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Perazzolli, M., Herrero, J., Sterck, L., Lenzi, L., Pellegrini, A., Puopolo, G., Van de Peer, Y., Pertot, I. (2016) Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat. BMC Genomics 17:838.

Le, P., Makhalanyane, T.P., Guerrero, L.D., Vikram, S., Van de Peer, Y., Cowan, D.A. (2016) Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts. Genome Biol. Evol. 8(9):2737-47.

Vlastaridis, P., Oliver, S., Van de Peer, Y., Amoutzias, G. (2015) The Challenges of Interpreting Phosphoproteomics Data: A Critical View Through the Bioinformatics Lens. CIBB 2015: Computational Intelligence Methods for Bioinformatics and Biostatistics pp 196-204.

Miclotte, G., Heydari, M., Demeester, P., Rombauts, S., Van de Peer, Y., Audenaert, P., Fostier, J. (2016) Jabba: Hybrid Error Correction for Long Sequencing Reads. Algorithms for Molecular Biology 11:10.

Van de Peer, Y., Pires, J.C. (2016) Editorial overview: Genome studies and molecular genetics: Of plant genes, genomes, and genomics. Curr. Opin. Plant Biol. 30:4-6.

Publications in Press
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Li, Z., R. De La Torre, A., Sterck, L., M. Canovas, F., Avila, C., Merino Sierra, I., Antonio Cabezas, J., Teresa Cervera, M., K. Ingvarsson, P., Van de Peer, Y. (2017) Single-copy genes as molecular markers for phylogenomic studies in seed plants. Genome Biol. Evol. (In Press).

De La Torre, A.R., Li, Z., Van de Peer, Y., Ingvarsson, P.K. (2017) Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Mol. Biol. Evol. (In Press).

Mizrachi, E., Verbeke, L. P. C., Christie, K.R., Fierro, A.C., Mansfield, S.D. , Davis, J., Gjersing, E., Tuskan, G., Van Montagu, M., Van de Peer, Y., Marchal, K., Myburg, A.A. (2016) Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. PNAS (In Press).

Vlastaridis, P., Kyriakidou, P., Chaliotis, A., Van de Peer, Y., Oliver, S., Amoutzias, G. (2016) Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. GigaScience (In Press).

Yao, Y., Storme, V., Marchal, K., Van de Peer, Y. (2016) Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment. PeerJ (In Press).

Cormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., Godfroy, O., Lipinska, A., Perrineau, M.-M., Van de Peer, Y., Hitte, C., Corre, E., Coelho, S., Cock, M. (2016) Re-annotation, improved large-scale assembly and establishment of a catalogue of non-coding loci for the genome of the model brown alga Ectocarpus. New Phytologist (In press).

Thi Ngoc Cao, P., Greenhalgh, R., Dermauw, W., Rombauts, S., Bajda, S., Zhurov, V., Grbić, M., Van de Peer, Y., Van Leeuwen, T., Rouzé, P., M. Clark, R. (2016) Complex evolutionary dynamics of massively expanded chemosensory receptor families in an extreme generalist chelicerate herbivore. Genome Biol. Evol. (In Press).

Van Parys, T., Melckenbeeck, I., Houbraken, M., Audenaert, P., Colle, J., Pickavet, M., Demeester, P., Van de Peer, Y. (2017) A Cytoscape app for motif enumeration with ISMAGS. Bioinformatics (In Press).

Christie, K.R., Myburg, A.A., Joubert, Y., Murray, S.L., Carstens, M., Lin, Y.-C., Meyer, J., Crampton, B.G., Christensen, S.A., Ntuli, J.F., Wighard, S.S., Van de Peer, Y., Berger, D.K. (2016) Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem. The Plant Journal (In Press).

Ebert, M.K., Faino, L., Rivera-Varas, V., de Jonge, R., Van de Peer, Y., Thomma, B. PHJ., Secor, G.A., D. Bolton, M. (2016) RNA-Sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction. Fungal Genetics and Biology (In Press).

Meysman, P., Saeys, Y., Sabaghian, E., Bittremieux, W., Van de Peer, Y., Goethals, B., Laukens, K. (2016) Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics (In Press).

Kerchev, P.I., Waszczak, C., Lewandowska, A., Willems, A., Shapiguzov, A., Li, Z., Alseekh, S., Mühlenbock, P., Hoebrichts, F., Huang, J., Van Der Kelen, K., Kangasjarvi, J., Fernie, A., De Smet, R., Van de Peer, Y., Messens, W., Van Breusegem, F. (2016) Lack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient Arabidopsis. Plant Physiol. (In Press).

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