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Research Output 2008 2020

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Article
2020

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 journalArticleAcademicpeer-review

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

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 journalArticleAcademicpeer-review

Open Access
Sus scrofa
prioritization
pig
Nucleotides
nucleotides

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 journalArticleAcademicpeer-review

Open Access
Quantitative Trait Loci
Caenorhabditis elegans
Gene expression
quantitative trait loci
Genes
2019
5 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

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
1 Citation (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 journalArticleAcademicpeer-review

Open Access
Comparative Genomics
Genomics
Genome
Genes
Bioinformatics

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
Horizontal Gene Transfer
Lycopersicon esculentum
Pollen
gene conversion
tomatoes

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
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
2018
6 Citations (Scopus)

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 journalArticleAcademicpeer-review

Open Access
Chickens
genomics
purebreds
egg
chickens
73 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. 118-135

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genomics
Genes
Genome
Computational Biology
Bioinformatics
1 Citation (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 journalArticleAcademicpeer-review

Open Access
Genome
DNA
Chromosomes
Technology
4 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 journalArticleAcademicpeer-review

Open Access
Lycopersicon esculentum
Zea mays
Arabidopsis
nucleotide sequences
tomatoes

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 journalArticleAcademicpeer-review

Open Access
Proteome
Genomics
Homology
Proteins
Fungi
12 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. 387-403

Research output: Contribution to journalArticleAcademicpeer-review

Polyploidy
Nucleotides
Haplotypes
Ploidies
Polymorphism
6 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. 1403-1413

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Phytophthora infestans
Systems Biology
genome
metabolism
Genome
11 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.e14

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
DNA-Directed RNA Polymerases
Transcription
Bacteria
Compaction
DNA
2 Citations (Scopus)

Predicting variant deleteriousness in non-human species: Applying the CADD approach in mouse

Groß, C., de Ridder, D. & Reinders, M., 12 Oct 2018, In : BMC Bioinformatics. 19, 1, 373.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Depletion
Annotation
Mouse
Dependent
Genomics
2 Citations (Scopus)

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Motazedi, E., de Ridder, D., Finkers, R., Baldwin, S., Thomson, S., Monaghan, K. & Maliepaard, C., 15 Nov 2018, In : Bioinformatics. 34, 22, p. 3864-3872

Research output: Contribution to journalArticleAcademicpeer-review

Polyploidy
Haplotype
Haplotypes
Sequencing
Chromosomes
2017
4 Citations (Scopus)

AraQTL - Workbench and Archive for systems genetics in Arabidopsis thaliana

Nijveen, H., Ligterink, W., Keurentjes, J. J. B., Loudet, O., Long, J., Sterken, M. G., Prins, P., Hilhorst, H. W., De Ridder, D., Kammenga, J. E. & Snoek, B. L., 2017, In : The Plant Journal. 89, 6, p. 1225-1235

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Quantitative Trait Loci
Arabidopsis
quantitative trait loci
Arabidopsis thaliana
Genomics
16 Citations (Scopus)
Open Access
Euchromatin
Lycopersicon esculentum
inbred lines
cold zones
tomatoes
2 Citations (Scopus)

Dysregulated signaling, proliferation and apoptosis impact on the pathogenesis of TCRγδ+ T cell large granular lymphocyte leukemia

Kallemeijn, M. J., de Ridder, D., Schilperoord-Vermeulen, J., van der Klift, M. Y., Sandberg, Y., van Dongen, J. J. M. & Langerak, A. W., 2017, In : PLoS ONE. 12, 4, e0175670.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Large Granular Lymphocytic Leukemia
T-cells
Lymphocytes
leukemia
lymphocytes
5 Citations (Scopus)
Open Access
Zimbabwe
Pichia
Microbiota
Biotechnology
Saccharomyces cerevisiae
5 Citations (Scopus)

Genomics of adaptation depends on the rate of environmental change in experimental yeast populations

Gorter, F. A., Derks, M. F. L., van den Heuvel, J., Aarts, M. G. M., Zwaan, B. J., de Ridder, D. & de Visser, J. A. G. M., 2017, In : Molecular Biology and Evolution. 34, 10, p. 2613-2626

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genomics
Nickel
nickel
yeast
Zinc
4 Citations (Scopus)

Sequence-based analysis of protein degradation rates

Correa Marrero, M., van Dijk, A-J. & de Ridder, D., 2017, In : Proteins : Structure, Function, and Bioinformatics. 85, 9, p. 1593-1601

Research output: Contribution to journalArticleAcademicpeer-review

Proteolysis
Sequence Analysis
Degradation
Proteins
Proteome
9 Citations (Scopus)

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Gritsenko, A. A., Weingarten-Gabbay, S., Elias-Kirma, S., Nir, R., de Ridder, D. & Segal, E., 18 Sep 2017, In : PLoS Computational Biology. 13, 9, 23 p., e1005734.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
ribosomes
Viruses
virus
Internal
RNA
20 Citations (Scopus)

The long reads ahead: De novo genome assembly using the MinION

de Lannoy, C., de Ridder, D. & Risse, J., 2017, In : F1000Research. 6, 1083.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Nanopores
Benchmarking
DNA Sequence Analysis
Genes
Genome
2016
13 Citations (Scopus)

Consumers’ choice-blindness to ingredient information

Cheung, T. T. L., Junghans, A. F., Dijksterhuis, G. B., Kroese, F., Johansson, P., Hall, L. & De Ridder, D. T. D., 1 Nov 2016, In : Appetite. 106, p. 2-12 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Blindness
Food Packaging
Nutrition Policy
Food Additives
Product Packaging
2 Citations (Scopus)

CyLineUp: A Cytoscape app for visualizing data in network small multiples

Nijveen, H., Dias Costa, M., Slijkhuis, T., Ligterink, W., Hilhorst, H. W. M. & de Ridder, D., 2016, In : F1000 Research. 5, 635.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Application programs
Color
Proteins
Visualization
Experiments
8 Citations (Scopus)

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

Ferreira de Carvalho, J., Oplaat, C., Pappas, N., Derks, M., de Ridder, D. & Verhoeven, K. J. F., 2016, In : BMC Genomics. 17, 203.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Taraxacum
DNA Transposable Elements
Clone Cells
Asexual Reproduction
Gene Expression
7 Citations (Scopus)

PanTools: representation, storage and exploration of pan-genomic data

Sheikhizadeh Anari, S., Schranz, M. E., Akdel, M., de Ridder, D. & Smit, S., 2016, In : Bioinformatics. 32, 17, p. i487-i493

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genomics
Genome
Genes
Gene
De Bruijn Graph
39 Citations (Scopus)

The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots

Santuari, L., Sanchez-Perez, G. F., Luijten, M., Rutjens, B., Terpstra, I., Berke, L., Gorte, M., Prasad, K., Bao, D., Timmermans-Hereijgers, J. L. P. M., Maeo, K., Nakamura, K., Shimotohno, A., Pencik, A., Novak, O., Ljung, K., Van Heesch, S., De Bruijn, E., Cuppen, E., Willemsen, V. & 6 others, Mähönen, A. P., Lukowitz, W., Snel, B., De Ridder, D., Scheres, B. & Heidstra, R., 2016, In : The Plant Cell. 28, 12, p. 2937-2951

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Regulatory Networks
Arabidopsis
cell differentiation
Cell Differentiation
Growth
2015
7 Citations (Scopus)

ACE: accurate correction of errors using K-mer tries

Sheikhizadeh Anari, S. & de Ridder, D., 2015, In : Bioinformatics. 31, 19, p. 3216-3218

Research output: Contribution to journalArticleAcademicpeer-review

Sequencing
High Throughput
Substitution
Coverage
Substitution reactions
29 Citations (Scopus)

Chromosomal copy number variation in Saccharomyces pastorianus is evidence for extensive genome dynamics in industrial lager brewing strains

van den Broek, M., Bolat, I., Nijkamp, J. F., Ramos, E., Luttik, M. A. H., Koopman, F., Geertman, J. M., de Ridder, D., Pronk, J. T. & Daran, J. M., 2015, In : Applied and Environmental Microbiology. 81, 18, p. 6253-6267

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Saccharomyces
brewing
genome
Genome
chromosome
34 Citations (Scopus)

Circulating human CD27-IgA+ memory B cells recognize bacteria with polyreactive Igs

Berkowska, M. A., Schickel, J. N., Grosserichter-Wagener, C., De Ridder, D., Ng, Y. S., Van Dongen, J. J. M., Meffre, E. & Van Zelm, M. C., 2015, In : The Journal of Immunology. 195, 4, p. 1417-1426

Research output: Contribution to journalArticleAcademicpeer-review

Immunoglobulin A
B-Lymphocytes
Bacteria
T-Lymphocytes
Mucous Membrane
6 Citations (Scopus)

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

Aflitos, S. A., Severing, E. I., Sanchez Perez, G. F., Peters, S. A., de Jong, H. & de Ridder, D., 2015, In : BMC Bioinformatics. 16, 1, 10 p., 352.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Cnidaria
Transcriptome
Cluster Analysis
Genome
Genes
2 Citations (Scopus)

Insight into Neutral and Disease-Associated Human Genetic Variants through Interpretable Predictors

van den Berg, B. A., Reinders, M. J. T., de Ridder, D. & de Beer, T. A. P., 2015, In : PLoS ONE. 10, 3, 17 p., e0120729.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Medical Genetics
single nucleotide polymorphism
Polymorphism
Single Nucleotide Polymorphism
Support vector machines
14 Citations (Scopus)

Introgression Browser: High throughput whole-genome SNP visualization

Aflitos, S. A., Sanchez Perez, G. F., de Ridder, D., Fransz, P., Schranz, M. E., de Jong, J. H. S. G. M. & Peters, S. A., 2015, In : The Plant Journal. 82, 1, p. 174-182

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
introgression
Single Nucleotide Polymorphism
Genome
genome
Lycopersicon esculentum
21 Citations (Scopus)

Making the difference: integrating structural variation detection tools

Lin, K., Smit, S., Bonnema, A. B., Sanchez Perez, G. F. & de Ridder, D., 2015, In : Briefings in Bioinformatics. 16, 5, p. 852-864

Research output: Contribution to journalArticleAcademicpeer-review

Genomic Structural Variation
Metagenomics
Eukaryota
Pipelines
Technology
15 Citations (Scopus)

Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection

Brand, H. K., Ahout, I. M. L., de Ridder, D., van Diepen, A., Li, Y., Zaalberg, M., Andeweg, A., Roeleveld, N., de Groot, R. & Warris, A., 2015, In : PLoS ONE. 10, 7, 14 p., e0131927.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Respiratory Syncytial Virus Infections
Pediatrics
Viruses
disease severity
Gene expression
15 Citations (Scopus)

Single-molecule protein sequencing through fingerprinting: computational assessment

Yao, Y., Docter, M., van Ginkel, J., de Ridder, D. & Joo, C., 2015, In : Physical Biology. 12, 5, 6 p., 055003.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Protein Sequence Analysis
Proteomics
Amino Acids
Proteins
Biological Science Disciplines
36 Citations (Scopus)
Open Access
Operophtera brumata
Moths
sexual dimorphism
Sex Characteristics
moth
12 Citations (Scopus)

Unbiased quantitative models of protein translation derived from ribosome profiling data

Gritsenko, A. A., Hulsman, M., Reinders, M. J. T. & de Ridder, D., 2015, In : PLoS Computational Biology. 11, 8, 26 p., e1004336.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Protein Biosynthesis
Profiling
ribosomes
Ribosomes
translation (genetics)
2014
36 Citations (Scopus)

Beyond genomic variation - comparison and functional annotation in three Brassica rapa genotypes: a turnip, a rapid cycling and a Chinese cabbage

Lin, K., Zhang, N., Severing, E. I., Nijveen, H., Cheng, F., Visser, R. G. F., Wang, X., de Ridder, D. & Bonnema, A. B., 2014, In : BMC Genomics. 15, 34 p., 250.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Brassica napus
Brassica rapa
Brassica
Genotype
Genome
149 Citations (Scopus)
Solanum
Lycopersicon esculentum
tomatoes
Single Nucleotide Polymorphism
Genome
4 Citations (Scopus)

Protein redesign by learning from data

van den Berg, B. A., Reinders, M. J. T., van der Laan, J. M., Roubos, J. A. & de Ridder, D., 2014, In : Protein Engineering, Design & Selection. 27, 9, p. 281-288

Research output: Contribution to journalArticleAcademicpeer-review

Learning
Proteins
Enzymes
Mutation
inulinase
2012
144 Citations (Scopus)

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Nijkamp, J. F., van den Broek, M., Datema, E., de Kok, S., Bosman, L., Luttik, M. A., Daran-Lapujade, P., Vongsangnak, W., Nielsen, J., Heijne, W. H. M., Klaassen, P., Paddon, C. J., Platt, D., Kotter, P., van Ham, R. C. H. J., Reinders, M. J. T., Pronk, J. T., de Ridder, D. & Daran, J. M., 2012, In : Microbial Cell Factories. 11, 36.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Biotechnology
Yeast
Saccharomyces cerevisiae
Genes
Genome
2008
170 Citations (Scopus)

The importance of social learning and culture for sustainable water management

Pahl-Wostl, C., Tabara, D., Bouwen, R., Craps, M., Dewulf, A., Mostert, E., de Ridder, D. & Taillieu, T., 2008, In : Ecological Economics. 64, 3, p. 484-495

Research output: Contribution to journalArticleAcademicpeer-review

water management
learning
resource management
paradigm shift
dike