-review
Open Access -
Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration
Yang, M., Smit, S., de Ridder, D., Feng, J., Liu, T., Xu, J., van der Lee, T. A. J., Zhang, H. & Chen, W., 5 Aug 2024, (E-pub ahead of print) In: Advanced Science. 2401899.Research output: Contribution to journal › Article › Academic › peer-review
Open Access -
A generic pipeline for CADD Score generation: chickenCADD and turkeyCADD
Lensing, K., van Schipstal, J. G. C., de Ridder, D., Groenen, M. A. M. & Derks, M. F. L., 3 Nov 2024, BioRxiv.Research output: Working paper › Preprint
Datasets
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Profile hidden Markov models trained on aligned KEGG Orthology sequences for enzyme annotation
Rodenburg, Y. A. (Creator), de Ridder, D. (Contributor), Govers, F. (Contributor) & Seidl, M. F. (Creator), Wageningen University & Research, 7 Oct 2019
DOI: 10.4121/uuid:9b6e6aa0-b815-409f-9e96-04828b03290b
Dataset
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Single-molecule protein sequencing through fingerprinting: computational assessment
Yao, Y. (Creator), Docter, M. W. (Creator), van Ginkel, H. G. T. M. (Creator), de Ridder, D. (Creator) & Joo, C. (Creator), TU Delft, 19 Jan 2018
DOI: 10.4121/uuid:08a078fc-9d4c-44d1-88c9-9cb412b83a46
Dataset
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Olfactomedin 4 serves as a marker for disease severity in pediatric Respiratory Syncytial Virus (RSV) infection
Brand, K. H. (Creator), Ahout, I. M. (Creator), de Ridder, D. (Creator), van Diepen, A. (Creator), Li, Y. (Creator), Zaalberg, M. (Creator), Andeweg, A. (Creator), Roeleveld, N. (Creator), de Groot, R. (Creator), Warris, A. (Creator), Hermans, P. W. (Creator), Ferwerda, G. (Creator) & Staal, F. J. (Creator), Wageningen University, 6 Jun 2015
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69606
Dataset
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The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots
Santuari, L. (Creator), Sanchez-Perez, G. F. (Creator), Luijten, M. (Creator), Rutjens, B. (Creator), Terpstra, I. (Creator), Berke, L. (Creator), Gorte, M. (Creator), Prasad, K. (Creator), Bao, D. (Creator), Timmermans-Hereijgers, J. L. P. M. (Creator), Maeo, K. (Creator), Nakamura, K. (Creator), Shimotohno, A. (Creator), Pencik, A. (Creator), Novak, O. (Creator), Ljung, K. (Creator), Van Heesch, S. (Creator), De Bruijn, E. (Creator), Cuppen, E. (Creator), Willemsen, V. (Creator), Mähönen, A. P. (Creator), Lukowitz, W. (Creator), Snel, B. (Creator), De Ridder, D. (Creator), Scheres, B. (Creator) & Heidstra, R. (Creator), Wageningen University & Research, 31 Mar 2016
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79755
Dataset
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Dataset underlying the publication: "MoGAAAP: A modular Snakemake workflow for automated genome assembly and annotation with quality assessment"
van Workum, D.-J. M. (Creator), Dey, K. K. (Creator), Kozik, A. (Creator), Lavelle, D. (Creator), de Ridder, D. (Creator), Schranz, E. (Creator), Michelmore, R. (Creator) & Smit, S. (Creator), Wageningen University & Research, 17 Feb 2025
DOI: 10.4121/4b39da65-2eef-4e05-8583-25f8850cf932
Dataset
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AI in bioinformatics research & education
de Ridder, D. (Speaker)
1 Mar 2024Activity: Talk/presentation/lecture › Oral presentation › Academic
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Digital Twins in the Living Environment
de Ridder, D. (Contributor), van der Heide, J. (Contributor) & Knibbe, W. J. (Speaker)
1 Nov 2021Activity: Talk/presentation/lecture › Lecture/seminar/webinar › Academic
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6th Conference New Technologies in Agriculture.
Knibbe, W. J. (Invited speaker), de Ridder, D. (Contributor) & van der Heide, J. (Contributor)
9 Dec 2021Activity: Talk/presentation/lecture › Oral presentation › Academic
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From GWAS Peak to Causal Mutation; Utilizing p(ig)CADD Scores to Prioritize Sequence Variation
Derks, M. (Speaker), Gross, C. (Contributor), Lopes, M. S. (Contributor), Reinders, M. J. T. (Contributor), Bosse, M. (Contributor), Gjuvsland, A. B. (Contributor), Megens, H.-J. (Contributor), de Ridder, D. (Contributor) & Groenen, M. (Contributor)
11 Jan 2020 → 15 Jan 2020Activity: Talk/presentation/lecture › Lecture/seminar/webinar › Other
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A survey of deleterious variants in highly managed commercial layer lines
Derks, M. F. L. (Presenter), Megens, H. J. W. C. (Contributor), Bosse, M. (Contributor), Gross, C. (Contributor), Reinders, M. (Contributor), de Ridder, D. (Contributor) & Groenen, M. (Contributor)
4 Apr 2017Activity: Other › Other
Press/Media
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Dutch cabinet invests EUR42 million in CROP-XR institute for faster development of resilient agricultural crops
Immink, R., Testerink, C., de Ridder, D. & van Dijk, A.-J.
18/04/22
1 Media contribution
Press/Media: Research › Popular
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Smart search for traits
Testerink, C., de Ridder, D. & van Dijk, A.-J.
29/09/21 → 30/09/21
2 Media contributions
Press/Media: Research › Professional
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Genoomrecherche is (n)iets op het spoor in Wuhan; Ophef
10/04/21
1 Media contribution
Press/Media: Research › Popular
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Forecasting with digital doppelgängers
10/06/20 → 11/06/20
2 Media contributions
Press/Media: Expert Comment › Other
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WUR is investing four million euros on self-learning models: A digital twins baby boom
de Ridder, D., Knibbe, W. J., Afman, L., Been, T. & Evers, J.
27/02/20 → 28/02/20
2 Media contributions
Press/Media: Research › Other
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Computational pangenomics
Flege, P. (PhD candidate), de Ridder, D. (Promotor) & Smit, S. (Co-promotor)
1/12/24 → …
Project: PhD
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Ecosystem within (EcoWhite): Exploring the virome and other microbiome members in whiteflies.
Patiño Medina, L. (PhD candidate), de Ridder, D. (Promotor), van Oers, M. (Promotor), Bryon, A. (Co-promotor) & Kupczok, A. (Co-promotor)
15/09/24 → …
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), Peters, S. (Co-promotor) & Nijveen, H. (Other)
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