If you made any changes in Pure these will be visible here soon.

Research Output 2008 2020

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
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. 38-40

Research output: Contribution to journalComment/Letter to the editorAcademic

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 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

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 paperAcademic

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 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

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 conferenceAbstractAcademic

Open Access
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

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 conferencePosterAcademic

Open Access
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

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 conferencePosterAcademic

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

AraQTL – Arabidopsis eQTL analysis platform

Nijveen, H., Ligterink, W., de Ridder, D. & Snoek, L. B., Dec 2016.

Research output: Contribution to conferencePoster

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

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 conferencePosterAcademic

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 journalArticleAcademicpeer-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 conferenceAbstractAcademic

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-i493

Research output: Contribution to journalArticleAcademicpeer-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 conferencePosterAcademic

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 conferencePosterAcademic

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. 16

Research output: Contribution to journalEditorialAcademic

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, 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