Dick de Ridder

Search results

• 2023

  Advanced drinking water production by 1 kDa hollow fiber nanofiltration - Biological activated carbon filtration (HFNF - BACF) enhances biological stability and reduces micropollutant levels compared with conventional surface water treatment

  Schurer, R., de Ridder, D. J., Schippers, J. C., Hijnen, W. A. M., Vredenbregt, L. & van der Wal, A., Apr 2023, In: Chemosphere. 321, 16 p., 138049.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Nanofiltration 100%
  • Surface waters 95%
  • Water Purification 86%
  • Potable water 80%
  • Water treatment 79%
  3 Citations (Scopus)

• baseLess: lightweight detection of sequences in raw MinION data

  Noordijk, B., Nijland, R., Carrion, V. J., Raaijmakers, J. M., de Ridder, D. & de Lannoy, C., 15 Feb 2023, In: Bioinformatics Advances. 3, 1, vbad017.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Nucleic acids 100%
  • Costs and Cost Analysis 85%
  • Fish 74%
  • Nucleic Acids 67%
  • Target tracking 64%

• Beyond sequence: Structure-based machine learning

  Durairaj, J., de Ridder, D. & van Dijk, A. D. J., 2023, In: Computational and Structural Biotechnology Journal. 21, p. 630-643

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Machine Learning 100%
  • Proteins 80%
  • Machine learning 64%
  • Protein Structure 43%
  • Protein 36%
  2 Citations (Scopus)

• Genomic prediction in plants: opportunities for ensemble machine learning based approaches

  Farooq, M., van Dijk, A. D. J., Nijveen, H., Mansoor, S. & de Ridder, D., 10 Jan 2023, In: F1000 Research. 11, 802.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Machine Learning 100%
  • Statistical Ensemble 87%
  • Hilbert Space 52%
  • Nucleotide 48%
  • Marker 25%
  1 Citation (Scopus)

• Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors

  Correa Marrero, M., Capdevielle, S., Huang, W., Al-subhi, A. M., Busscher, M., Busscher-Lange, J., van der Wal, F., de Ridder, D., van Dijk, A. D. J., Hogenhout, S. A. & Immink, G. H., 15 Nov 2023, (E-pub ahead of print) In: The Plant Journal.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Phytoplasma 100%
  • Protein Interaction Mapping 93%
  • transcription factors 39%
  • Transcription Factors 38%
  • phytoplasmal diseases 19%

• Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning

  Nieuwkoop, T., Terlouw, B. R., Stevens, K. G., Scheltema, RA., De Ridder, D., Van der Oost, J. & Claassens, NJ., 21 Mar 2023, In: Nucleic acids research. 51, 5, p. 2363-2376

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Machine Learning 100%
  • Codon 87%
  • Random Allocation 86%
  • Genes 35%
  • Proteins 32%
  3 Citations (Scopus)

• The use of proton transfer reaction mass spectrometry for high throughput screening of terpene synthases

  Di Girolamo, A., Pedrotti, M., Koot, A., Verstappen, F., van Houwelingen, A., Vossen, C., Bouwmeester, H., de Ridder, D. & Beekwilder, J., 31 May 2023, In: Journal of Mass Spectrometry. 58, 6, p. e4951 12 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Proton Transfer Reaction Mass Spectrometry 100%
  • Terpene 75%
  • High Throughput Screening 70%
  • Gas Chromatography Mass Spectrometry (GCMS) 49%
  • Sample Preparation 36%
  1 Citation (Scopus)
• 2022

  A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories

  Götz, M., Barth, A., Bohr, S. S. R., Börner, R., Chen, J., Cordes, T., Erie, D. A., Gebhardt, C., Hadzic, M. C. A. S., Hamilton, G. L., Hatzakis, N. S., Hugel, T., Kisley, L., Lamb, D. C., de Lannoy, C., Mahn, C., Dunukara, D., de Ridder, D., Sanabria, H., Schimpf, J., & 9 othersSeidel, C. A. M., Sigel, R. K. O., Sletfjerding, M. B., Thomsen, J., Vollmar, L., Wanninger, S., Weninger, K. R., Xu, P. & Schmid, S., 14 Sept 2022, In: Nature Communications. 13, 1, p. 5402

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • smFRET Spectroscopy 100%
  • Benchmarking 72%
  • Degradation Rate 64%
  • trajectories 52%
  • Kinetics 48%
  14 Citations (Scopus)

• Digital twins in the green life sciences

  Knibbe, W. J., Afman, L., Boersma, S., Bogaardt, M-J., Evers, J., Van Evert, F., Van der Heide, J., Hoving, I., Van Mourik, S., De Ridder, D. & De Wit, A., 2022, In: NJAS: Impact in Agricultural and Life Sciences. 94, 1, p. 249-279

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Biological Science Disciplines 100%
  • life science 98%
  • Life Sciences 90%
  • life sciences 85%
  • advice 42%

• 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 Access

  • Domestication 100%
  • Lycopersicon esculentum 87%
  • domestication 81%
  • recombination 69%
  • Genetic Recombination 60%
  10 Citations (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

  Open Access

• PanTools v3: functional annotation, classification and phylogenomics

  Jonkheer, E. M., van Workum, F. J. M., Sheikhizadeh Anari, S., Brankovics, B., de Haan, J. R., Berke, L., van der Lee, T. A. J., de Ridder, D. & Smit, S., 15 Sept 2022, In: Bioinformatics. 38, 18, p. 4403-4405

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Phylogeny 100%
  • Annotation 96%
  • Genome 77%
  • Genomics 72%
  • Plant Genome 56%
  5 Citations (Scopus)

• Prioritizing candidate eQTL causal genes in Arabidopsis using RANDOM FORESTS

  Hartanto, M., Sami, A. A., de Ridder, D. & Nijveen, H., Nov 2022, In: G3 (Bethesda, Md.). 12, 11, jkac255.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Arabidopsis 100%
  • Quantitative Trait Loci 96%
  • Genes 30%
  • Protein Interaction Domains and Motifs 12%
  • Gene Expression 10%
  2 Citations (Scopus)

• The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency

  Garassino, F., Wijfjes, R. Y., Boesten, R., Reyes Marquez, F., Becker, F. F. M., Clapero, V., van den Hatert, I., Holmer, R., Schranz, E., Harbinson, J., de Ridder, D., Smit, S. & Aarts, M. G. M., Dec 2022, In: Plant Journal. 112, 5, p. 1298-1315

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Hirschfeldia incana 100%
  • Brassicaceae 92%
  • Brassica rapa 78%
  • Photosynthesis 61%
  • Mustard Plant 61%
  1 Citation (Scopus)

• 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 Access

  • T-Cell Prolymphocytic Leukemia 100%
  • MicroRNAs 18%
  • Gene Expression Profiling 7%
  • T-Cell Antigen Receptor 7%
  • Leukocyte Count 6%
  5 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. 2229-2239

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Swine 100%
  • Phenotype 76%
  • Biological Science Disciplines 22%
  • Genotype 12%
  • Genes 7%
  9 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 Access

  • Multigene Family 100%
  • Genes 87%
  • Genomics 43%
  • Genome 22%
  • Biological Products 16%
  65 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, 1

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Cucumis melo 100%
  • Cucurbitaceae 84%
  • Breeding 62%
  • poly A-T 14%
  • Selective Breeding 12%
  5 Citations (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 Access

  • Forster resonance energy transfer 100%
  • Molecules 61%
  • Proteins 58%
  • DNA 21%
  • Arginine 18%
  8 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. 3253-3260

  Research output: Contribution to journal › Article › Academic › peer-review

  • Energy Transfer 100%
  • Statistical Models 28%
  • Datasets 20%
  • Statistics 19%
  • Software 19%
  2 Citations (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 Access

  • Nanopores 100%
  • Molecules 65%
  • Proteins 61%
  • Proteasome Endopeptidase Complex 43%
  • Costs 4%
  7 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, 3

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Coevolution 100%
  • Sesquiterpenes 89%
  • coevolution 82%
  • Positive ions 81%
  • Specificity 79%
  8 Citations (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 Access

  • artificial intelligence 100%
  • plant breeding 85%
  • phenotype 41%
  • genotype 25%
  • genotyping 20%
  100 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 Access

  • Arabidopsis 100%
  • Breeding 89%
  • Multifactorial Inheritance 63%
  • Gene Ontology 58%
  • Genomics 51%
  4 Citations (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 Sept 2021, In: PLoS ONE. 16, 9 September, e0253102.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Molecules 100%
  • Genomics 71%
  • DNA 35%
  • Throughput 23%
  • Labeling 16%
  1 Citation (Scopus)

• 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 Sept 2019

  Research output: Patent

  Open Access

  • radiant energy 100%
  • barcoding 49%
  • proteins 22%
  • amino acids 12%
  • oligonucleotides 11%

• 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 Access

  • Pectobacterium 100%
  • Gene Pool 78%
  • Genes 21%
  • Solanum tuberosum 15%
  • Genome 11%
  19 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 Access

  • Systems Biology 100%
  • Genome 56%
  • Phytophthora infestans 53%
  • Oomycetes 47%
  • Workflow 30%
  3 Citations (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 Access

  • Exome 100%
  • Virulence 72%
  • Machine Learning 31%
  • Software 20%
  21 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 Access

  • Protein Structure 100%
  • Proteins 93%
  • Feature extraction 78%
  • Machine Learning 77%
  • Machine learning 74%
  14 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. 191-201

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Gene expression regulation 100%
  • Machine Learning 59%
  • Gene expression 57%
  • Gene Expression Regulation 56%
  • Machine learning 38%
  24 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-i725

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Moment Invariants 100%
  • Protein Structure 87%
  • Protein 65%
  • Proteins 56%
  • Libraries 33%
  12 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 Access

  • Haplotype 100%
  • Polyploidy 92%
  • DNA Sequencing 91%
  • Haplotypes 69%
  • Simulation 46%
  8 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. 480-492

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Lycopersicon esculentum 100%
  • Horizontal Gene Transfer 95%
  • Pollen 85%
  • gene conversion 60%
  • pollen 56%
  10 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 Access

  • Haplotypes 100%
  • haplotypes 90%
  • Error 79%
  • application coverage 29%
  • Nucleotide 24%
  5 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. 4215-4226

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Germination 100%
  • Arabidopsis 91%
  • Seeds 71%
  • Gene Expression Regulation 30%
  • Regulator Genes 28%
  4 Citations (Scopus)

• Oomycete metabolism is highly dynamic and reflects lifestyle adaptations

  Rodenburg, Y. A., de Ridder, D., Govers, F. & Seidl, M. F., 12 Feb 2020, BioRxiv, 41 p.

  Research output: Working paper › Preprint

  Open Access

  • Oomycetes 100%
  • lifestyle 87%
  • metabolism 50%
  • symbiosis 10%
  • biochemical pathways 8%

• 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 Access

  • Sus scrofa 100%
  • prioritization 99%
  • pig 74%
  • Nucleotides 60%
  • nucleotides 52%
  13 Citations (Scopus)

• pCADD scripts data

  Groß, C., Derks, M., Megens, H. J., Bosse, M., Groenen, M. A. M., Reinders, M. & De Ridder, D., 2020

  Research output: Non-textual form › Software

  Open Access

  • Boidae 100%
  • Sus 98%
  • Python 98%
  • Magic 97%
  • prioritization 92%

• 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 Sept 2020, In: Plos Genetics. 16, 9, 1009027.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • genomics 100%
  • Chickens 96%
  • genome 93%
  • chickens 69%
  • Genome 67%
  3 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 Access

  • Peronospora 100%
  • heterozygosity 35%
  • Oomycetes 35%
  • promoter regions 29%
  • Genome 28%
  13 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 Access

  • pinene cyclase I 100%
  • Cinnamomum camphora 94%
  • Sesquiterpenes 63%
  • Monoterpene 55%
  • Terpene 53%
  7 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 Access

  • Genetics 100%
  • Quantitative Trait Loci 93%
  • Mining 84%
  • Caenorhabditis elegans 81%
  • Gene expression 81%
  13 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. 157-165

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

  • Sesquiterpenes 100%
  • plant analysis 88%
  • terpene synthase 86%
  • Sesquiterpene 81%
  • sesquiterpenoids 74%
  35 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 journal › Comment/Letter to the editor › Academic

  Open Access
  6 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 Access

  • Polyploidy 100%
  • Haplotypes 74%
  • Alleles 58%
  • Genotype 28%
  • Tetraploidy 26%
  11 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 Access

  • Comparative Genomics 100%
  • Genome 70%
  • Genomics 66%
  • Bioinformatics 52%
  • Computational Biology 40%
  2 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 Access

  • Plant Genome 100%
  • Lycopersicon esculentum 28%
  • Datasets 16%
  • Arabidopsis 13%
  • Zea mays 12%
  3 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

  • Protein-protein Interaction 100%
  • Protein 66%
  • Proteins 58%
  • Mutation 53%
  • Contact 53%
  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 › Academic