20052020

Research output per year

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Research Output

2005

Factors affecting duration of the expulsive stage of parturition and piglet birth intervals in sows with uncomplicated, spontaneous farrowings

van Dijk, A. D. J., van Rens, B. T. T. M., van der Lende, T. & Taverne, M. A. M., 2005, In : Theriogenology. 64, 7, p. 1573-1590

Research output: Contribution to journalArticleAcademicpeer-review

79 Citations (Scopus)

Identification of sow and piglet factors affecting the duration of the expulsive stage of farrowing and piglet birth intervals

van Dijk, A. D. J., van Rens, B. T. T. M., van der Lende, T. & Taverne, M. A. M., 2005.

Research output: Contribution to conferenceAbstractAcademic

2006

Acid-base balance of umbilical artery blood of liveborn piglets at birth and its relation with factors affecting delivery of individual piglets

van Dijk, A. D. J., van der Lende, T. & Taverna, M. A., 2006, In : Theriogenology. 66, 8, p. 1824-1833

Research output: Contribution to journalArticleAcademicpeer-review

21 Citations (Scopus)

The progress of delivery affects the acid-base balance of umbilical artery blood at birth in liveborn piglets

van Dijk, A. D. J., van der Lende, T. & Taverna, M. A., 2006.

Research output: Contribution to conferenceConference paperAcademic

2007

Dietary specific antibodies in spray-dried immune plasma prevent enterotoxigenic Escherichia coli F4 (ETEC) post weaning in diarrhoea in piglets

Niewold, T. A., van Dijk, A. D. J., Geenen, P. L., Roodink, H., Margry, R. & van der Meulen, J., 2007, In : Veterinary Microbiology. 124, 3-4, p. 362-369

Research output: Contribution to journalArticleAcademicpeer-review

31 Citations (Scopus)
2008

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control

van Dijk, A. D. J., ter Braak, C. J. F., Immink, G. H., Angenent, G. C. & van Ham, R. C. H. J., 2008, In : Bioinformatics. 24, 1, p. 26-33

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)

Predicting sub-Golgi localization of type II membrane proteins

van Dijk, A. D. J., Bosch, H. J., ter Braak, C. J. F., van der Krol, A. R. & van Ham, R. C. H. J., 2008, In : Bioinformatics. 24, 16, p. 1779-1786

Research output: Contribution to journalArticleAcademicpeer-review

25 Citations (Scopus)
2009

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome

Severing, E. I., van Dijk, A. D. J., Stiekema, W. & van Ham, R. C. H. J., 2009, In : BMC Genomics. 10, 13 p., 154.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
39 Citations (Scopus)

Continuous-time modeling of cell fate determination in Arabidopsis flowers

van Mourik, S., van Dijk, A. D. J., de Gee, M., Immink, G. H., Kaufmann, K., Angenent, G. C., van Ham, R. C. H. J. & Molenaar, J., 2009.

Research output: Contribution to conferencePosterProfessional

Open Access

SEPALLATA3: the 'glue' for MADS box transcription factor complex formation

Immink, G. H., Tonaco, I. A. N., de Folter, S., Shchennikova, A., van Dijk, A. D. J., Busscher-Lange, J., Borst, J. W. & Angenent, G. C., 2009, In : Genome Biology. 10, 16 p., R24.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
165 Citations (Scopus)

SLIDER: Mining correlated motifs in protein-protein interaction networks

Boyen, P., van Dijk, A. D. J., van Ham, R. C. H. J. & Neven, F., 2009.

Research output: Contribution to conferenceConference paperAcademic

Open Access
5 Citations (Scopus)
2010

Bayesian Markov Random Rield Analysis for Protein Function Prediction Based on Network Data

Kourmpetis, Y. I. A., van Dijk, A. D. J., Bink, M. C. A. M., van Ham, R. C. H. J. & ter Braak, C. J. F., 2010, In : PLoS ONE. 5, 2, 10 p., e9293.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
70 Citations (Scopus)

Conserved and variable correlated mutations in the plant MADS protein network

van Dijk, A. D. J. & van Ham, R. C. H. J., 2010, In : BMC Genomics. 11, 607.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Continuous-time modeling of cell fate determination in Arabidopsis flowers

van Mourik, S., van Dijk, A. D. J., de Gee, M., Immink, R. G. H., Kaufmann, K., Angenent, G. C., van Ham, R. C. H. J. & Molenaar, J., 2010, In : BMC Systems Biology. 4, 13 p., 101.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Modeling of auxin-induced flower patterns

van Mourik, S., Merks, R., Guravage, M., van Dijk, A. D. J., de Gee, M., Immink, R., Kaufmann, K., Angenent, G. C. & Molenaar, J., 2010.

Research output: Contribution to conferencePosterProfessional

Open Access

Quantitative modelling of the regulatory network of flowering time genes

Valentim, F. L., van Mourik, S., Immink, R. G. H., Angenent, G. C., van Ham, R. C. H. J. & van Dijk, A. D. J., 2010.

Research output: Contribution to conferenceConference paperAcademic

Quantitativ modelling of the gene regulatory network underlying floral timing

Valentim, F. H., Immink, R. G. H., van Mourik, S., van Ham, R. C. H. J., Angenent, G. C. & van Dijk, A. D. J., 2010.

Research output: Contribution to conferencePosterProfessional

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

van Dijk, A. D. J., Morabito, G., Fiers, M. A., van Ham, R. C. H. J., Angenent, G. C. & Immink, R. G. H., 2010, In : PLoS Computational Biology. 6, 11 p., e1001017.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
39 Citations (Scopus)
2011

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
27 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
8 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

29 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

38 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
14 Citations (Scopus)

SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks

Boyen, P., van Dyck, D., Neven, F., van Ham, R. C. H. J. & van Dijk, A. D. J., 2011, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 5, p. 1344-1357

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)
2012

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

144 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

97 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

19 Citations (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
1 Citation (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
8 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
42 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
27 Citations (Scopus)
2013

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
425 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

58 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
9 Citations (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

1 Citation (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

41 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

20 Citations (Scopus)
2014

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

6 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
2 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
16 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

143 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
21 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

50 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

47 Citations (Scopus)
2015

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
21 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
4 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

62 Citations (Scopus)