Publications


The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining.
Szakonyi, D. et al. Current Plant Biology 2, 1-11 (2015)

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin
de Boer, J.M. et al. BMC Genomics 16 (2015)

Introgression browser: High-throughput whole-genome SNP visualization
Aflitos, S.A. et al. Plant Journal 82, 174-182 (2015)

Towards recommendations for metadata and data handling in plant phenotyping
Krajewski, P. et al. Journal of Experimental Botany 66, 5417-5427 (2015)

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Aflitos, S. et al. Plant Journal (2014).

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis
Zhang, Y. et al. Nature chemical biology 10, 1028-1033 (2014)

Making the difference: Integrating structural variation detection tools
Lin, K., Bonnema, G., Sanchez-Perez, G. & De Ridder, D. Briefings in Bioinformatics 16, 852-864 (2014)

The genome of the stress-tolerant wild tomato species Solanum pennellii
Bolger, A. et al. Nature Genetics 46, 1034-1038 (2014)

Biological Process Annotation of Proteins Across the Plant Kingdom
Bargsten, J.W. et al. Current Plant Biology (2014) 1: 73–82

Prioritization of candidate genes in QTL regions based on associations between traits and biological processes
Bargsten, J.W. et al. BMC Plant Biology, (2014) 14:330.

A large-scale evaluation of computational protein function prediction
Radivojac, P., et al. Nat Methods, (2013) 10: p. 221-227.

MSClust: a tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data
Tikunov YM, Laptenok S, Hall RD, Bovy A, de Vos RC. Metabolomics, (2012)

The tomato genome sequence provides insights into fleshy fruit evolution
Sato, S. et al. Nature 485, 635-641 (2012)

Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources
Kourmpetis, Y.A., et al. Plant Physiol, (2011) 155(1): p. 271-81.

Genome sequence and analysis of the tuber crop potato
Xu, X. et al. Nature 475, 189-195 (2011)

PRI-CAT: A web-tool for the analysis, storage and visualization of plant ChIP-seq experiments
Muiño, J.M., Hoogstraat, M., Van Ham, R.C.H.J. & Van Dijk, A.D.J. Nucleic Acids Research 39, W524-W527 (2011)

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. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, 1344-1357 (2011)

Bayesian Markov Random Field analysis for protein function prediction based on network data
Kourmpetis, Y.A., et al., PLoS One, 2010. 5(2): p. e9293