Research output per year
Research output per year
- 1 - 50 out of 93 results
Search results
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2022
Domestication Shapes Recombination Patterns in Tomato
Fuentes, R. R., de Ridder, D., van Dijk, A. D. J. & Peters, S. A., 7 Jan 2022, In: Molecular Biology and Evolution. 39, 1, msab287.Research output: Contribution to journal › Article › Academic › peer-review
Open Access1 Citation (Scopus) -
Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics
van Dijk, A-J., Shiu, S. H. & de Ridder, D., 27 Jun 2022, In: Frontiers in Artificial Intelligence. 5, 959470.Research output: Contribution to journal › Editorial › Academic › peer-review
Open Access -
The miR-200c/141-ZEB2-TGFβ axis is aberrant in human T-cell prolymphocytic leukemia
Erkeland, S. J., Stavast, C. J., Schilperoord-Vermeulen, J., Collo, G. D., van de Werken, H. J. G., Leon, L. G., van Hoven-Beijen, A., van Zuijen, I., Mueller, Y. M., Bindels, E. M., de Ridder, D., Kappers-Klunne, M. C., van Lom, K., van der Velden, V. H. J. & Langerak, A. W., Jan 2022, In: Haematologica. 107, 1, p. 143-153 11 p.Research output: Contribution to journal › Article › Academic › peer-review
Open Access2 Citations (Scopus) -
2021
Accelerated discovery of functional genomic variation in pigs
Derks, M. F. L., Gross, C., Lopes, M. S., Reinders, M. J. T., Bosse, M., Gjuvsland, A. B., de Ridder, D., Megens, H. J. & Groenen, M. A. M., Jul 2021, In: Genomics. 113, 4, p. 2229-2239Research output: Contribution to journal › Article › Academic › peer-review
Open Access4 Citations (Scopus) -
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
Kautsar, S. A., van der Hooft, J. J. J., de Ridder, D. & Medema, M. H., 13 Jan 2021, In: GigaScience. 10, 1, giaa154.Research output: Contribution to journal › Article › Academic › peer-review
Open Access32 Citations (Scopus) -
Chasing breeding footprints through structural variations in Cucumis melo and wild relatives
Demirci, S., Fuentes, R., van Dooijeweert, W., Aflitos, S. A., Schijlen, E. G. W. M., Hesselink, T., de Ridder, D., van Dijk, A. D. J. & Peters, S. A., 26 Jan 2021, In: G3 : Genes Genomes Genetics. 11, 1Research output: Contribution to journal › Article › Academic › peer-review
Open Access1 Citation (Scopus) -
Evaluation of FRET X for single-molecule protein fingerprinting
De Lannoy, C. V., Filius, M., Van Wee, R., Joo, C. & De Ridder, D., 19 Nov 2021, In: iScience. 24, 11, 103239.Research output: Contribution to journal › Article › Academic › peer-review
Open Access3 Citations (Scopus) -
FRETboard: semisupervised classification of FRET traces
de Lannoy, C. V., Filius, M., Kim, S. H., Joo, C. & de Ridder, D., 2021, In: Biophysical Journal. 120, 16, p. 3253-3260Research output: Contribution to journal › Article › Academic › peer-review
1 Citation (Scopus) -
In silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection
De Lannoy, C., Lucas, F. L. R., Maglia, G. & De Ridder, D., 22 Oct 2021, In: iScience. 24, 10, 103202.Research output: Contribution to journal › Article › Academic › peer-review
Open Access3 Citations (Scopus) -
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
Durairaj, J., Melillo, E., Bouwmeester, H. J., Beekwilder, M. J., de Ridder, D. & van Dijk, A. D. J., 22 Mar 2021, In: PLoS Computational Biology. 17, 3Research output: Contribution to journal › Article › Academic › peer-review
Open Access1 Citation (Scopus) -
Machine learning in plant science and plant breeding
van Dijk, A. D. J., Kootstra, G., Kruijer, W. & de Ridder, D., 22 Jan 2021, In: iScience. 24, 1, 101890.Research output: Contribution to journal › Article › Academic › peer-review
Open Access31 Citations (Scopus) -
Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana
Farooq, M., van Dijk, A. D. J., Nijveen, H., Aarts, M. G. M., Kruijer, W., Nguyen, T. P., Mansoor, S. & de Ridder, D., 20 Jan 2021, In: Frontiers in Genetics. 11, p. 1-17 17 p., 609117.Research output: Contribution to journal › Article › Academic › peer-review
Open Access1 Citation (Scopus) -
Signal-based optical map alignment
Akdel, M., Van De Geest, H., Schijlen, E., Van Rijswijck, I. M. H., Smid, E. J., Sanchez-Perez, G. & De Ridder, D., 30 Sep 2021, In: PLoS ONE. 16, 9 September, e0253102.Research output: Contribution to journal › Article › Academic › peer-review
Open Access -
Single-molecule fret for protein characterization
Joo, C., Filius, M., De Lannoy, C. & De Ridder, D., 18 Mar 2021, Patent No. WO2021049940, Priority date 12 Sep 2019Research output: Patent
Open Access -
The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool
Jonkheer, E. M., Brankovics, B., Houwers, I. M., van der Wolf, J. M., Bonants, P. J. M., Vreeburg, R. A. M., Bollema, R., de Haan, J. R., Berke, L., Smit, S., de Ridder, D. & van der Lee, T. A. J., 14 Apr 2021, In: BMC Genomics. 22, 1, 265.Research output: Contribution to journal › Article › Academic › peer-review
Open Access8 Citations (Scopus) -
Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models
Rodenburg, S. Y. A., Seidl, M. F., de Ridder, D. & Govers, F., 11 Oct 2021, In: Frontiers in Microbiology. 12, 748178.Research output: Contribution to journal › Article › Academic › peer-review
Open Access1 Citation (Scopus) -
2020
CAPICE: A computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations
Li, S., Van Der Velde, K. J., De Ridder, D., Van Dijk, A. D. J., Soudis, D., Zwerwer, L. R., Deelen, P., Hendriksen, D., Charbon, B., Van Gijn, M. E., Abbott, K., Sikkema-Raddatz, B., Van Diemen, C. C., Kerstjens-Frederikse, W. S., Sinke, R. J. & Swertz, M. A., 24 Aug 2020, In: Genome Medicine. 12, 1, 75.Research output: Contribution to journal › Article › Academic › peer-review
Open Access8 Citations (Scopus) -
Caretta – A multiple protein structure alignment and feature extraction suite
Akdel, M., Durairaj, J., de Ridder, D. & van Dijk, A. D. J., 2020, In: Computational and Structural Biotechnology Journal. 18, p. 981-992 12 p.Research output: Contribution to journal › Article › Academic › peer-review
Open Access10 Citations (Scopus) -
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., Feb 2020, In: Trends in Biotechnology. 38, 2, p. 191-201Research output: Contribution to journal › Article › Academic › peer-review
Open Access12 Citations (Scopus) -
Geometricus represents protein structures as shape-mers derived from moment invariants
Durairaj, J., Akdel, M., de Ridder, D. & van Dijk, A. D. J., Dec 2020, In: Bioinformatics (Oxford, England). 36, 2, p. i718-i725Research output: Contribution to journal › Article › Academic › peer-review
Open Access4 Citations (Scopus) -
Hap10: Reconstructing accurate and long polyploid haplotypes using linked reads
Majidian, S., Kahaei, M. H. & De Ridder, D., 18 Jun 2020, In: BMC Bioinformatics. 21, 1, 253.Research output: Contribution to journal › Article › Academic › peer-review
Open Access3 Citations (Scopus) -
Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing
Rommel Fuentes, R., Hesselink, T., Nieuwenhuis, R., Bakker, L. V., Schijlen, E. G. W. M., van Dooijeweert, W., Diaz Trivino, S., de Haan, J. R., Sanchez Perez, G. F., Zhang, X., Fransz, P., de Jong, J. H. S. G. M., van Dijk, A. D. J., de Ridder, D. & Peters, S. A., May 2020, In: The Plant Journal. 102, 3, p. 480-492Research output: Contribution to journal › Article › Academic › peer-review
Open Access4 Citations (Scopus) -
Minimum error correction-based haplotype assembly: Considerations for long read data
Majidian, S., Kahaei, M. H. & de Ridder, D., 12 Jun 2020, In: PLoS ONE. 15, 6, e0234470.Research output: Contribution to journal › Article › Academic › peer-review
Open Access4 Citations (Scopus) -
Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana
Hartanto, M., Joosen, R. V. L., Snoek, B. L., Willems, L. A. J., Sterken, M. G., de Ridder, D., Hilhorst, H. W. M., Ligterink, W. & Nijveen, H., Nov 2020, In: G3 : Genes Genomes Genetics. 10, 11, p. 4215-4226Research output: Contribution to journal › Article › Academic › peer-review
Open Access1 Citation (Scopus) -
PCADD: SNV prioritisation in Sus scrofa
Groß, C., Derks, M., Megens, H. J., Bosse, M., Groenen, M. A. M., Reinders, M. & De Ridder, D., 7 Feb 2020, In: Genetics Selection Evolution. 52, 1, 4.Research output: Contribution to journal › Article › Academic › peer-review
Open Access7 Citations (Scopus) -
pCADD scripts data
Groß, C., Derks, M., Megens, H. J., Bosse, M., Groenen, M. A. M., Reinders, M. & De Ridder, D., 2020Research output: Non-textual form › Software › Other research output
Open Access -
Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD
Groß, C., Bortoluzzi, C., de Ridder, D., Megens, H-J., Groenen, M. A. M., Reinders, M. & Bosse, M., 23 Sep 2020, In: Plos Genetics. 16, 9, 1009027.Research output: Contribution to journal › Article › Academic › peer-review
Open Access2 Citations (Scopus) -
The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters
Thines, M., Sharma, R., Rodenburg, S. Y. A., Gogleva, A., Judelson, H. S., Xia, X., van den Hoogen, J., Kitner, M., Klein, J., Neilen, M., de Ridder, D., Seidl, M. F., van den Ackerveken, G., Govers, F., Schornack, S. & Studholme, D. J., 1 Apr 2020, In: Molecular Plant-Microbe Interactions. 33, 5, p. 742-753 12 p.Research output: Contribution to journal › Article › Academic › peer-review
Open Access8 Citations (Scopus) -
The santalene synthase from Cinnamomum camphora: Reconstruction of a sesquiterpene synthase from a monoterpene synthase
Di Girolamo, A., Durairaj, J., van Houwelingen, A. M. M. L., Verstappen, F. W. A., Bosch, H. J., Cankar, K., Bouwmeester, H. J., de Ridder, D., van Dijk, A. D. J. & Beekwilder, M. J., 30 Nov 2020, In: Archives of Biochemistry and Biophysics. 695, 12 p., 108647.Research output: Contribution to journal › Article › Academic › peer-review
Open Access4 Citations (Scopus) -
WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans
Snoek, B. L., Sterken, M. G., Hartanto, M., Van Zuilichem, A-J., Kammenga, J. E., De Ridder, D. & Nijveen, H., 21 Jan 2020, In: Database : the Journal of Biological Databases and Curation. 2020, baz149.Research output: Contribution to journal › Article › Academic › peer-review
Open Access9 Citations (Scopus) -
2019
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. 157-165Research output: Contribution to journal › Article › Academic › peer-review
Open Access20 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. 38-40Research output: Contribution to journal › Comment/Letter to the editor › Academic
Open Access5 Citations (Scopus) -
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 journal › Article › Academic › peer-review
Open Access7 Citations (Scopus) -
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 journal › Article › Academic › peer-review
Open Access2 Citations (Scopus) -
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 journal › Article › Academic › peer-review
Open Access2 Citations (Scopus) -
Improved inference of intermolecular contacts through protein–protein interaction prediction using coevolutionary analysis
Correa Marrero, M., Immink, G. H., de Ridder, D. & van Dijk, A. D. J., Jun 2019, In: Bioinformatics. 35, 12, p. 2036-2042 7 p.Research output: Contribution to journal › Article › Academic › peer-review
7 Citations (Scopus) -
Integrative pangenome analysis of the Pectobacterium genus
Jonkheer, E., Brankovics, B., Houwers, I. M., van der Wolf, J. M., Bonants, P. J. M., Vreeburg, R. A. M., Sheikhizadeh Anari, S., de Ridder, D., Smit, S. & van der Lee, T. A. J., Apr 2019.Research output: Contribution to conference › Poster
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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 journal › Article › Academic › peer-review
Open Access16 Citations (Scopus) -
PanTools
Nijveen, H., Smit, S., Medema, M. H., de Ridder, D., van Dijk, A. D. J., Jonkheer, E. M., van der Hooft, J. J. J., van Lankveld, T., Moed, M. & van Workum, F. J. M., 2019Research output: Non-textual form › Software › Other research output
Open Access -
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 journal › Article › Academic › peer-review
1 Citation (Scopus) -
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 paper
Open Access -
2018
A survey of functional genomic variation in domesticated chickens
Derks, M. F. L., Megens, H. J., Bosse, M., Visscher, J., Peeters, K., Bink, M. C. A. M., Vereijken, A., Gross, C., De Ridder, D., Reinders, M. J. T. & Groenen, M. A. M., 16 Apr 2018, In: Genetics Selection Evolution. 50, 1, 17.Research output: Contribution to journal › Article › Academic › peer-review
Open Access20 Citations (Scopus) -
Computational pan-genomics: status, promises and challenges
Marschall, T., de Ridder, D., Sheikhizadeh Anari, S. & Smit, S., 1 Jan 2018, In: Briefings in Bioinformatics. 19, 1, p. 118-135Research output: Contribution to journal › Article › Academic › peer-review
Open Access158 Citations (Scopus) -
Correcting palindromes in long reads after whole-genome amplification
Warris, S., Schijlen, E. G. W. M., van de Geest, H. C., Vegesna, R., Hesselink, T., te Lintel Hekkert, B., Sanchez Perez, G. F., Medvedev, P., Makova, K. D. & de Ridder, D., 6 Nov 2018, In: BMC Genomics. 19, 798.Research output: Contribution to journal › Article › Academic › peer-review
Open Access6 Citations (Scopus) -
DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom
Demirci, S., Peters, S. A., de Ridder, D. & van Dijk, A. D. J., 1 Aug 2018, In: Plant Journal. 95, 4, p. 686-699 14 p.Research output: Contribution to journal › Article › Academic › peer-review
Open Access11 Citations (Scopus) -
Efficient inference of homologs in large eukaryotic pan-proteomes
Sheikhizadeh Anari, S., de Ridder, D., Schranz, M. E. & Smit, S., 26 Sep 2018, In: BMC Bioinformatics. 19, 1, 11 p.Research output: Contribution to journal › Article › Academic › peer-review
Open Access3 Citations (Scopus) -
Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study
Motazedi, E., Finkers, H. J., Maliepaard, C. A. & de Ridder, D., May 2018, In: Briefings in Bioinformatics. 19, 3, p. 387-403Research output: Contribution to journal › Article › Academic › peer-review
27 Citations (Scopus) -
Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Rodenburg, Y. A., Seidl, M. F., de Ridder, D. & Govers, F., Jun 2018, In: Molecular Plant Pathology. 19, 6, p. 1403-1413Research output: Contribution to journal › Article › Academic › peer-review
Open Access20 Citations (Scopus) -
Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription
Janissen, R., Arens, M. M. A., Vtyurina, N. N., Rivai, Z., Sunday, N. D., Eslami-Mossallam, B., Gritsenko, A. A., Laan, L., de Ridder, D., Artsimovitch, I., Dekker, N. H., Abbondanzieri, E. A. & Meyer, A. S., 23 Aug 2018, In: Cell. 174, 5, p. 1188-1199.e14Research output: Contribution to journal › Article › Academic › peer-review
Open Access43 Citations (Scopus) -
In silico predictions of variant deleteriousness in the genomes of pig species
Gross, C., Derks, M., de Ridder, D. & Reinders, M., 12 Dec 2018. 1 p.Research output: Contribution to conference › Abstract
Open Access