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Research Output 2005 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
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)

Comprehensive phenotyping reveals interactions and functions of Arabidopsis thaliana TCP genes in yield determination

van Es, S. W., van der Auweraert, E., Rodrigues da Silveira, S., Angenent, G. C., van Dijk, A. D. J. & Immink, G. H., 22 Mar 2019, In : The Plant Journal.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Arabidopsis
seed yield
Arabidopsis thaliana
vegetative growth
phenotype
1 Citation (Scopus)
Protein-protein Interaction
Contact
Proteins
Protein
Mutation
Horizontal Gene Transfer
Lycopersicon esculentum
Pollen
gene conversion
tomatoes
2018
5 Citations (Scopus)

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Aerts, N., de Bruijn, S., van Mourik, H., Angenent, G. C. & van Dijk, A. D. J., 25 Jun 2018, In : BMC Plant Biology. 18, 1, 131.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Arabidopsis thaliana
transcription factors
DNA-binding domains
protein binding
ecotypes
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
3 Citations (Scopus)
cauliflower
ambient temperature
gene
curds (plant)
flowering
9 Citations (Scopus)

Transcription factor mediated control of anthocyanin biosynthesis in vegetative tissues

Outchkourov, N. S., Karlova, R. B., Hölscher, M., Schrama, X., Blilou, I., Jongedijk, E. J., Diez Simon, C., van Dijk, A. D. J., Bosch, H. J., Hall, R. D. & Beekwilder, M. J., Feb 2018, In : Plant Physiology. 176, 2, p. 1862-1878

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Anthocyanins
anthocyanins
Transcription Factors
transcription factors
biosynthesis
6 Citations (Scopus)

Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control

Leeggangers, H. A. C. F., Rosilio-Brami, T., Nadal Bigas, J., Rubin, N., van Dijk, A. D. J., Nunez de Caceres Gonzalez, F. F., Saadon-Shitrit, S., Nijveen, H., Hilhorst, H. W. M., Immink, G. H. & Zaccai, M., Jan 2018, In : Plant and Cell Physiology. 59, 1, p. 90-106

Research output: Contribution to journalArticleAcademicpeer-review

Tulipa
Tulipa gesneriana
Lilium
Lilium longiflorum
Ethanolamine
2017
15 Citations (Scopus)

An interactomics overview of the human and bovine milk proteome over lactation

Zhang, L., van Dijk, A-J. & Hettinga, K., 2017, In : Proteome Science. 15, 1.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Human Milk
Proteome
Lactation
Milk
Milk Proteins
31 Citations (Scopus)

Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation

Bemer, M., van Dijk, A-J., Immink, R. G. H. & Angenent, G. C., 2017, In : Trends in Plant Science. 22, 1, p. 66-80

Research output: Contribution to journalArticleAcademicpeer-review

transcription factors
genes
gene expression
protein-protein interactions
DNA
16 Citations (Scopus)
Open Access
Euchromatin
Lycopersicon esculentum
inbred lines
cold zones
tomatoes
8 Citations (Scopus)

Divergent regulation of Arabidopsis SAUR genes: A focus on the SAUR10-clade

van Mourik, H., van Dijk, A. D. J., Stortenbeker, N., Angenent, G. C. & Bemer, M., 19 Dec 2017, In : BMC Plant Biology. 17, 245.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
auxins
Arabidopsis
RNA
genes
transcription factors
4 Citations (Scopus)

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time

van Dijk, A. D. J. & Molenaar, J., 2017, In : PeerJ. 5, 4, 18 p., e3197.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene expression
Cues
Genes
flowering
Gene Expression

Plant genomics databases

van Dijk, A. D. J. (ed.), 2017, Springer. 337 p. (Methodes in Molecular Biology; vol. 1533)

Research output: Book/ReportBook editingAcademic

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

Similarities between plant traits based on their connection to underlying gene functions

Nap, J. P., Sanchez-Perez, G. F. & van Dijk, A-J., 2017, In : PLoS ONE. 12, 8, e0182097.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genes
Phenotype
phenotype
genes
Metabolites

Species-specific genome sequence databases: A practical review

van Dijk, A-J., 2017, Plant genomics databases: Methods and Protocols. van Dijk, A. D. J. (ed.). Humana Press Inc., p. 173-181 (Methods in Molecular Biology; vol. 1533).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
Databases
Proteins
2016
114 Citations (Scopus)

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 others, Cao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Törönen, P., Koskinen, P., Holm, L., Chen, C. T., Hsu, W. L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., BKC, D., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L. C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeño-Cortés, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernández, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A-J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., 2016, In : Genome Biology. 17, 1, 184.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
protein
prediction
Proteins
proteins
methodology
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
2015
20 Citations (Scopus)

A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network

Valentim, F. L., van Mourik, S., Posé, D., Kim, M. C., Schmid, M., van Ham, R. C. H. J., Busscher, M., Sanchez Perez, G. F., Molenaar, J., Angenent, G. C., Immink, R. G. H. & van Dijk, A. D. J., 2015, In : PLoS ONE. 10, 2, e0116973.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Regulatory Networks
Arabidopsis
dynamic models
Dynamic models
Genes
4 Citations (Scopus)

The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Szakonyi, D., van Landeghem, S., Baerenfaller, K., Baeyens, L., Blomme, J., Casanova-Saéz, R., De Bodt, S., Esteve-Bruna, D., Fiorani, F., Gonzalez, N., Grønlund, J., Immink, R. G. H., Jover-Gil, S., Kuwabara, A., Muñoz-Nortes, T., van Dijk, A. D. J., Wilson-Sánchez, D., Buchanan-Wollaston, V., Angenent, G. C., Van de Peer, Y. & 5 others, Inzé, D., Micol, J. L., Gruissem, W., Walsh, S. & Hilson, P., 2015, In : Current Plant Biology. 2, p. 1-11

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Data Mining
Growth and Development
Arabidopsis
Data mining
growth and development
61 Citations (Scopus)

Towards recommendations for metadata and data handling in plant phenotyping

Krajewski, P., Chen, D., Cwiek, H., van Dijk, A. D. J., Fiorani, F., Kersey, P., Klukas, C., Lange, M., Markiewicz, A., Nap, J. P. H., van Oeveren, J., Pommier, P., Scholz, U., van Schriek, M., Usadel, B. & Weise, S., 2015, In : Journal of Experimental Botany. 66, 18, p. 5417-5427

Research output: Contribution to journalArticleAcademicpeer-review

phenotype
Plant Development
standardization
plant development
Phenotype
2014
6 Citations (Scopus)

Biological process annotation of proteins across the plant kingdom

Bargsten, J. W., Severing, E. I., Nap, J. P. H., Sanchez Perez, G. F. & van Dijk, A. D. J., 2014, In : Current Plant Biology. 1, p. 73-82

Research output: Contribution to journalArticleAcademicpeer-review

Molecular Sequence Annotation
Biological Phenomena
Plant Proteins
plant proteins
prediction
2 Citations (Scopus)

Inferring the Gene Network Underlying the Branching of Tomato Inflorescence

Astola, L., Stigter, J. D., van Dijk, A. D. J., van Daelen, R. & Molenaar, J., 2014, In : PLoS ONE. 9, 4, 7 p., e89689.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Inflorescence
Gene Regulatory Networks
Lycopersicon esculentum
branching
inflorescences
15 Citations (Scopus)

Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

Bargsten, J. W., Nap, J. P. H., Sanchez Perez, G. F. & van Dijk, A. D. J., 2014, In : BMC Plant Biology. 14, 330.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
prioritization
quantitative trait loci
genes
quantitative traits
flowering
138 Citations (Scopus)

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis

Zhang, Y., van Dijk, A. D. J., Scaffidi, A., Flematti, G. R., Hofmann, M., Charnikhova, T., Verstappen, F. W. A., Hepworth, J., van der Krol, A. R. & Leyser, O., 2014, In : Nature Chemical Biology. 10, p. 1028-1033

Research output: Contribution to journalArticleAcademicpeer-review

Cytochrome P-450 Enzyme System
Carotenoids
Growth
Enzymes
Dioxygenases
21 Citations (Scopus)

Structural determinants of DNA recognition by plant MADS-domain transcription factors

Muino Acuna, J. M., Smaczniak, C., Angenent, G. C., Kaufmann, K. & van Dijk, A. D. J., 2014, In : Nucleic acids research. 42, 4, p. 2138-2146

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Plant DNA
MADS Domain Proteins
Transcription Factors
DNA
Binding Sites
49 Citations (Scopus)

The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction; a two decades history

Pajoro, A., Biewers, S., Dougali, E., Valentim, F. L., Mendes, M. A., Porri, A., Coupland, G., Van de Peer, Y., van Dijk, A. D. J., Colombo, L., Davies, B. & Angenent, G. C., 2014, In : Journal of Experimental Botany. 65, 17, p. 4731-4745

Research output: Contribution to journalArticleAcademicpeer-review

plant reproduction
Gene Regulatory Networks
Arabidopsis
Reproduction
History
46 Citations (Scopus)

Valencene synthase from the heartwood of Nootka cypress (Callitropsis nootkatensis) for biotechnological production of valencene

Beekwilder, M. J., van Houwelingen, A. M. M. L., Cankar, K., van Dijk, A. D. J., de Jong, R., Stoopen, G. M., Bouwmeester, H. J., Achkar, J., Sonke, T. & Bosch, H. J., 2014, In : Plant Biotechnology Journal. 12, 2, p. 174-182

Research output: Contribution to journalArticleAcademicpeer-review

nootkatone
Cupressus
Xanthocyparis nootkatensis
heartwood
terpenoids
2013
421 Citations (Scopus)

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Kourmpetis, Y. A. I., van Dijk, A. D. J. & Friedberg, I., 2013, In : Nature Methods : techniques for life scientists and chemists. 10, p. 221-227

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Molecular Sequence Annotation
Proteins
Genome
Genes
Experiments
57 Citations (Scopus)

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

Danisman, S., van Dijk, A. D. J., Bimbo, A., van der Wal, F., Hennig, L., de Folter, S., Angenent, G. C. & Immink, R. G. H., 2013, In : Journal of Experimental Botany. 64, 18, p. 5673-5685

Research output: Contribution to journalArticleAcademicpeer-review

Arabidopsis
Transcription Factors
transcription factors
Computational Biology
bioinformatics
9 Citations (Scopus)

Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes

Kourmpetis, Y. A. I., van Dijk, A. D. J. & ter Braak, C. J. F., 2013, In : Algorithms for Molecular Biology. 8, 1, 10.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Ontology
Labeling
Ontology
Annotation
Genome
1 Citation (Scopus)

Mining minimal motif pair sets maximally covering interactions in a protein-protein interaction network

Boyen, P., Neven, F., Valentim, F. L. & van Dijk, A. D. J., 2013, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10, 1, p. 73-86

Research output: Contribution to journalArticleAcademicpeer-review

Protein Interaction Maps
Set Covering
Protein Interaction Networks
Protein-protein Interaction
Mining
40 Citations (Scopus)

N-glycan occupancy of Arabidopsis N-glycoproteins

Song, W., Mentink, R., Henquet, M. G. L., Cordewener, J. H. G., van Dijk, A. D. J., Bosch, H. J., America, A. H. P. & van der Krol, A. R., 2013, In : Journal of Proteomics. 93, p. 343-355

Research output: Contribution to journalArticleAcademicpeer-review

Arabidopsis
Polysaccharides
Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase
Glycoproteins
Glycopeptides
20 Citations (Scopus)

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

Kastritis, P. L., Visscher, K. M., van Dijk, A. D. J. & Bonvin, A. M. J. J., 2013, In : Proteins : Structure, Function, and Bioinformatics. 81, 3, p. 510-518

Research output: Contribution to journalArticleAcademicpeer-review

Water
Proteins
Hydrophobic and Hydrophilic Interactions
Hydrophobicity
Amino Acids
2012
140 Citations (Scopus)

Arabidopsis Class I and Class II TCP Transcription Factors Regulate Jasmonic Acid Metabolism and Leaf Development Antagonistically.

Danisman, S., van der Wal, F., Dhondt, S., Waites, R., de Folter, S., Bimbo, A., van Dijk, A. D. J., Muino Acuna, J., Cutri, L., Dornelas, M. C., Angenent, G. C. & Immink, R. G. H., 2012, In : Plant Physiology. 159, 4, p. 1511-1523

Research output: Contribution to journalArticleAcademicpeer-review

leaf development
jasmonic acid
Cell Size
Arabidopsis
Transcription Factors
96 Citations (Scopus)

Characterization of SOC1’s Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators1[C][W]

Immink, R. G. H., Posé, D., Ferrario, S. I. T., Ott, F., Kaufmann, K., Valentim, F. L., de Folter, S., van der Wal, F., van Dijk, A. D. J., Schmid, M. & Angenent, G. C., 2012, In : Plant Physiology. 160, 1, p. 433-449

Research output: Contribution to journalArticleAcademicpeer-review

MADS Domain Proteins
Homeodomain Proteins
flowering
Arabidopsis
regulatory sequences
19 Citations (Scopus)

Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.

Kastritis, P. L., van Dijk, A. D. J. & Bonvin, A. M., 2012, Computational Drug Discovery and Design . Baron, R. (ed.). New York: Springer Science + Business Media, p. 355-374 (Methods in Molecular Biology ; vol. 819).

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecules
Water
Proteins
Hydrogen bonds
Crystal structure
meristems
auxins
flowers
plant hormones
transcription factors
1 Citation (Scopus)

Interactome-Wide Prediction of Protein-Protein Binding Sites Reveals Effects of Protein Sequence Variation in Arabidopsis thaliana

Valentim, F. L., Neven, F., Boyen, P. & van Dijk, A. D. J., 2012, In : PLoS ONE. 7, 10, e47022.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
protein binding
Arabidopsis
Protein Binding
binding sites
amino acid sequences
8 Citations (Scopus)

Mutational Robustness of Gene Regulatory Networks

van Dijk, A. D. J., van Mourik, S. & van Ham, R. C. H. J., 2012, In : PLoS ONE. 7, 1, 9 p., e30591.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Regulatory Networks
Transcription Factors
transcription factors
Genes
mutation
42 Citations (Scopus)

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

Severing, E. I., van Dijk, A. D. J., Morabito, G., Busscher-Lange, J., Immink, G. H. & van Ham, R. C. H. J., 2012, In : PLoS ONE. 7, 1, 13 p., e30524.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
MADS Domain Proteins
Plant Proteins
alternative splicing
Alternative Splicing
proteins
26 Citations (Scopus)

Simulation of Organ Patterning on the Floral Meristem Using a Polar Auxin Transport Model

van Mourik, S., Kaufmann, K., van Dijk, A. D. J., Angenent, G. C., Merks, R. M. H. & Molenaar, J., 2012, In : PLoS ONE. 7, 1, 9 p., e28762.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Indoleacetic Acids
Meristem
meristems
auxins
calyx
2011
27 Citations (Scopus)

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

Severing, E. I., van Dijk, A. D. J. & van Ham, R. C. H. J., 2011, In : BMC Plant Biology. 11, 10 p., 82.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
alternative splicing
proteome
proteomics
Arabidopsis thaliana
transcriptomics
8 Citations (Scopus)

Correlated mutations via regularized multinomial regression

Sreekumar, J., ter Braak, C. J. F., van Ham, R. C. H. J. & van Dijk, A. D. J., 2011, In : BMC Bioinformatics. 12, 13 p., 444.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sequence Alignment
Mutation
Regression
Multiple Sequence Alignment
Proteins
29 Citations (Scopus)

Genome-wide computational function prediction of Arabidopsis thaliana proteins by integration of multiple data sources

Kourmpetis, Y. I. A., van Dijk, A. D. J., van Ham, R. C. H. J. & ter Braak, C. J. F., 2011, In : Plant Physiology. 155, p. 271-281

Research output: Contribution to journalArticleAcademicpeer-review

Arabidopsis Proteins
Information Storage and Retrieval
Arabidopsis thaliana
Genome
genome
37 Citations (Scopus)

N-glycoproteomics in plants: Perspectives and challenges

Song, W., Henquet, M. G. L., Mentink, R., van Dijk, A. D. J., Cordewener, J. H. G., Bosch, H. J., America, A. H. P. & van der Krol, A. R., 2011, In : Journal of Proteomics. 74, 8, p. 1463-1474

Research output: Contribution to journalArticleAcademicpeer-review

Polysaccharides
Plant Development
Glycopeptides
Golgi Apparatus
Processing
14 Citations (Scopus)

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.

Muino, J. M., Hoogstraat, M., van Ham, R. C. H. J. & van Dijk, A. D. J., 2011, In : Nucleic acids research. 39, suppl. 2, p. W524-W527

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Research
Workflow
Arabidopsis
Genome
DNA