20052020

Research output per year

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Research Output

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)

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)

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

5 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
118 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
16 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
21 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

143 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
27 Citations (Scopus)

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
69 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

6 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)

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)

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
5 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
4 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, G. H., Kaufmann, K., Angenent, G. C., van Ham, R. C. H. J. & Molenaar, J., 2009.

Research output: Contribution to conferencePosterProfessional

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)

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)

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

32 Citations (Scopus)

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

1 Citation (Scopus)

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)
Open Access
16 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
9 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
4 Citations (Scopus)
3 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)

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)

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
4 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)

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)

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

1 Citation (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)

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)

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)

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

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)
Open Access

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)

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)

Plant genomics databases

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

Research output: Book/ReportBook editingAcademic

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)

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)

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)

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)