Research Output per year
Research Output 2008 2020
- 1 - 50 out of 65 results
- Publication Year, Title (descending)
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. 191-201Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 157-165Research output: Contribution to journal › Article › Academic › peer-review
Sesquiterpenes
sesquiterpenoids
terpenoids
Databases
Mutagenesis
4
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 Access
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
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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-review
Open Access
Plant Genome
Lycopersicon esculentum
Workflow
Arabidopsis
Zea mays
1
Citation
(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
Contact
Proteins
Protein
Mutation
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
Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing
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., 9 Dec 2019, In : The Plant Journal.Research output: Contribution to journal › Article › Academic › peer-review
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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-review
Nanopores
Nanopore
Benchmarking
Benchmark
Sequencing
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 › Academic
Peronospora
heterozygosity
Oomycetes
promoter regions
genome
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 journal › Article › Academic › peer-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. 118-135Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 387-403Research output: Contribution to journal › Article › Academic › peer-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. 1403-1413Research output: Contribution to journal › Article › Academic › peer-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.e14Research output: Contribution to journal › Article › Academic › peer-review
Open Access
DNA-Directed RNA Polymerases
Transcription
Bacteria
Compaction
DNA
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 › Academic
Open Access
Pangenome analysis and its application on Pectobacterium
Jonkheer, E., Smit, S., de Ridder, D., Brankovics, B., Houwers, I. M., van der Wolf, J. M., Bonants, P. J. M., Vreeburg, R. A. M. & van der Lee, T. A. J., 2018.Research output: Contribution to conference › Abstract › Academic
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 journal › Article › Academic › peer-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. 3864-3872Research output: Contribution to journal › Article › Academic › peer-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. 1225-1235Research output: Contribution to journal › Article › Academic › peer-review
Open Access
Quantitative Trait Loci
Arabidopsis
quantitative trait loci
Arabidopsis thaliana
Genomics
A survey of deleterious variants in highly managed commercial layer lines
Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 2017.Research output: Contribution to conference › Poster › Academic
Open Access
16
Citations
(Scopus)
Distribution, position, and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between S. lycopersicum and S. pimpinellifolium
Demirci, S., van Dijk, A. D. J., Sanchez Perez, G. F., Aflitos, S. A., de Ridder, D. & Peters, S. A., 2017, In : The Plant Journal. 89, 3, p. 554-564Research output: Contribution to journal › Article › Academic › peer-review
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 journal › Article › Academic › peer-review
Open Access
Large Granular Lymphocytic Leukemia
T-cells
Lymphocytes
leukemia
lymphocytes
5
Citations
(Scopus)
Genome sequences of cyberlindnera fabianii 65, pichia kudriavzevii 129, and saccharomyces cerevisiae 131 isolated from fermented masau fruits in Zimbabwe
van Rijswijck, I. M. H., Derks, M. F. L., Abee, T., de Ridder, D. & Smid, E. J., 2017, In : Genome Announcements. 5, 14, p. e0006417Research output: Contribution to journal › Article › Academic › peer-review
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. 2613-2626Research output: Contribution to journal › Article › Academic › peer-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. 1593-1601Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-review
Open Access
ribosomes
Viruses
virus
Internal
RNA
Survey of deleterious variants in highly managed commercial layer lines
Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., Apr 2017.Research output: Contribution to conference › Poster › Academic
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 journal › Article › Academic › peer-review
Open Access
Nanopores
Benchmarking
DNA Sequence Analysis
Genes
Genome
2016
AraQTL – Arabidopsis eQTL analysis platform
Nijveen, H., Ligterink, W., de Ridder, D. & Snoek, L. B., Dec 2016.Research output: Contribution to conference › Poster
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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-review
Open Access
Application programs
Color
Proteins
Visualization
Experiments
Detection of deleterious genomic variation in domesticated animals
Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 19 Apr 2016.Research output: Contribution to conference › Poster › Academic
Open Access
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 journal › Article › Academic › peer-review
Open Access
Taraxacum
DNA Transposable Elements
Clone Cells
Asexual Reproduction
Gene Expression
Metabolic network construction of the Phytophthora infestans – tomato pathosystem
Rodenburg, Y. A., Seidl, M. F., de Ridder, D. & Govers, F., 1 Aug 2016, p. 11.Research output: Contribution to conference › Abstract › Academic
Phytophthora infestans
tomatoes
genome
pathogens
metabolism
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-i493Research output: Contribution to journal › Article › Academic › peer-review
Open Access
Genomics
Genome
Genes
Gene
De Bruijn Graph
Predicting Impact of Variation in Livestock
Gross, C., Reinders, M., de Ridder, D., Derks, M. F. L., Bosse, M., Megens, H. J. W. C. & Groenen, M., 19 Apr 2016.Research output: Contribution to conference › Poster › Academic
Predicting the impact of genetic variation in livestock
Gross, C., Reinders, M., de Ridder, D., Derks, M. F. L., Bosse, M., Megens, H. J. W. C. & Groenen, M., 3 Sep 2016.Research output: Contribution to conference › Poster › Academic
2
Citations
(Scopus)
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016
van Dijk, A-J., Lähdesmäki, H., de Ridder, D. & Rousu, J., 2016, In : BMC Bioinformatics. 17, suppl. 16Research output: Contribution to journal › Editorial › Academic
Open Access
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, , 2016, In : The Plant Cell. 28, 12, p. 2937-2951Research output: Contribution to journal › Article › Academic › peer-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. 3216-3218Research output: Contribution to journal › Article › Academic › peer-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. 6253-6267Research output: Contribution to journal › Article › Academic › peer-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. 1417-1426Research output: Contribution to journal › Article › Academic › peer-review
Immunoglobulin A
B-Lymphocytes
Bacteria
T-Lymphocytes
Mucous Membrane