Publications

2014

Vanneste, K., Maere, S., Van de Peer, Y. (2014) Tangled up in two: A burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philosophical Transactions B 369, 20130353 .

Myburg, A.A., Grattapaglia, D., Tuskan, G., Hellsten, U., Hayes, R.D., Grimwood, J., Jenkins, B., Lindquist, E., Tice, H., Bauer, D., Goodstein, D., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A.R.K., van Jaarsveld, I., Hussey, S.G., Pinard, D., van der Merwe, K., Singh, N., Silva-Junior, O.B., Togawa, R.C., Pappas, M.R., Faria, D.A., Sansaloni, C.P., Petrol, C.D., Yang, X., Ranjan, P., Tschaplinski, T.J., Ye, Z., Li, T., Sterck, L., Vanneste, K., Murat, C., Soler, M., San Clemente, H., Saidi, N., Cassan-Wang, H., Dunand, C., Hefer, C.A., Bornberg-Bauer, E., Kersting, A.R., Vining, K., Amarasinghe, V., Ranik, M., Naithani, S., Elser, J., Boyd, A.E., Liston, A., Spatafora, J.W., Dharmwardhana, P., Raja, R., Sullivan, C., Romanel, E., Alves-Ferreira, M., Külheim, C., Foley, W., Carocha, V., Paiva, J., Kudrna, D., Brommonschenkel, S.H., Pasquali, G., Byrne, K., Rigault, P., Tibbits, J., Spokevicius, A., Jones, R.C., Steane, D.A., Vaillancourt, R.E., Potts, B.M., Joubert, Y., Barry, K., Pappas Jr., G.J., Strauss, S.H., Jaiswal, P., Grima-Pettenati, J., Salse, J., Van de Peer, Y., Rokhsar, D., Schmutz, J. (2014) Genome sequence of Eucalyptus grandis: A global tree crop for fiber and energy. Nature 510, 356–362.

* Pajoro, A., * Biewers, S., * Dougali, E., * Leal Valentim, F., * Adelina Mendes, M., * Porri, A., Coupland, G., Van de Peer, Y., van Dijk, A.D.J., Colombo, L., Davies, B., Angenent, G.C. (2014) The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction, a two decades history. Journal of Experimental Botany pii: eru233. *contributed equally

Chaves, I., Lin, Y.-C., Pinto Ricardo, C., Van de Peer, Y., Miguel, C. (2014) miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns. Tree Genetics & Genomes 10,721-737.

Vanneste, K., Baele, G., Maere, S., Van de Peer, Y. (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications at the Cretaceous-Tertiary boundary. Genome Res. gr. 168997.113.

Yao, Y., Marchal, K., Van de Peer, Y. (2014) Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments. PLOS One 9,e90695.

Morreel, K., Saeys, Y., Dima, O., Lu, F., Van de Peer, Y., Vanholme, R., Ralph, S., Vanholme, B., Boerjan, W. (2014) Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks. The Plant Cell 26,929-945.

Bolton, M.D., * de Jonge, R., * Inderbitzin, P., Liu, Z., Birla, K., Van de Peer, Y., Subbarao, K.V., Thomma, B. PHJ., Secor, G.A. (2014) The heterothallic sugarbeet pathogen Cercospora beticolacontains exon fragments of both MAT genes that are homogenized by concerted evolution. Fungal Genetics and Biology 62,43-54. *contributed equally

Ciesielska, K., Van Bogaert, M., Chevineau, S., Li, B., Groeneboer, S., Soetaert, W., Van de Peer, Y., Devreese, B. (2014) Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids. J. Proteomics 1874-3919.

Zhurov, V., Navarro, M., Bruinsma, K.A., Arbona, V., Santamaria, M.E., Wybouw, M.C.N., Osborne, E.J., Ens, C., Rioja, C., Vermeirssen, V., Rubio-Somoza, I., Krishna, P., Diaz, I., Schmid, M., Gómez-Cadenas, A., Van de Peer, Y., Grbic, M., Clark, R.M., Van Leeuwen, T., Grbic, V. (2014) Reciprocal responses in the interaction between Arabidopsis and the cell-content feeding chelicerate herbivore Tetranychus urticae. Plant Physiol. 164,384-399.

GIGA Community of Scientists, , Van de Peer, Y., Voolstra, C.R., Welch, D.M., Winston, J., Zhou, X. (2014) The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of Heredity 105, 1-18.

2013

Van Bel, M., Proost, S., Van Neste, C., Deforce, D., Van de Peer, Y., Vandepoele, K. (2013) TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biology 14:R134.

Verhelst, B., Van de Peer, Y., Rouzé, P. (2013) The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution. Genome Biology and Evolution 5,2393-401.

De Clercq, I., Vermeirssen, V., Van Aken, O., Vandepoele, K., Murcha, M., Law, S., Inzé, A., Ng, S., Ivanova, A., Rombaut, D., Van de Cotte, B., Jaspers, P., Van de Peer, Y., Kangasjarvi, J., Whelan, J., Van Breusegem, F. (2013) The membrane-bound NAC transcription factor ANAC013 is a regulator of mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. The Plant Cell 25, 3472-90.

Ciesielska, K., Li, B., Groeneboer, S., Van Bogaert, M., Lin, Y.-C., Soetaert, W., Van de Peer, Y., Devreese, B. (2013) SILAC-based proteome analysis of Starmerella bombicola sophorolipid production. Journal of Proteome Research 12,4376-4392.

Hakala, K., Van Landeghem, S., Salakoski, T., Van de Peer, Y., Ginter, F. (2013) EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction. Proceedings of the BioNLP Shared Task 2013 Workshop 26-34.

Van Landeghem, S., Kaewphan, S., Ginter, F., Van de Peer, Y. (2013) Evaluating large-scale text mining applications beyond the traditional numeric performance measures. Proceedings of the BioNLP 2013 Workshop 63-71.

Zimmer, A., Lang, D., Buchta, K., Rombauts, S., Nishiyama, T., Hasebe, M., Van de Peer, Y., Rensing, S.A., Reski, R. (2013) Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics 14.

Vandepoele, K., Van Bel, M., Richard, G., Van Landeghem, S., Verhelst, B., Moreau, H., Van de Peer, Y., Grimsley, N., Piganeau, G. (2013) pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. Environ. Microbiol. 15, 2147-2153.

Galagan, J. E., Minch, K., Peterson, M., Lyubetskaya, A., Azizi, E., Sweet, L., Gomes, A., Rustad, T., Dolganov, G., Glotova, I., Abeel, T., Mahwinney, C., Kennedy, A. D., Allard, R., Brabant, W., Krueger, A., Jaini, S., Honda, B., Yu, W., Hickey, M. J., Zucker, J., Garay, C., Weiner, J., Sisk, P., Stolte, C., Winkler, J. K., Van de Peer, Y., Iazzetti, P., Camacho, D.M., Dreyfuss, J., Liu, Y., Dorhoi, A., Mollenkopf, H., Drogaris, P., Lamontagne, J., Zhou, K., Piquenot, J., Tae Park, S., Raman, S., H.E. Kaufmann, S., P. Mohney, R., Chelsky, D., Branch Moody, D., R. Sherman, D., K. Schoolnik, G. (2013) The Mycobacterium tuberculosis regulatory network and hypoxia. Nature 499, 178-183.

De Tiège, A., Tanghe, K., Braeckman, J., Van de Peer, Y. (2013) From DNA- to NA-centrism and the conditions for gene-centrism revisited. Biol. Philos. 28.

* Ruttink, T., * Sterck, L., Rohde, A., Bendixen, C., Rouzé, P., Aslankoohi, E., Van de Peer, Y., Roldán-Ruiz, I. (2013) Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. Plant Biotechnol J. 11, 605–617. *contributed equally

Read, B. A., Kegel, J., Klute, M. J., Kuo, Y.-C., Lefebvre, S. C., Maumus, F., Mayer, K., Miller, G., Monier, A., Salamov, A., Young, N.D., Aguilar, ., Aguilar, ., Claverie, J., Frickenhaus, S., Gonzalez, A., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Schmutz, J., Schroeder, D., de Vargas, C., Vérret, F., von Dassow, P., Valentin, K., Van de Peer, Y., Rouzé, P., Wheeler, G., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, D., Jenkins, B., Jones, B. M., Leese, F., Lobanov, A., Lawson, T., Lindquist, E., Marsh, M. E., Lomsadze, A., Mueller-Roeber, B., Lucas, S., Malik, S.-B., Pagarete, A., Mock, T., Probert, I., Parker, M.S., Quesneville, H., Raines, C., Rensing, S.A., Mauricio Riano-Pachon, D., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., van der Giezen, M., Wahlund, T. M., Williams, C., Wilson, W., Wolfe, K., Wurch, L. L., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, A. Z., Zhang, J., V. Grigoriev, I. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-13.

Nystedt, B., Street, N. R., Zuccolo, A., Lin, Y.-C., Wetterbom, A., Vezzi, A., Scofield, D. G., Delhomme, N., Alexeyenko, A., Giacomello, S., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Olson, A., Niittylä, T., Ritland, K., Rilakovic, N., Rosselló, J. A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Vanneste, K., Tuominen, H., Zhang, J., Wu, Z., Zerbe, P., Bhalerao, R.P., Bohlmann, J., Arvestad, L., Bousquet, J., Garcia Gil, R., de Jong, P.J., Hvidsten, T. R., MacKay, J., Ritland, K., Morgante, M., Sundberg, B., Van de Peer, Y., Lee Thompson, S., Nilsson, O., Andersson, B., Lundeberg, J., Jansson, S. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497,579-84.

Van Landeghem, S., Björne, J., Wei, C.-H., Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H.-Y., Lu, Z., Salakoski, T., Van de Peer, Y., Ginter, F. (2013) Large-scale event extraction from literature with multi-level gene normalization. PLOS One 8: e55814.

Van Bogaert, M., Holvoet, K., Roelants, S. L.K.W, Li, B., Lin, Y.-C., Van de Peer, Y., Soetaert, W. (2013) The biosynthetic gene cluster for sophorolipids: a biotechnological interesting biosurfactant produced by Starmerella bombicola. Molecular Microbiology 88,501-9.

Van Landeghem, S., De Bodt, S., Drebert, Z. J., Inzé, D., Van de Peer, Y. (2013) The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. The Plant Cell 25, 794-807.

Roelants, S. L.K.W, Saerens, K.M., Derycke, T., Li, B., Lin, Y.-C., Van de Peer, Y., De Maeseneire, S.L., Van Bogaert, M., Soetaert, W. (2013) Candida bombicola as a platform organism for the production of tailor-made biomolecules. Biotechnol. Bioeng. 110,2494-503.

De Smet, R., Adams, K., Vandepoele, K., Van Montagu, M., Maere, S., Van de Peer, Y. (2013) Convergent gene loss following gene and genome duplications createssingle-copy families in flowering plants. PNAS 110, 2898-2903.

Fawcett, J., Van de Peer, Y., Maere, S. (2013) Significance and biological consequences of polyploidization in land plant evolution. . Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, Greilhuber, J., Doležel, J., and Wendel, J. F. (Eds). Vienna, Springer-Verlag 277-294 .

Vanneste, K., Van de Peer, Y., Maere, S. (2013) Inference of genome duplications from age distributions revisited. Mol. Biol. Evol. 30, 177-90.

2012

Andolfo, G., Sanseverino, W., Rombauts, S., Van de Peer, Y., Bradeen, J. M., Carputo, D., Frusciante, L., Ercolano, M. (2012) Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytol. 197,223-37.

Hakala, K., Van Landeghem, S., Kaewphan, S., Salakoski, T., Van de Peer, Y., Ginter, F. (2012) CyEVEX: Literature-scale network integration and visualization through Cytoscape. Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine (SMBM) p. 91-96.

Sterck, L., Billiau, K., Abeel, T., Rouzé, P., Van de Peer, Y. (2012) ORCAE: online resource for community annotation of eukaryotes. Nat. Methods 9, 1041.

Cock, M., Sterck, L., Ahmed, S., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Arun, A., Aury, J., Badger, J. H., Beszteri, B., Billiau, K., Bonnet, E., H. Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, S.M., Collen, J., Le Corguille, G., Corre, E., Dartevelle, L., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Godfroy, O., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Luthringer, R., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Macaisne, N., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D.R., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Scornet, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Rouzé, P., Van de Peer, Y., Wincker, P. (2012) The Ectocarpus Genome and Brown Algal Genomics. Adv. Bot. Res. 64: 141-184.

Klochendler, A., Weinberg-Corem, N., Moran, M., Swisa, A., Pochet, N., Savova, V., Vikesa, J., Van de Peer, Y., Brandeis, M., Regev, A., Nielsen, FC., Dor, Y., Eden, A. (2012) A Transgenic Mouse Marking Live Replicating Cells Reveals In Vivo Transcriptional Program of Proliferation. Dev. Cell 23,681-90.

* Vekemans, D., * Proost, S., Vanneste, K., Coenen, H., Viaene, T., Ruelens, P., Maere, S., Van de Peer, Y., Geuten, K. (2012) Gamma paleohexaploidy in the stem-lineage of core eudicots: significance for MADS-box gene and species diversification. Mol. Biol. Evol. 29,3793-806. *contributed equally

Milner, DA Jr., Pochet, N., Krupka, M., Williams, C., Seydel, K., Taylor, J.S., Van de Peer, Y., Regev, A., Wirth, D., Daily, J.P., Mesirov, J.P. (2012) Transcriptional Profiling of Plasmodium falciparum Parasites from Patients with Severe Malaria Identifies Distinct Low vs. High Parasitemic Clusters. PLOS One 7, e40739.

Brown, M.T., Hanna, M., Tesar, B., Pochet, N., Vartanov, A., Fernandes, M., Werner, G., Ash, M., Roden, C., MacConaill, L., Hainz, U., Longtine, J., Wang, X., Correll, M., Van de Peer, Y., Regev, A., Wu, C., Neuberg, D., Freedman, A. (2012) Germline Copy Number Variation Associated with Mendelian Inheritance of CLL in Two Families. Leukemia 26, 1710-3.

Murat, C., Van de Peer, Y., Salse, J. (2012) Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol. Evol. 4, 805-16.

Moreau, H., Verhelst, B., Couloux, A., Derelle, E., Rombauts, S., Grimsley, N., Van Bel, M., Poulain, J., Katinka, M., Hohmann-Marriott, M., Piganeau, G., Rouzé, P., Da Silva, C., Wincker, P., Van de Peer, Y., Vandepoele, K. (2012) Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage . Genome Biol. 13, R74.

Amoutzias, G., He, Y., Lilley, K., Van de Peer, Y., Oliver, S. (2012) Evaluation and properties of the budding yeast phosphoproteome. Molecular and Cellular Proteomics 11, M111.009555.

Van Landeghem, S., Hakala, K., Rönnqvist, S., Salakoski, T., Van de Peer, Y., Ginter, F. (2012) Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology and Indirect Associations. Advances in Bioinformatics 2012,582765.

Tomato Genome Consortium (TGC): ..., ..., Rombauts, S., Fawcett, J., Van de Peer, Y., ..., ... (2012) The tomato genome sequence provides insights intofleshy fruit evolution. Nature 485,635-41.

Brown, M.T., Hanna, M., Tesar, B., Werner, G., Pochet, N., Asara, J., Wang, X., dal Cin, P., Fernandes, M., Thompson, C., MacConaill, L., Wu, C., Van de Peer, Y., Correll, M., Regev, A., Neuberg, D., Freedman, A. (2012) Integrative Genomic Analysis Implicates Gain of PIK3CA at 3q26 and MYC at 8q24 in Chronic Lymphocytic Leukemia. Clin. Cancer Res. 18, 3791-3802.

Van Landeghem, S., Björne, J., Abeel, T., De Baets, B., Salakoski, T., Van de Peer, Y. (2012) Semantically linking molecular entities in literature through entity relationships. BMC Bioinformatics 13,S6.

Kaewphan, S., Peltonen, S., Van Landeghem, S., Van de Peer, Y., Jones, P., Ginter, F. (2012) Integrating large-scale text mining and co-expression networks: Targeting NADP(H) metabolism in E. coli with event extraction. Proceedings of the LREC workshop on Building and Evaluating Resources for Biomedical Text Mining. Istanbul, Turkey.

Björne, J., Van Landeghem, S., Pyysalo, S., Ohta, T., Ginter, F., Van de Peer, Y., Ananiadou, S., Salakoski, T. (2012) PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. Proceedings of the 2012 Workshop on Biomedical Natural Language Processing(BioNLP) NAACL Workshop. Montreal, Canada. pp. 82-90 .

De Smet, R., Van de Peer, Y. (2012) Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr. Opin. Plant Biol. 15,168-176.

Van de Peer, Y., Pires, J.C. (2012) Getting up to speed. Curr. Opin. Plant Biol. 15,111-4.

Whitford, R., Fernandez, A., Tejos, R., Cuellar Perez, A., Kleine-Vehn, J., Vanneste, S., Drozdzecki, A., Leitner, J., Abas, L., Aerts, M., Hoogewijs, K., Baster, P., De Groodt, R., Lin, Y.-C., Storme, V., Van de Peer, Y., Beeckman, T., Madder, A., Devreese, B., Luschnig, C., Friml, J., Hilson, P. (2012) GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Dev. Cell 22,678-85.

Fawcett, J., Rouzé, P., Van de Peer, Y. (2012) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol. Biol. Evol. 29,849-59.

Hacquard, S., Joly, D., Lin, Y.-C., Tisserant, E., Feau, N., Delaruelle, C., Legué, V., Kohler, A., Tanguay, P., Petre, B., Frey, P., Van de Peer, Y., Rouzé, P., Martin, F., Hamelin, R., Duplessis, S. (2012) A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici- populina (poplar leaf rust). Mol. Plant Microbe In. 25,279-293.

* Van Bel, M., * Proost, S., Wischnitzki, E., Movahedi, S., Scheerlinck, C., Van de Peer, Y., Vandepoele, K. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158,590-600. *contributed equally

Malacarne, G., Perazzolli, M., Cestaro, A., Sterck, L., Fontana, P., Van de Peer, Y., Viola, R., Velasco, R., Salamini, F. (2012) Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes . PLOS One 7,e29762.

* Proost, S., * Fostier, J., De Witte, D., Dhoedt, B., Demeester, P., Van de Peer, Y., Vandepoele, K. (2012) i-ADHoRe 3.0 - Fast and Sensitive Detection of Genomic Homology in Extremely Large Data Sets. Nucleic Acids Res. 40,e11. *contributed equally

Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y. (2012) GenomeView: a next-generation genome browser. Nucleic Acids Res. 40,e12.

2011

Kano, Y., Björne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L.E., Kilicoglu, H., Bergler, S., Van Landeghem, S., Van Parys, T., Van de Peer, Y., Miwa, S., Ananiadou, S., Neves, M., Pascual-Montano, A., Ozgur, A., Radev, D.R., Riedel, S., Saetre, R., Chun, H.W., Kim, J.R., Pyysalo, S., Ohta, T., Tsujii, J. (2011) U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12,481.

Van Landeghem, S., De Baets, B., Van de Peer, Y., Saeys, Y. (2011) High-precision bio-molecular event extraction from text using parallel binary classifiers. Comput. Intell. 27,645-664.

Grbic, M., Van Leeuwen, T., Clark, T. G., Rombauts, S., Rouzé, P., Grbic, V., Osborne, E., Dermauw, W., Thi Ngoc Cao, P., Ortego, F., Hernandez-Crespo, P., Diaz, I., Martinez, N.J., Navajas, M., Sucena, E., Magalhaes, S., Nagy, L., Pace, N.R., Djuranovic, S., Smagghe, G., Iga, M., Christiaens, M., Veenstra, J., Ewer, J., Mancilla Villalobos, R., Hutter, J., Hudson, A., Velez, M., Yi, S., Zeng, Q., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, SR., Gregory, R., Mathieu, J., Verdon, L., Farinelli, L., Schmutz, J., Lindquist, E., Feyereisen, R., Van de Peer, Y. (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479,487-492.

Young, N.D., Debelle, F., Oldroyd, G.E., Geurts, P., Cannon, S.B., Udvardi, M., Benedito, V., Mayer, K., Gouzy, J.P., Schoof, H., Van de Peer, Y., Proost, S., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, K., Mudge, J., Bharti, A., Murray, J.A.H., Naoumkina, M., Rosen, B., Silverstein, K., Tang, H., Rombauts, S., Zhao, Q., Zhou, K., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, J., Bidwell, S.L., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, Y., Doyle, J., Dudez, A., Farmer, E.E., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., Gonzalez, A., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D., Jing, Y., Jöcker, A., Kenton, S., Kim, J.R., Klee, K., Lai, M.-H., Lang, D., Lin, S., Macmil, S., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E., Mun, J., Najar, F., Nicholson, C., Noirot, C., OBleness, M., Paule, C., Poulain, J., Prion, F., Qin, B., Qu, D., Retzel, E., Riddle, C., Sallet, E., Samain, S., Samson, G., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Ségurens, B., Severin, A., Sherrier, J., Shi, J., Sims, S., Singer, S., Sinharoy, S., Sterck, L., Viollet, A., Wang, X., Wang, X., Wang, X., Wang, X., Warfsmann, J., Weissenbach, J., White, O., White, O., Wiley, G., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, K., Zuber, A., Denarie, J., Dixon, R., May, G., Schwartz, D., Rogers, J., Quetier, F., Town, C.D., Roe, B. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480,520-4.

Coyne, R. S., Hannick, L., Shanmugam, D., Hostetler, J. B., Brami, D., Joardar, V. S., Johnson, P.J., Radune, D., Singh, N., Kumar, U., Saier, M., Wang, X., Cai, H., Gu, J., Mather, M. W., Vaidya, A. B., Wilkes, D. E., Rajagopalan, V., Asai, D. J., Pearson, C. G., Findly, R. C., Dickerson, H. W., Badger, J. H., Wu, M., Martens, C., Van de Peer, Y., Roos, D. S., Cassidy-Hanley, D. M., Clark, T. G. (2011) Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol. 12,R100.

Cock, M., Colle, J., Sterck, L., Rouzé, P., Scornet, D., Anthouard, V., Artiguenave, F., Aury, J., Billiau, K., Bonnet, E., H.F. Bothwell, J., Brillet, L., Carre, W., Coelho, S.M., Corre, E., Da Silva, C., Jubin, C., Martens, C., Maumus, F., Miranda-Saavedra, D., Peters, S., Porcel, B., Quesneville, H., Boyen, C., Van de Peer, Y., Wincker, P. (2011) Nature, nurture and the structure of macroalgal genomes. Eur. J. Phycol. 46,39-39.

Michoel, T., Joshi, A., Nachtergaele, B., Van de Peer, Y. (2011) Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. Mol. BioSyst. 7,2769-2778.

Joshi, A., Van de Peer, Y., Michoel, T. (2011) Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. Nucleic Acids Res. 39,9108-17.

Chancerel, E., Lepoittevin, C., Le Provost, G., Lin, Y.-C., Pablo Jaramillo-Correa, J., J Eckert, A., L Wegrzyn, J., Zelenika, D., Boland, A., Frigerio, J., Chaumeil, P., Garnier-Géré, P., Boury, C., Grivet, D., C González-Martínez, S., Rouzé, P., Van de Peer, Y., B Neale, D., T Cervera, M., Kremer, A., Plomion, C. (2011) Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics 12,368.

Van Landeghem, S., Ginter, F., Van de Peer, Y., Salakoski, T. (2011) EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions. Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, ACL-HLT 2011 28-37, Portland, Oregon, USA.

Duplessis, S., A. Cuomo, C., Lin, Y.-C., Aerts, A., Tisserant, E., Veneault-Fourrey, C., L. Joly, D., Hacquard, S., Amselem, J., L. Cantarel, B., Chiu, C.-H., Couthinho, P., Feau, N., Field, M., Frey, P., Gelhaye, E., Goldberg, J., Grabherr, M., D. Kodira, C., Kohler, A., Kües, U., A. Lindquist, E., Lucas, S., Mago, R., Mauceli, E., Morin, E., Murat, C., L. Pangilinan, J., Park, R., Pearson, M., Quesneville, H., Rouhier, N., Sakthikumar, S., A. Salamov, A., Schmutz, J., Selles, B., Shapiro, H.J., Tangay, P., A. Tuskan, G., Henrissat, B., Van de Peer, Y., Rouzé, P., G. Ellis, J., N. Dodds, P., E. Schein, J., Zhong, S., C. Hamelin, R., V. Grigoriev, I., J. Szabon, L., Martina, F. (2011) Obligate Biotrophy Features Unraveled by the Genomic Analysis of Rust Fungi. Proc. Natl. Acad. Sci. USA 108,22.

Van de Peer, Y. (2011) A mystery unveiled. Genome Biol. 12,113.

Baele, G., Van de Peer, Y., Vansteelandt, S. (2011) Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. BMC Evol. Biol. 11,145.

Movahedi, S., Van de Peer, Y., Vandepoele, K. (2011) Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiology 156,1316-1330.

* Hu, T.T., * Pattyn, P., Bakker, E.G., Cao, J., Cheng, Y.-Y., Clarck, R.M., Fahlgren, N., Fawcette, J., Grimwood, J., Gundlach, H., Haberer, G., Hollister, J.D., Ossowski, S., Ottilar, R.P., Salamov, A., Schneeberger, K., Spannagl, M., Wang, X., Yang, L., Nasrallah, M.E., Bergelson, J., Carrington, J.C., Gaut, B.S., Schmutz, J., Mayer, K., Van de Peer, Y., Grigoriev, I., Nordborg, M., Weigel, D., Guo, Y-L. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 4,476-81. *contributed equally

* Audenaert, P., * Van Parys, T., Brondel, F., Pickavet, M., Demeester, P., Van de Peer, Y., Michoel, T. (2011) CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. Bioinformatics 27,1587-1588 . *contributed equally

Proost, S., Pattyn, P., Gerats, T., Van de Peer, Y. (2011) Journey through the past: 150 million years of plant genome evolution. Plant J. 66, 58-65.

* Fostier, J., * Proost, S., Dhoedt, B., Saeys, Y., Demeester, P., Van de Peer, Y., Vandepoele, K. (2011) A Greedy, Graph-Based Algorithm for the Alignment of Multiple Homologous Gene Lists. Bioinformatics 27, 749-56. *contributed equally

Van de Peer, Y. (2011) Genomes: the truth is in there. EMBO Rep. 12,93.

Armañanzas, R., Saeys, Y., Inza, I., Garcia-Torres, M., Bielza, C., Van de Peer, Y., Larrañaga, P. (2011) Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms. IEEE-ACM Trans. Comput. Biol. Bioinform. 8,760-74.

Yao, Y., Baele, G., Van de Peer, Y. (2011) A bio-inspired agent-based system for controlling robot behaviour. Proceedings of the IA - 2011 IEEE Symposium on Intelligent Agents organized in IEEE Symposium Series in Computational Intelligence 2011 Paris, France.

2010

Sanchez-Rodriguez, A., Martens, C., Engelen, K., Van de Peer, Y., Marchal, K. (2010) The Potential for Pathogenicity was Present in the Ancestor of the Ascomycete subphylum Pezizomycotina. BMC Evol. Biol. 10, 318.

Maere, S., Van de Peer, Y. (2010) Duplicate retention after small- and large-scale duplication. Evolution After Gene Duplication (Book Chapter, Ed. Dittmar, K., Liberles, D.) 31-56.

* Abeel, T., * Van Landeghem, S., Morante, R., Van Asch, V., Van de Peer, Y., Daelemans, W., Saeys, Y. (2010) Highlights of the BioTM 2010 workshop on advances in bio text mining. BMC Bioinformatics 11, I1. *contributed equally

* Van Landeghem, S., * Abeel, T., Saeys, Y., Van de Peer, Y. (2010) Discriminative and informative features for biomolecular text mining with ensemble feature selection. Bioinformatics 26, 554-560. *contributed equally

Bonnet, E., Michoel, T., Van de Peer, Y. (2010) Prediction of a regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 26, 638-644.

Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., Bhatnagar, S.K., Troggio, M., Pruss, D., Salvi, S., Pindo, M., Baldi, P., Castelletti, S., Cavaiuolo, M., Coppola, G., Costa, F., Cova, V., Dal Ri, A., Goremykin, V., Komjanc, M., Longhi, S., Magnago, P., Malacarne, G., Malnoy, M., Micheletti, D., Moretto, M., Perazzolli, M., Si-Ammour, A., Vezzulli, S., Zini, E., Eldredge, G., FitzGerald, L.M., Gutin, N., Lanchbury, J., Macalma, T., Mitchell, J.T., Reid, J., Wardell, B., Kodira, C., Chen, Z., Desany, B., Niazi, F., Palmer, L., Koepke, T., Jiwan, D., Schaeffer, S., Krishnan, V., Wu, C., Chu, V.T., King, S.T., Vick, J., Tao, Q., Mraz, A., Stormo, K., Stormo, K., Bogden, R., Ederle, D., Stella, A., Vecchietti, A., Kater, M.M., Masiero, S., Lasserre, P., Lespinasse, Y., Allan, A.C., Bus, V., Chagné, D., Crowhurst, R.N., Gleave, A.P., Lavezzo, E., Fawcett, J., Proost, S., Rouzé, P., Sterck, L., Toppo, S., Lazzari, B., Hellens, R.P., Durel, C., Gutin, A., Bumgarner, R.E., Gardiner, S.E., Skolnick, M., Egholm, M., Van de Peer, Y., Salamini, F., Viola, R. (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat. Genet. 42, 833–839.

Baele, G., Van de Peer, Y., Vansteelandt, S. (2010) Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. BMC Evol. Biol. 10, 244.

Van Landeghem, S., Pyysalo, S., Ohta, T., Van de Peer, Y. (2010) Integration of Static Relations to Enhance Event Extraction from Text. Proceedings of the 2010 Workshop on Biomedical Natural Language Processing 144-152. Uppsala, Sweden.

Baele, G., Van de Peer, Y., Vansteelandt, S. (2010) Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J. Mol. Evol. 71,34-50.

Michoel, T., Joshi, A., Bonnet, E., Vermeirssen, V., Van de Peer, Y. (2010) Towards system level modeling of functional modules and regulatory pathways using genome-scale data. Proceedings of the Seventh International Workshop on Computational Systems Biology (WCSB 2010) 71-74. Luxembourg, Luxembourg.

Fawcett, J., Van de Peer, Y. (2010) Angiosperm polyploids and their road to evolutionary success. Trends in Evolutionary Biology 2, e3, 16-21.

Martens, C., Van de Peer, Y. (2010) The hidden duplication past of the plant pathogen phytophthora and its consequences for infection. BMC Genomics 11, 353.

Cock, M., Sterck, L., Rouzé, P., Scornet, D., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J., Badger, J., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, S.M., Colln, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P. (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465, 617–621.

Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26, 1566-1568.

Bonnet, E., Tatari, M., Joshi, A., Michoel, T., Marchal, K., Berx, G., Van de Peer, Y. (2010) Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLOS One 5, e10162.

Amoutzias, G., Van de Peer, Y. (2010) Single-Gene and Whole-Genome Duplications and the Evolution of Protein-Protein Interaction Networks. Evolutionary Genomics and Systems Biology (Book Chapter, Ed. Caetano-Anollés, G.),413-429.

Joshi, A., Van Parys, T., Van de Peer, Y., Michoel, T. (2010) Characterizing regulatory path motifs in integrated networks using perturbational data. Genome Biol. 11, R32.

Saeys, Y., Van Landeghem, S., Van de Peer, Y. (2010) Event based text mining for integrated network construction. Journal of Machine Learning Research, Workshop and Conference proceedings 8, 112-121.

Amoutzias, G., He, Y., Gordon, J., Mossialos, D., Oliver, S., Van de Peer, Y. (2010) Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci 107, 2967-2971.

Huysman, M., Martens, C., Vandepoele, K., Gillard, J., Rayko, E., Heijde, M., Bowler, C., Inzé, D., Van de Peer, Y., De Veylder, L., Vyverman, W. (2010) Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signalling. Genome Biol. 11, R17.

Rehrauer, H., Aquino, C., Gruissem, W., Henz, SR., Hilson, P., Laubinger, S., Naouar, N., Patrignani, A., Rombauts, S., Shu, C.-L., Van de Peer, Y., Vuylsteke, M., Weigel, D., Zeller, G., Hennig, L. (2010) AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol. 152, 487-499.

Abeel, T., Helleputte, T., Van de Peer, Y., Dupont, C., Saeys, Y. (2010) Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics 26, 392-398.

Van de Peer, Y., Maere, S., Meyer, A. (2010) 2R or not 2R is not the question anymore. Nat. Rev. Genet. 11, 166.

2009

* Proost, S., * Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., Vandepoele, K. (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. The Plant Cell 21, 3718-3731. *contributed equally

Van de Peer, Y., Fawcett, J., Proost, S., Sterck, L., Vandepoele, K. (2009) The flowering world: a tale of duplications. Trends Plant Science 14, 680-688 .

Kernbach, S., Hamann, K., Stradner, J., Thenius, R., Schmickl, T., van Rossum, A. C., Sebag, M., Bredeche, N., Yao, Y., Baele, G., Van de Peer, Y., Timmis, K.N., Mokhtar, M., Tyrrell, A., Eiben, A. E., McKibbin, S. P., Liu, W., Winfield, A. F. T. (2009) On adaptive self-organization in artificial robot organisms. Computation World: Future Computing, Service Computation, Cognitive, Adaptive, Content, Patterns 33-43.

Mattanovich, D., Callewaert, L., Rouzé, P., Lin, Y.-C., Graf, A., Redl, A., Tiels, P., Gasser, B., De Schutter, K. (2009) Open access to sequence: Browsing the Pichia pastoris genome. Microbial Cell Factories 8, 53.

Saeys, Y., Van Landeghem, S., Van de Peer, Y. (2009) Integrated network construction using event based text mining. Proceedings of the 3rd Machine Learning in Systems Biology workshop (MLSB) 105-114.

* Piganeau, G., * Vandepoele, K., Gourbiere, S., Van de Peer, Y., Moreau, H. (2009) Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus. J. Mol. Evol. 69, 249-59. *contributed equally

Van de Peer, Y., Maere, S., Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725-32.

Vermeirssen, V., Joshi, A., Michoel, T., Bonnet, E., Casneuf, T., Van de Peer, Y. (2009) Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. Molecular BioSystems 5, 1817-30.

Mueller, L., Lankhorst, R., Tanksley, S., Giovannoni, J., White, O., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A., Menda, N., Tecle, I., Bombarely, A., Stack, S., Royer, S., Chang, Y., Shearer, L., Kim, J.R., Jo, S., Hur, C., Choi, D., Li, C., Zhao, Q., Jiang, H., Geng, Y., Dai, Y., Fan, M.-J., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Y.-Y., Li, C., Ling, H., Xue, Y., Wang, X., Seymour, G., Bishop, G., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A., Kumar, R., Gupta, A., Sharma, A., Khurana, J., Khurana, J., Tyagi, A., Sarita, ., Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, N., Kumar, A., Dixit, R., Singh, N., Praveen, S., Dalal, V., Yadav, M., Ghazi, I., Gaikwad, K., Raj Sharma, T., Mohapatra, T., Singh, N., Szinay, D., de Jong, P.J., Peters, S., van Staveren, M., Datema, E., Fiers, M., van Ham, R., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, M., Botella, M., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, J., He, Y., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, X., Ye, Z., Yang, W., Wang, X., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D?Agostino, N., Chiusano, M., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K., Guigó, R., Camara, F., Rombauts, S., Fawcett, J., Van de Peer, Y., Knapp, S., Zamir, D., Stiekema, W. (2009) A Snapshot of the Emerging Tomato Genome Sequence: The Tomato Genome Sequencing Consortium. The Plant Genome 2, 78-92.

De Bodt, S., Proost, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10, 288.

Abeel, T., Van de Peer, Y., Saeys, Y. (2009) Towards a gold standard for promoter prediction evaluation. Bioinformatics 25, i313-i320.

Dittami, S., Scornet, D., Petit, J., Ségurens, B., Da Silva, C., Corre, E., Dondrup, M., Glatting, K., Konig, R., Sterck, L., Rouzé, P., Van de Peer, Y., Cock, M., Boyen, C., Tonon, T. (2009) Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol. 10, R66.

De Schutter, K., Lin, Y.-C., Tiels, P., Van Hecke, A., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, L. (2009) Genome sequence of the recombinant protein production host Pichia pastoris, a methylotrophic yeast. Nature Biotechnology 27, 561-6.

Michoel, T., De Smet, R., Joshi, A., Van de Peer, Y., Marchal, K. (2009) Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. 3, 49.

Abeel, T., Van de Peer, Y., Saeys, Y. (2009) Java-ML: a machine learning library. J. Mach. Learn. Res. 10, 931-4.

Baele, G., Van de Peer, Y., Vansteelandt, S. (2009) Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences. BMC Evol. Biol. 9, 87.

Worden, A.Z., J-Lee, H., Mock, T., Rouzé, P., Simmons, M.P., Aerts, A., Allen, A., Cuvelier, M.L., Derelle, E., Everett, M.V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S.M., Parker, M.S., Rombauts, S., Salamov, A., Von, P. Dasso, Badger, J., Coutinho, P.M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J.E., John, U., Lanier, W., Lindquist, E., Lucas, S., Mayer, K., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, V., Bhattacharya, D., Goodenough, U.W., Van de Peer, Y., Grigoriev, I. (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324, 268-72.

Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., Van de Peer, Y. (2009) Unravelling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol. 150, 535-46.

Fawcett, J., Maere, S., Van de Peer, Y. (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci 106, 5737-42.

Michoel, T., De Smet, R., Joshi, A., Marchal, K., Van de Peer, Y. (2009) Reverse-engineering transcriptional modules from gene expression data. Ann. NY. Acad. Sci. 1158, 36-43 .

Joshi, A., De Smet, R., Marchal, K., Van de Peer, Y., Michoel, T. (2009) Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics 25, 490-6.

Baele, G., Bredeche, N., Haasdijk, E., Maere, S., Michiels, N., Van de Peer, Y., Schmickl, T., Schwarzer, C., Thenius, R. (2009) Open-ended On-board Evolutionary Robotics for Robot Swarms. Proceedings of the 2009 IEEE Congress On Evolutionary Computation. 1123-1130.

2008

Fierro, A.C., Vandenbussche, M., Engelen, K., Van de Peer, Y., Marchal, K. (2008) Meta Analysis of Gene Expression Data within and Across Species. Curr. Genomics 9, 525-34.

Bowler, C., * Allen, A., * Badger, J., * Grimwood, J., * Jabbari, K., * Kuo, Y.-C., * Maheswari, U., * Martens, C., * Maumus, F., * Otillar, R., * Rayko, E., * Salamov, A., * Vandepoele, K., Beszteri, B., Gruber, A., Heijde, M., Katinka, M., Mock, T., Valentin, K., Vérret, F., Berges, J., Brownlee, C., Cadoret, J., Chiovitti, A., Jae Choi, C., Coesel, S., Martino, A., Detter, J., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M., Jenkins, B., Jiroutova, K., Jorgensen, R., Joubert, Y., Kaplan, A., Kroeger, N., Kroth, P., Roche, J., Lindquist, E., Lommer, M., Martin-Jézéquel, V., Lopez, P., Lucas, S., Mangogna, M., McGinnis, K., Medlin, L., Montsant, A., Oudot-Secq, M., Napoli, C., Obornik, M., Petit, J., Porcel, B., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T., Schmutz, J., Schnitzler Parker, M., Shapiro, H.J., Siaut, M., Stanley, M., J.Sussman, M., Taylor, J.S., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L., Rokhsar, D., Weissenbach, J., Armbrust, V., Green, P.J., Van de Peer, Y., Grigoriev, I. (2008) The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature 456, 239-44. *contributed equally

Baele, G., Van de Peer, Y., Vansteelandt, S. (2008) A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. Syst. Biol. 57, 675-92.

Van Landeghem, S., Saeys, Y., De Baets, B., Van de Peer, Y. (2008) Extracting protein-protein interactions from text using rich feature vectors and feature selection. Proceedings of Third International Symposium on Semantic Mining in Biomedicine (SMBM 08) 77-84.

Saeys, Y., Abeel, T., Van de Peer, Y. (2008) Robust Feature Selection using Ensemble Feature Selection Techniques. Proceedings of ECML/PKDD 5212, 313-25.

Armañanzas, R., Inza, I., Santana, R., Saeys, Y., Flores, J., Lozano, J., Van de Peer, Y., Blanco, R., Robles, P., Bielza, C., Larrañaga, P. (2008) A review of estimation of distribution algorithms in bioinformatics. BioData Mining 1, 6.

Van Bel, M., Saeys, Y., Van de Peer, Y. (2008) FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. Bioinformatics 24, 1532-3.

Abeel, T., Saeys, Y., Rouzé, P., Van de Peer, Y. (2008) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 24, i24-i31.

Amoutzias, G., Van de Peer, Y., Mossialos, D. (2008) Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases. Future Microbiol. 3, 361-70.

Foissac, S., Gouzy, J.P., Rombauts, S., Mathé, C., Amselem, J., Sterck, L., Van de Peer, Y., Rouzé, P., Schiex, T. (2008) Genome Annotation in Plants and Fungi: EuGene as a model platform. Curr. Bioinform. 3, 87-97.

Amoutzias, G., Van de Peer, Y. (2008) Together We Stand: Genes Cluster to Coordinate Regulation. Dev. Cell 14, 640-2.

Amoutzias, G., Robertson, D., Van de Peer, Y., Oliver, S. (2008) Choose your partners: dimerization in eukaryotic transcription factors. Trends in Biochemical Sciences 33, 220-9.

Martin, F., Aerts, A., Ahrén, D., Brun, A., Duchaussoy, F., Gibon, J., Kohler, A., Lindquist, E., Pereda, V., Salamov, A., Shapiro, H.J., Wuyts, J., Blaudez, D., Buée, M., Brokstein, P., Canbäck, B., Cohen, D., Courty, P.E., Coutinho, P., Danchin, E.G.J., Delaruelle, C., Detter, J., Deveau, A., DiFazio, S., Duplessis, S., Fraissinet-Tachet, L., Lucic, E., Frey-Klett, P., Fourrey, C., Feussner, I., Gay, G., Gérard, J., Grimwood, J., Hoegger, P.J., Jain, P., Kilaru, S., Labbé, J., Lin, Y.-C., Legué, V., F LeTacon, ., Marmeisse, R., Melayah, D., Montanini, B., Muratet, M., Nehls, U., Niculita-Hirzel, H., Oudot-LeSecq, M.P., Peter, G., Quesneville, H., Rajashekar, B., Reich, M., Rouhier, N., Schmutz, J., Yin, T., Chalot, M., Henrissat, B., Kües, U., Lucas, S., Van de Peer, Y., Podila, G., Polle, A., Pukkila, PJ., Richardson, P., Rouzé, P., Sanders, I., Stajich, J.E., Tunlid, A., Tuskan, G., Grigoriev, I. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452, 88-92.

Martens, C., Vandepoele, K., Van de Peer, Y. (2008) Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc. Natl. Acad. Sci. USA 105, 3427-32.

Abeel, T., Saeys, Y., Bonnet, E., Rouzé, P., Van de Peer, Y. (2008) Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 18, 310-23.

Helaers, R., Tzika, A., Van de Peer, Y., Milinkovitch, M.C. (2008) MANTIS, a phylogenetic framework for multi-species genome comparisons. Bioinformatics 24, 151-7.

Vandenbroucke, K., Robbens, S., Vandepoele, K., Inzé, D., Van de Peer, Y., Van Breusegem, F. (2008) Hydrogen Peroxide-Induced Gene Expression across Kingdoms: A Comparative Analysis. Mol. Biol. Evol. 25, 507-16.

Rensing, S.A., Lang, D., Zimmer, A., Terry, A., Salamov, A., H,Shapiro, , Nishiyama, T., P.-Perroud, F., Lindquist, E., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., Shin-I, T., Kuroki, Y., Toyoda, A., Suzuki, Y., S.-Hashimoto, I., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Ashton, N., Anterola, A., Aoki, S., Barbazuk, W.B., Barker, E., Bennetzen, J., Blankenship, R., Cho, S.H., Dutcher, S., Estelle, M., Fawcett, J., Gundlach, H., Hanada, K., Heyl, A., Hicks, K. A., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, D.R., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, P., Sanderfoot, A., Schween, G., S.-Shiu, H., Stueber, K., Theodoulou, F.L., Tu, H., Van de Peer, Y., Verrier, P.J., Waters, E., Wood, A., Yang, G., Cove, D., Cuming, A.C., Hasebe, M., Lucas, S., Mishler, B.D., Reski, R., Grigoriev, I., Quatrano, R.S., Boore, J.L. (2008) The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319, 64-9.

Joshi, A., Van de Peer, Y., Michoel, T. (2008) Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24, 176-83.

Robbens, S., Rouzé, P., Cock, M., Spring, J., Worden, A.Z., Van de Peer, Y. (2008) The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. J. Mol. Evol. 66, 80-4.

John, U., Beszteri, B., Derelle, E., Van de Peer, Y., Read, B., Moreau, H., Cembella, A. (2008) Novel Insights into Evolution of Protistan Polyketide Synthases through Phylogenomic Analysis. Protist 159, 21-30.

Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008) i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24, 127-8.

2007

Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., FitzGerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J., Sterck, L., Vandepoele, K., Grando, M.S., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F., Viola, R. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLOS One 2, e1326.

Casneuf, T., Van de Peer, Y., Huber, H. (2007) In situ Analysis of Cross-Hybridisation on Microarrays and the Inference of Expression Correlation. BMC Bioinformatics 8,461 .

Merks, R.M.H., Van de Peer, Y., Inzé, D., Beemster, G.T.S. (2007) Canalization without flux sensors: a traveling-wave hypothesis. Trends Plant Science 12, 384-90.

Van Hellemont, R., Blomme, T., Van de Peer, Y., Marchal, K. (2007) Divergence of regulatory sequences in duplicated fish genes. Genome Dyn 3, 81-100.

Rensing, S.A., Ick, J., Fawcett, J., Lang, D., Zimmer, A., Van de Peer, Y., Reski, R. (2007) An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol. Biol. 7,130.

Van de Peer, Y. (2007) The future for plants and plants for the future. Genome Biol. 8, 308.

Saeys, Y., Abeel, T., Degroeve, S., Van de Peer, Y. (2007) Translation initiation site prediction on a genomic scale: beauty in simplicity. Bioinformatics 23, 418-23.

Bonet, I., Lorenzo, M., Saeys, Y., Van de Peer, Y., Grau, R. (2007) Predicting Human Immunodeficiency Virus (HIV) Drug Resistance using Recurrent Neural Networks. Lect. Notes in Comput. Sci. 4527, 234-43.

* Michoel, T., * Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data. BMC Bioinformatics 8, S5. *contributed equally

Palenik, B., Grimwood, J., Aerts, A., Rouzé, P., Salamov, A., Putnam, N., Zhou, K., Jorgensen, R., Derelle, E., Rombauts, S., Otillar, R., Merchant, S., Podell, S., Gaasterland, T., Manuell, A., Napoli, C., Gendler, K., Vallon, O., Peyretaillade, E., Jancek, S., Piganeau, G., Heijde, M., Jabbari, K., Bowler, C., Werner, G., Robbens, S., Pazour, G., Dubchak, I., Ren, Q., Delwiche, C., Paulsen, I., De Boever, P., Schmutz, J., Rokhsar, D., Van de Peer, Y., Moreau, H., Grigoriev, I. (2007) The Tiny Eukaryote Ostreococcus Provides Genomic Insights Into The Paradox Of Plankton Speciation. Proc. Natl. Acad. Sci. USA 104, 7705-10.

Robbens, S., Petersen, J., Brinkmann, H., Rouzé, P., Van de Peer, Y. (2007) Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus. J. Mol. Evol. 64, 601-4.

Saeys, Y., Rouzé, P., Van de Peer, Y. (2007) In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi, and protists. Bioinformatics 23, 414-20.

Carlton, J.M., Hirt, H., Silva, E.P., Delcher, A.L., Schatz, M., Zhao, Q., Wortman, J.R., Bidwell, S.L., Alsmark, C.M., Besteiro, S., Sicheritz-Ponten, T., Noel, C.J., Dacks, J.B., Foster, P.G., Simillion, C., Van de Peer, Y., Barton, G.J., Westrop, G.D., Müller, S., Dessi, D., Fiori, L.P., Paulsen, I., Zhang, J., Bastida-Corcuera, F.D., Barbosa, A., Brown, M.T., Hayes, R.D., Mukherjee, M., Okumura, C.Y., Schneider, M., Villalvazo, M., Haase, G., Pertea, M., Feldblyum, T., Utterback, T.R., Shu, C.-L., Osoegawa, K., de Jong, P.J., Dolezal, P., Hrd, I., Malik, S.-B., Logsdon, Jr., Henze, K., Gupta, A., Wang, X., Dunne, R.L., Upcroft, J.A., Upcroft, P., White, O., Salzberg, S.L., Tanghe, K., Chiu, C.-H., Embley, T.M., Coombs, G.H., Mottram, J.C., Tachezy, J., Fraser-Liggett, C.M., Johnson, P.J. (2007) Draft Genome Sequence of the Sexually-Transmitted Pathogen Trichomonas vaginalis. Science 315, 207-12.

Robbens, S., Derelle, E., Ferraz, C., Wuyts, J., Moreau, H., Van de Peer, Y. (2007) The Complete Chloroplast and Mitochondrial DNA Sequence of Ostreococcus tauri: Organelle Genomes of the Smallest Eukaryote are Examples of Compaction. Mol. Biol. Evol. 24, 956-68.

Saeys, Y., Van de Peer, Y. (2007) Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection. Lect. Notes in Bioinf. 4366, 107-118.

Sterck, L., Rombauts, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2007) How many genes are there in plants (... and why are they there)?. Curr. Opin. Plant Biol. 10, 199-203.

2006

Vandepoele, K., Casneuf, T., Van de Peer, Y. (2006) Identification of novel regulatory modules in dicot plants using expression data and comparative genomics. Genome Biol. 7,R103.

* Cannon, S.B., * Sterck, L., * Rombauts, S., Sato, S., Wang, X., Mudge, J., Vasdewani, J., Cheung, F., Gouzy, J.P., Schiex, T., Spanngl, M., Schoof, H., Nicholson, C., Humphrays, S., Mayer, K., Rogers, J., Quetier, F., Oldroyd, G.E., Debelle, F., Cook, D.R., Town, C.D., Roe, B.A., Tabata, S., Van de Peer, Y., Young, N.D. (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl. Acad. Sci. USA 103, 14959-64. *contributed equally

Tuskan, G., * DiFazio, S., * Jansson, S., * Bohlmann, J., * Grigoriev, I., * Hellsten, U., * Putnam, N., * Ralph, S., * Rombauts, S., * Salamov, A., * Schein, J., * Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J., Locascio, P., Luo, Y., Lucas, S., Martin, F., Montanini, B., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouzé, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y., Rokhsar, D. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313, 1596-604. *contributed equally

* Derelle, E., * Ferraz, C., * Rombauts, S., * Rouzé, P., Worden, A.Z., Robbens, S., Partensky, F., Degroeve, S., Echeynie, S., Cooke, R., Saeys, Y., Wuyts, J., Panaud, O., Piegu, B., Ball, S., Ral, J.P., Bouget, F.-Y., Piganeau, G., De Baets, B., Picard, A., Delseny, M., Demaille, J., Van de Peer, Y., Moreau, H. (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl. Acad. Sci. USA 103, 11647-52. *contributed equally

Saeys, Y., Van de Peer, Y. (2006) Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection. Proceedings of the 15th Dutch Belgian Machine Learning Conference (Benelearn 2006), pp. 105-112..

Bonet, I., Garcia, M.M., Salazar, S., Sanchex, R., Saeys, Y., Van de Peer, Y., Grau, R. (2006) Feature Extraction Using Clustering of Proteins. Lect. Notes in Comput. Sci. (vol. 4225) pp. 614-623..

Bonet, I., Garcia, M.M., Salazar, S., Sanchex, R., Saeys, Y., Van de Peer, Y., Grau, R. (2006) Predicting Human Immunodeficiency Virus (HIV) Drug Resistance using Recurrent Neural Networks. Proceedings of the 10th International Electronic Conference on Synthetic Organic Chemistry, 2006.

Van den Bulcke, T., Lemmens, K., Van de Peer, Y., Marchal, K. (2006) Inferring transcriptional networks by mining 'omics' data. Curr. Bioinform. 1, 301-313.

Baele, G., Raes, J., Van de Peer, Y., Vansteelandt, S. (2006) An improved statistical method for detecting heterotachy in nucleotidesequences. . Mol. Biol. Evol. 23, 1397-405.

Bonnet, E., Van de Peer, Y., Rouzé, P. (2006) The small RNA world of plants. New Phytol. 171, 451-68.

De Bodt, S., Theissen, G., Van de Peer, Y. (2006) Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. Mol. Biol. Evol. 23, 1293-303.

Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., Van de Peer, Y. (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7, R43.

Gevers, D., Van de Peer, Y. (2006) Gene duplicates in vibrio genomes. Invited book chapter in The Biology of Vibrios. Editors: Thompson, F.L., Austin, B. & Swings, J. ASM press. pp. 76-83.

Faes, P., Minnaert, B., Christiaens, M., Bonnet, E., Saeys, Y., Stroobandt, D., Van de Peer, Y. (2006) A Scalable Hardware Accelerator for Comparing Protein Sequences.. Proceedings of the First International Conference on Scalable Information Systems. Hong Kong, April 2006, on CD..

Michoel, T., Van de Peer, Y. (2006) A helicoidal transfer matrix model for inhomogeneous DNA melting. Physical Review E. 73, 011908.

Van de Peer, Y. (2006) When duplicated genes don't stick to the rules. Heredity 96, 204-5.

Casneuf, T., De Bodt, S., Raes, J., Maere, S., Van de Peer, Y. (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol. 7, R13.

2005

Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., Van de Peer, Y. (2005) Predicting splice sites from high-dimensional local context representations. Bioinformatics 21, 1332-8.

* Maere, S., * De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., Van de Peer, Y. (2005) Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102, 5454-9. *contributed equally

Aubourg, S., Brunaud, V., Bruyere, C., Cooke, R., Cottet, A., Couloux, A., Dehais, P., Deleage, G., Duclert, A., Echeverria, M., Eschbach, A., Falconet, D., Filippi, G., Gaspin, C., Geourjon, C., Grienenberger, J.M., Houlne, G., Jamet, E., Lechauve, F., Leleu, O. L., Leroy, P., Mache, R., Meyer, C., Nedjari, H., Negrutiu, I., Orsini, V., Peyretaillade, E., Raes, J., Risler, J.L., Riviere, S., Rombauts, S., Rouzé, P., Schneider, M., Schwob, P., Small, I., Soumayet-Kampetenga, G., Stankovski, D., Toffano, C., Tognolli, M., Caboche, M., Lecharny, A. (2005) GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Res. 33, D641-6.

Van Hellemont, R., Monsieurs, P., Thijs, G., De Moor, B., Van de Peer, Y., Marchal, K. (2005) A novel approach to identifying regulatory motifs in distantly related genomes. Genome Biol. 6, R113.

Vandepoele, K., Vlieghe, K., Florquin, K., Hennig, L., Beemster, G.T.S., Gruissem, W., Van de Peer, Y., Inzé, D., De Veylder, L. (2005) Genome-wide identification of potential plant E2F target genes. Plant Physiol. 139, 316-28.

Beysen, D., Raes, J., Leroy, B.P., Lucassen, A., Yates, J.R., Clayton-Smith, J., Ilyina, H., Sklower Brooks, S., Christin-Maitre, S., Fellous, M., Fryns, J.P., Kim, J.R., Lapunzina, P., Lemyre, E., Meire, F., Messiaen, L.M., Oley, C., Splitt, M., Thomson, J., Van de Peer, Y., Veitia, R.A., De Paepe, A., De Baere, E. (2005) Deletions involving long-range conserved non-genic sequences (CNGs) upstream and downstream of FOXL2 as novel disease-causing mechanism in bpes. Am. J. Hum. Genet. 77, 205-18.

* De Bodt, S., * Maere, S., Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-7. *contributed equally

Gevers, D., Cohan, F.M., Lawrence, J.G., Spratt, B.G., Coenye, T., Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005) Re-evaluating prokaryotic species. Nature Rev. Micriobiol. 3, 733-9.

Meyer, A., Van de Peer, Y. (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27, 937-45.

* Coenye, T., * Gevers, D., Van de Peer, Y., Vandamme, P., Swings, J. (2005) Review: Towards a prokaryotic genomic taxonomy. Fems Microbiol. Rev. 29, 147-67. *contributed equally

Saeys, Y., Degroeve, S., Van de Peer, Y. (2005) Feature ranking using an EDA-based wrapper approach. Invited book chapter in 'Towards a new evolutionary computation : advances in Estimation of Distribution algorithms.' Editors: Jose A. Lozano, Pedro Larranaga, Inaki Inza and Endika Bengoetxea.

Van de Peer, Y., Meyer, A. (2005) Large-scale gene and ancient genome duplications. Book chapter in: The Evolution of the Genome, edited by T.R. Gregory. Elsevier, San Diego..

Florquin, K., Degroeve, S., Saeys, Y., Van de Peer, Y. (2005) Large-scale structural analysis of the core promoter inMammalian and plant genomes. Nucleic Acids Res. 33, 4255-64.

Robbens, S., Khadaroo, B., Camasses, A., Derelle, E., Ferraz, C., Inzé, D., Van de Peer, Y., Moreau, H. (2005) Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri. Mol. Biol. Evol. 22, 589-97.

Van de Peer, Y. (2005) Horizontal plant biology on the rise. Genome Biol. 6, 302.

Vandepoele, K., Van de Peer, Y. (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol. 137, 31-42.

Sterck, L., Rombauts, S., Jansson, S., Sterky, F., Rouzé, P., Van de Peer, Y. (2005) EST data suggest that poplar is an ancient polyploid. New Phytol. 167, 165-70.

Paterson, A.H., Bowers, J. E., Van de Peer, Y., Vandepoele, K. (2005) Ancient duplication of cereal genomes. . New Phytol. 165, 658-61.

Raes, J., Van de Peer, Y. (2005) Functional divergence of proteins through frameshift mutations. Trends Genet. 21, 428-31.

2004

* Bonnet, E., * Wuyts, J., Rouzé, P., Van de Peer, Y. (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20, 2911-7. *contributed equally

Bonnet, E., Wuyts, J., Rouzé, P., Van de Peer, Y. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important new target genes. Proc. Natl. Acad. Sci. USA 101, 11511-6.

Saeys, Y., Degroeve, S., Aeyels, D., Rouzé, P., Van de Peer, Y. (2004) Feature selection for splice site prediction: A new method using EDA-based feature ranking. BMC Bioinformatics 5, 64.

Vandepoele, K., De Vos, W., Taylor, J.S., Meyer, A., Van de Peer, Y. (2004) Major events in the genome evolution of vertebrates: paranome age and size differs considerably between fishes and land vertebrates. Proc. Natl. Acad. Sci. USA 101, 1638-43.

Wuyts, J., Perriere, G., Van de Peer, Y. (2004) The European ribosomal RNA database. Nucleic Acids Res. 32, D101-3.

Degroeve, S., Saeys, Y., De Baets, B., Van de Peer, Y., Rouzé, P. (2004) Splice site prediction in eukaryote genome sequences: the algorithmic issues. The New Avenues in Bioinformatics J. Seckbach (ed.) another book of the Cellular Origin and Life in Extreme Habitats Book Series. Kluwer Academic Publishers, Dordrecht, The Netherlands. (2004).

Gevers, D., Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. 12, 148-54.

Simillion, C., Vandepoele, K., Saeys, Y., Van de Peer, Y. (2004) Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 14, 1095-106.

Alvares, L.E., Wuyts, J., Van de Peer, Y., Silva, E.P., Coutinho, L.L., Brison, O., Ruiz, I.R.G. (2004) The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2. Genome 47, 421-8.

Khadaroo, B., Robbens, S., Ferraz, C., Derelle, E., Eychenie, S., Cooke, R., Peaucellier, G., Delseny, M., Demaille, J., Van de Peer, Y., Picard, A. (2004) The First Green Lineage cdc25 Dual-Specificity Phosphatase. Cell Cycle 3, 513-8.

Trindade, G.S., Da Fonseca, F.G., Marques, J.T., Diniz, S., Leite, J.A., De Bodt, S., Van de Peer, Y., Bonjardim, C.A., Ferreira, P.C.P., Kroon, E.G. (2004) The Belo Horizonte virus: a vaccinia-like virus lacking the A-type inclusion body gene isolated from infected mice. J. Gen. Virol. 85, 2015-21.

Rombauts, S., Lescot, M., Zhang, J., Aubourg, S., Mathé, C., Jansson, S., Rouzé, P., Boerjan, W. (2004) Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements. Theor. Appl. Genet. 109, 10-22.

Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) The quest for genomic homology. Curr. Genomics 5, 299-308.

Saeys, Y., Degroeve, S., Aeyels, D., Rouzé, P., Van de Peer, Y. (2004) Selecting relevant features for gene structure prediction. Proceedings of Benelearn 13, 103-109.

Simillion, C., Vandepoele, K., Van de Peer, Y. (2004) Recent developments in computational approaches for uncovering genomic homology. BioEssays 26, 1225-35.

Saeys, Y., Degroeve, S., Van de Peer, Y. (2004) Digging into acceptor splice site prediction: an iterative feature selection approach. Proceedings of ECML/PKDD , Lecture Notes in Artificial Intelligence 3202, 386-397.

Van de Peer, Y. (2004) Computational approaches to unveiling ancient genome duplications. Nat. Rev. Genet. 5, 752-63.

Van de Peer, Y. (2004) Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids. Genome Biol. 5, 250.

2003

Thareau, V., D?hais, P., Hilson, P., Rouzé, P., Aubourg, S. (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics 19, 2191-8.

Vlieghe, K., Florquin, K., Vuylsteke, M., Rombauts, S., Van Hummelen, P., Van de Peer, Y., Inzé, D., De Veylder, L. (2003) Microarray analysis of E2Fa-DPa-overexpressingplants uncovers a cross-talking genetic networkbetween DNA replication and nitrogen assimilation. J. Cell Sci. 116, 4249-59.

Vandenbussche, M., Theissen, G., Van de Peer, Y., Gerats, T. (2003) Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations. Nucleic Acids Res. 31, 4401-9.

Rombauts, S., Van de Peer, Y., Rouzé, P. (2003) AFLPInsilico, simulating AFLP fingerprints. Bioinformatics 19, 776-7.

Crowe, M.L., Serizet, C., Thareau, V., Aubourg, S., Rouzé, P., Hilson, P., Beynon, J., Weisbeek, P., Van Hummelen, P., Reymond, P., Paz-Ares, J., Nietfeld, W., Trick, M. (2003) CATMA: a complete Arabidopsis GST database. Nucleic Acids Res. 31, 156-8.

Raes, J., Rohde, A., Holst-Christensen, J., Boerjan, W. (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 133, 1051-71.

De Bodt, S., Raes, J., Van de Peer, Y., Theissen, G. (2003) And then there were many: MADS goes genomic. Trends Plant Science 8, 475-83.

Paraskevis, D., Lemey, P., Salemi, M., Suchard, M., Van de Peer, Y., Vandamme, A.-M. (2003) Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using Bayesian inference: implications for the origin of HIV-1. Mol. Biol. Evol. 20, 1986-96.

Vandepoele, K., Simillion, C., Van de Peer, Y. (2003) Evidence that rice, and other cereals, are ancient aneuploids. The Plant Cell 15, 2192-202.

Saeys, Y., Degroeve, S., Aeyels, D., Van de Peer, Y. (2003) Fast feature selection using a simple Estimation of Distribution Algorithm: A case study on splice site prediction. Bioinformatics 19 Suppl 2, II179-II188.

Raes, J., Van de Peer, Y. (2003) Gene duplications, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico. Applied Bioinformatics 2, 91-101.

* Rombauts, S., * Florquin, K., Lescot, M., Marchal, K., Rouzé, P., Van de Peer, Y. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 132, 1162-76. *contributed equally

Taylor, J.S., Braasch, I., Frickey, T., Meyer, A., Van de Peer, Y. (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res. 13, 382-90.

Van de Peer, Y. (2003) Phylogeny inference based on distance methods. in The phylogenetic handbook Cambridge University Press, UK.

Van de Peer, Y. (2003) Analysis of nucleotide sequences using TREECON. in The phylogenetic handbook Cambridge University Press, UK.

Meyer, A., Van de Peer, Y. (2003) Natural selection merely modified while redundancy created - Susumu Ohnos idea of the evolutionary importance of gene and genome duplications. J. Struct. Func. Genomics. 3, vii-ix.

Van de Peer, Y., Taylor, J.S., Meyer, A. (2003) Are all fishes ancient polyploids?. J. Struct. Func. Genomics. 3, 65-73.

Raes, J., Vandepoele, K., Saeys, Y., Simillion, C., Van de Peer, Y. (2003) Investigating ancient duplication events in the Arabidopsis genome. J. Struct. Func. Genomics. 3, 117-29.

Blayo, P., Rouzé, P., Sagot, M.F. (2003) Orphan gene finding - an exon assembly approach. Theor. Comput. Sci. 290, 1407-1431..

De Bodt, S., Raes, J., Florquin, K., Rombauts, S., Rouzé, P., Theissen, G., Van de Peer, Y. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J. Mol. Evol. 56, 573-86.

2002

Bonnet, E., Van de Peer, Y. (2002) ZT: a software tool for simple and partial Mantel tests. J. Stat. Softw. 7, 1-12.

Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M., Van de Peer, Y. (2002) The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99, 13627-32.

Mathé, C., Sagot, M.F., Schiex, T., Rouzé, P. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30, 4103-17.

Van de Peer, Y., Frickey, T., Taylor, J.S., Meyer, A. (2002) Dealing with saturation at the amino acid level: A case study involving anciently duplicated zebrafish genes. Gene 295, 205-11.

Oborn?k, M., Van de Peer, Y., Hyp?a, V., Frickey, T., ?lapeta, J.R., Meyer, A., Luke?, J. (2002) Phylogenetic analyses suggest a possible lateral gene transfer from the mitochondrion to the apicoplast. Gene 285, 109-18.

Lescot, M., Dehais, P., Moreau, Y., Van de Peer, Y., Rouzé, P., Rombauts, S. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30, 325-7.

Wuyts, J., Van de Peer, Y., Winkelmans, T., De Wachter, R. (2002) The European database on small subunit ribosomal RNA. Nucleic Acids Res. 30, 183-5.

Van de Peer, Y., Taylor, J.S., Joseph, J., Meyer, A. (2002) Wanda: A database of duplicated fish genes. Nucleic Acids Res. 30, 109-12.

Van de Peer, Y., De Rijk, P., Wuyts, J., Winkelmans, T., De Wachter, R. (2002) The European small subunit ribosomal RNA database. Nucleic Acids Res. 30, 183-5.

Van de Peer, Y. (2002) ZT: a software tool for simple and partial Mantel tests. J. Stat. Softw. 7, 1-12..

Rensing, S.A., Rombauts, S., Van de Peer, Y., Reski, R. (2002) Moss transcriptome and beyond. Trends Plant Science 7, 535-8.

Vandepoele, K., Simillion, C., Van de Peer, Y. (2002) Detecting the undetectable: Uncovering duplicated segments in Arabidopsis through rice. Trends Genet. 18, 606-8.

Degroeve, S., De Baets, B., Van de Peer, Y., Rouzé, P. (2002) Feature subset selection for splice site prediction. Bioinformatics 18 Suppl 2, S75-83.

Ben Ali, A., De Baere, R., De Wachter, R., Van de Peer, Y. (2002) Evolutionary relationships among heterokont algae (the autotroph stramenopiles) based on a combined analysis of small and large subunit ribosomal RNA. Protist 153, 123-32.

Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., Van de Peer, Y. (2002) The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12, 1792-801.

Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput. Biol. 9, 447-64.

Vandepoele, K., Raes, J., De Veylder, L., Rouzé, P., Rombauts, S., Inzé, D. (2002) Genome-wide analysis of core cell cycle genes in Arabidopsis. The Plant Cell 14, 903-16.

Thijs, G., Moreau, Y., De Smet, F., Mathys, J., Lescot, M., Rombauts, S., Rouzé, P., De Moor, B., Marchal, K. (2002) INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics 18, 331-2.

2001

Wuyts, J., Van de Peer, Y., De Wachter, R. (2001) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res. 29, 5017-28.

Taylor, J.S., Van de Peer, Y., Braasch, I., Meyer, A. (2001) Comparative genomics provides evidence for an ancient genome duplication in fish. Philos. T. Roy. Soc. 356, 1661-79.

Wuyts, J., De Rijk, P., Van de Peer, Y., Winkelmans, T., De Wachter, R. (2001) The European large subunit ribosomal RNA database. Nucleic Acids Res. 29, 175-7.

De Rijk, P., Wuyts, J., Van de Peer, Y., Winkelmans, T., De Wachter, R. (2001) The European large subunit ribosomal RNA database. Nucleic Acids Res. 29, 175-7.

Taylor, J.S., Van de Peer, Y., Meyer, A. (2001) Revisiting recent tests of the ancient fish-specific genome duplication hypothesis. Curr. Biol. 11, R1005-R1007..

Van de Peer, Y., Taylor, J.S., Braasch, I., Meyer, A. (2001) The ghost of selection past: rates of evolution and functional divergence in anciently duplicated genes. J. Mol. Evol. 53, 436-46.

Taylor, J.S., Van de Peer, Y., Meyer, A. (2001) Genome duplication, divergent resolution and speciation. Trends Genet. 17, 299-301.

Ben Ali, A., De Baere, R., Van der Auwera, G., De Wachter, R., Van de Peer, Y. (2001) Phylogenetic relationships among different groups of algae based on complete large subunit ribosomal RNA sequences. Int. J. Syst. Evol. Microbiol. 51, 737- 749..

Thijs, G., Lescot, M., Rombauts, S., Marchal, K., De Moor, B., Moreau, Y., Rouzé, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics 17, 1113-22.

2000

Wuyts, J., De Rijk, P., Van de Peer, Y., Pison, G., Rousseeuw, P., De Wachter, R. (2000) Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res. 28, 4698-708.

Van de Peer, Y., Ben Ali, A., Meyer, A. (2000) Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi. Gene 246, 1-8.

Mathé, C., Dehais, P., Pavy, N., Rombauts, S., Van Montagu, M., Rouzé, P. (2000) Gene prediction and gene classes in Arabidopsis thaliana. J. Biotechnol. 78, 293-9.

Van de Peer, Y., Baldauf, S., Doolittle, W.F., Meyer, A. (2000) An updated and comprehensive phylogeny of the rRNA crown eukaryotes based on rate calibrated evolutionary distances. J. Mol. Evol. 51, 565-76.

Lockhart, P.J., Huson, D., Maier, U.-G., Fraunholz, M.J., Van de Peer, Y., Barbrook, A.C., Howe, C.J., Steel, M.A. (2000) How molecules evolve on the eubacterial tree. Mol. Biol. Evol. 17, 835-838..

1999

Ben Ali, A., Wuyts, J., De Wachter, R., Meyer, A., Van de Peer, Y. (1999) Construction of a variability map for eukaryotic large subunit ribosomal RNA. Nucleic Acids Res. 27, 2825-31.

Terryn, N., Heijnen, L., De Keyser, A., Van Asseldonck, M., De Clercq, R., Verbakel, H., Gielen, J., Zabeau, M., Villarroel, R., Jesse, T., Neyt, P., Hogers, R., Van Den Daele, H., Ardiles, W., Schueller, C., Mayer, K., Dehais, P., Rombauts, S., Van Montagu, M., Rouzé, P., De Vos, P. (1999) Evidence for an ancient chromosomal duplication in Arabidopsis thaliana bysequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445, 237-45.

De Rijk, P., Robbrecht, E., de Hoog, S., Caers, A., Van de Peer, Y., De Wachter, R. (1999) Database on the structure of small subunit ribosomal RNA. Nucleic Acids Res. 27, 174-8.

Van de Peer, Y., Robbrecht, E., de Hoog, S., Caers, A., De Rijk, P., De Wachter, R. (1999) Database on the structure of small subunit ribosomal RNA. Nucleic Acids Res. 27, 179-83.

Rombauts, S., D?hais, P., Van Montagu, M., Rouzé, P. (1999) PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res. 27, 295-6.

Raes, J., Van de Peer, Y. (1999) ForCon : a software tool for the conversion of sequence alignments. Embnet. News 6, 10-12..

Andersen, R.A., Van de Peer, Y., Potter, D., Sexton, J.P., Kawachi, M., LaJeunesse, T. (1999) Phylogenetic analysis of the SSU rDNA from members of the Chrysophyceae. Protist 150, 71-84.

Van de Peer, Y. (1999) Molecular evolution and the incorporation of site-to-site rate variation in distance tree construction methods. Belg. J. Zool. 129, 5-16..

Pavy, N., Rombauts, S., D?hais, P., Mathé, C., Ramana, D.V., Leroy, P., Rouzé, P. (1999) Evaluation of gene prediction software using a genomic data set: application of Arabidopsis thaliana sequences. Bioinformatics 15, 887-99.

Rouzé, P., Pavy, N., Rombauts, S. (1999) Genome annotation: which tools do we have for it?. Curr. Opin. Plant Biol. 2, 90-5.

Pavy, N., Mathé, C., Rombauts, S., Rouzé, P. (1999) Genomics and bio-computing (in French). OCL-OLEAGINEUX CORPS GRAS LIPIDES 6,148-154.

1998

De Rijk, P., Caers, A., Van de Peer, Y., De Wachter, R. (1998) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 26, 183-6.

Van de Peer, Y., Caers, A., De Rijk, P., De Wachter, R. (1998) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 26, 179-82.

Wenderoth, K., Marquardt, J., Fraunholz, M.J., Van de Peer, Y., Wastl, J., Maier, U.-G. (1998) The taxonomic position of Chlamydomyxa labyrinthuloides. Eur. J. Phycol. 34, 97-108..

Winnepenninckx, B., Van de Peer, Y., Backeljau, T. (1998) Metazoan relationships on the basis of 18S rRNA sequences: a few years later. Amer. Zool. 38 888-906..

Vandamme, P., Segers, P., Ryll, M., Hommez, J., Vancanneyt, M., Coopman, R., De Baere, R., Van de Peer, Y., Kersters, K., De Wachter, R., Hinz, K.H. (1998) Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory diseases in pigeons: taxonomic structure and phylogenetid allocations. Int. J. Syst. Bacteriol. 48 Pt 2, 431-40.

Zwart, G., Huismans, R., van Agterveld, M.P., Van de Peer, Y., De Rijk, P., Eenhoorn, H., Muyzer, G., Van Hannen, E.J., Gons, H.J., Laanbroek, H.J. (1998) Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake. FEMS Microbiol. Lett. 25, 159-169..

1997

De Rijk, P., Van de Peer, Y., De Wachter, R. (1997) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 25, 117-22.

Van de Peer, Y., Jansen, A., De Rijk, P., De Wachter, R. (1997) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 25, 111-6.

Van de Peer, Y., De Wachter, R. (1997) Evolutionary relationships among the eukaryotic crown taxa taking into account site to site rate variation in 18S rRNA. J. Mol. Evol. 45, 619-30.

Capesius, I., Van de Peer, Y. (1997) Secondary Structure of the large ribosomal subunit RNA of the moss Funaria hygrometrica. J. Plant Physiol. 151, 239-241..

Rensing, S.A., Obrdlik, P., Rober-Kleber, N., M?ller, S., Hofmann, C.J.B., Van de Peer, Y., Maier, U.-G. (1997) Molecular phylogeny of the stress-70 protein family with certain emphasis on algal relationships. Eur. J. Phycol. 32, 279-285..

Kral`ova, I., Van de Peer, Y., Jirku, M., Van Ranst, M., Scholz, T., Lukes, J. (1997) Phylogenetic analysis of a fish tapeworm Proteocephalus exiguus, La Rue, 1911, based on the small subunit rRNA gene. Mol. Biochem. Parasitol. 84, 263-6.

Van de Peer, Y., De Wachter, R. (1997) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Applic. Biosci. 13, 227-30.

1996

Van de Peer, Y., Chapelle, S., De Wachter, R. (1996) A quantitative map of nucleotide substitution rates in bacterial ribosomal subunit RNA. Nucleic Acids Res. 24, 3381-91.

Van de Peer, Y., Rensing, S.A., Maier, U.-G., De Wachter, R. (1996) Substitution rate calibration of small ribosomal subunit RNA identifies chlorarachniophyte nucleomorphs as remnants of green algae. Proc. Natl. Acad. Sci. USA 93, 7732-6.

De Rijk, P., Van de Peer, Y., De Wachter, R. (1996) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 24, 92-7.

Van de Peer, Y., Nicolai, S., De Wachter, R. (1996) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 24, 86-91.

Chalwatzis, N., Hauf, J., Van de Peer, Y., Kinzelbach, R., Zimmerman, F.K. (1996) 18S ribosomal RNA genes of insects: primary structure of the genes and molecular phylogeny of the Holometabola. Ann. Entomol. Soc. Am. 89, 788-803..

Moore, E.R.B., Mau, M., Arnscheidt, A., Van de Peer, Y., De Wachter, R., Collins, M.D., B?ttger, R., Timmis, K.N. (1996) Determination and comparison of the 16S rRNA gene sequences of Pseudomonas (sensu stricto) and estimation of intrageneric relationships. Syst. Appl. Microbiol. 19, 478-492..

Van de Peer, Y., Vancanneyt, M., De Wachter, R. (1996) Compilation of Pseudomonad sequences present in a database on the structure of ribosomal RNA. Syst. Appl. Microbiol. 19, 493-500..

Van de Peer, Y., Janssens, W., Heyndrickx, L., Fransen, K., Van der Groen, G., De Wachter, R. (1996) Phylogenetic analysis of the env gene of HIV-1 isolates taking into account individual nucleotide substitution rates. AIDS 10, 1485-94.

Van de Peer, Y., Van der Auwera, G., De Wachter, R. (1996) The evolution of stramenopiles and alveolates as derived by substitution rate calibration of small ribosomal subunit RNA. J. Mol. Evol. 42, 201-10.

Moens, L., Vanfleteren, J., Van de Peer, Y., Peeters, K., Kapp, O., Czelusniak, J., Goodman, M., Vinogradov, S. (1996) Globins in non-vertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. Mol. Biol. Evol. 13, 324-33.

1995

Nelissen, B., Van de Peer, Y., Wilmotte, A., De Wachter, R. (1995) Early divergence of plastids within the cyanobacterial divergence as deduced on the basis of complete 16S rRNA sequences. Mol. Biol. Evol. 12, 1166-73.

De Rijk, P., Van de Peer, Y., Van den Broeck, I., De Wachter, R. (1995) Evolution according to large ribosomal subunit RNA. J. Mol. Evol. 41, 366-75.

Van der Auwera, G., De Baere, R., Van de Peer, Y., De Rijk, P., Van den Broeck, I., De Wachter, R. (1995) The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. Mol. Biol. Evol. 12, 671-8.

Haase, G., Sonntag, L., Van de Peer, Y., Uithoff, J.M.J., Podbielski, A., Melzer-Krick, B., de Hoog, S. (1995) Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences. Antonie Van Leeuwenhoek 68, 19-33.

Winnepenninckx, B., Van de Peer, Y., Backeljau, T., De Wachter, R. (1995) CARD: A drawing tool for RNA secondary structure models. Biotechniques 18, 1060-3.

Van de Peer, Y., De Wachter, R. (1995) Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA. in Molecular Microbial Ecology Manual 3.3.4. pp. 1-12..

1994

De Rijk, P., Van de Peer, Y., Chapelle, S., De Wachter, R. (1994) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 22, 3495-501.

Van de Peer, Y., Van den Broeck, I., De Rijk, P., De Wachter, R. (1994) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 22, 3488-94.

Van de Peer, Y., De Wachter, Y. (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10, 569-70.

Vanfleteren, J., Van de Peer, Y., Blaxter, M.L., Tweedie, S.A.R., Trotman, C., Lu, L., Van Hauwaert, M.-L., Moens, L. (1994) Molecular genealogy of some Nematode taxa as based on cytochrome c and globin amino acid sequences. Mol. Phyl. Evol. 3, 92-101.

Van de Peer, Y., Neefs, J.-M., De Rijk, P., De Vos, P., De Wachter, R. (1994) About the order of divergence of the major bacterial taxa during evolution. Syst. Appl. Microbiol. 17, 32-38..

Janssens, W., Heyndrickx, L., Van de Peer, Y., Bouckaert, A., Fransen, K., Motte, J., Gershy-Damet, G.M., Peeters, K., Van der Groen, G., Piot, P. (1994) Molecular phylogeny of part of the env-gene of human immunodeficiency virus type I isolated in Ivory Coast. AIDS 8, 21-6.

1993

Neefs, J.-M., Van de Peer, Y., De Rijk, P., Chapelle, S., De Wachter, R. (1993) Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21, 3025-49.

Wilmotte, A., Van de Peer, Y., Goris, A., Chapelle, S., De Baere, R., Nelissen, B., Neefs, J.-M., Hennebert, G.L., De Wachter, R. (1993) Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis. Syst. Appl. Microbiol. 16, 436-444..

Van de Peer, Y., Neefs, J.-M., De Rijk, P., De Wachter, R. (1993) Reconstructing evolution from eukaryotic small ribosomal subunit RNA sequence: Calibration of the molecular clock. J. Mol. Evol. 37, 221-32.

Van de Peer, Y., De Wachter, R. (1993) TREECON: a software package for the construction and drawing of evolutionary trees. Comput. Applic. Biosci. 9, 177-82.

Van de Peer, Y., Neefs, J.-M., De Rijk, P., De Wachter, R. (1993) Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences. Biochem. Syst. Ecol. 21, 43-55..

Van Camp, G., Van de Peer, Y., Nicolai, S., Neefs, J.-M., Vandamme, P., De Wachter, R. (1993) Structure of 16S and 23S ribosomal RNA genes in Campylobacter species: phylogenetic analysis of the genus Campylobacter and presence of internal transcribed spacers. Syst. Appl. Microbiol. 16, 361-368..

1992

Winnepenninckx, B., Backeljau, T., Van de Peer, Y., De Wachter, R. (1992) Structure of the small ribosomal subunit RNA of the pulmonate snail Limicolaria kambeul and phylogenetic analysis of the Metazoa. FEBS Lett. 309, 123-6.

De Rijk, P., Neefs, J.-M., Van de Peer, Y., De Wachter, R. (1992) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 20 Suppl, 2075-89.

De Wachter, R., Neefs, J.-M., Goris, A., Van de Peer, Y. (1992) The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron. Nucleic Acids Res. 20, 1251-7.

Winnepenninckx, B., Van de Peer, Y., Peeters, K., De Baere, I., Moens, L. (1992) Study of invertebrate and plant globins: templates and evolutionary trees. Belg. J. Bot. 125, 191-200..

Wilmotte, A., Turner, S., Van de Peer, Y., Pace, N.R. (1992) Taxonomical study of marine oscillatorian strains (Cyanobacteria) with narrow trichomes. II. Nucleotide sequence analysis of the 16S ribosomal RNA. J. Phycol. 28, 828-838..

Van de Peer, Y., Neefs, J.-M., De Rijk, P., De Baere, R., Goris, A., Hendriks, L., De Wachter, R. (1992) Ribosomal RNA as a tool for studying evolution. Belg. J. Bot. 125, 174-190..

Van de Peer, Y., Hendriks, L., Goris, A., Neefs, J.-M., Vancanneyt, M., Kersters, K., Berny, J., Hennebert, G.L., De Wachter, R. (1992) Evolution of basidiomycetous yeasts as deduced from small ribosomal subunit RNA sequences. Syst. Appl. Microbiol. 15, 250 -258..

Nelissen, B., Wilmotte, A., De Baere, R., Haes, F., Van de Peer, Y., Neefs, J.-M., De Wachter, R. (1992) Phylogenetic study of cyanobacteria on the basis of 16S ribosomal RNA sequences. Belg. J. Bot. 125, 210-213..

Hendriks, L., Goris, A., Van de Peer, Y., Neefs, J.-M., Vancanneyt, M., Kersters, K., Berny, J., Hennebert, G.L., De Wachter, R. (1992) Phylogenetic relationships among ascomycetes and ascomycete-like yeasts as deduced from small ribosomal subunit RNA sequences. Syst. Appl. Microbiol. 15, 98-104..

1991

Neefs, J.-M., Van de Peer, Y., De Rijk, P., Goris, A., De Wachter, R. (1991) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 19 Suppl, 1987-2015.

Hendriks, L., Goris, A., Van de Peer, Y., Neefs, J.-M., Vancanneyt, M., Kersters, K., Hennebert, G.L., De Wachter, R. (1991) Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences. J. Gen. Microbiol. 137, 1223-30.

Hendriks, L., De Baere, R., Van de Peer, Y., Neefs, J.-M., Goris, A., De Wachter, R. (1991) The evolutionary position of the rhodophyte Porphyra umbilicalis and the basidiomycete Leucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA. J. Mol. Evol. 32, 167-77.

1990

Hendriks, L., Van de Peer, Y., Van Herck, M., Neefs, J.-M., De Wachter, R. (1990) The 18S ribosomal RNA sequence of the sea anemone Anemonia sulcata and its evolutionary position among other eukaryotes. FEBS Lett. 269, 445-9.

Moens, L., Van Hauwaert, M.-L., De Smet, K., Ver Donck, K., Van de Peer, Y., Van Beeumen, J., Wodak, S., Alard, P., Trotman, C. (1990) Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin. J. Biol. Chem. 265, 14285-91.

Neefs, J.-M., Van de Peer, Y., Hendriks, L., De Wachter, R. (1990) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 18 Suppl, 2237-317.

Van de Peer, Y., Neefs, J.-M., De Wachter, R. (1990) Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins. J. Mol. Evol. 30, 463-76.

Van de Peer, Y., De Baere, R., Cauwenberghs, J., De Wachter, R. (1990) Evolution of green plants and their relationship with other photosynthetic eukaryotes as deduced from 5S ribosomal RNA sequences. Pl. System. Evol. 170, 85-96..

Van den Eynde, H., Van de Peer, Y., Vandenabeele, H., Van Bogaert, M., De Wachter, R. (1990) 5S rRNA sequences of Myxobacteria and radioresistant bacteria and implications for eubacterial evolution. Int. J. Syst. Bacteriol. 40, 399-404.

Van den Eynde, H., Van de Peer, Y., Perry, J., De Wachter, R. (1990) 5S ribosomal RNA sequences of representatives of the genera Chlorobium, Prosthecochloris, Thermomicrobium, Cytophaga, Flavobacterium, Flexibacter and Saprospira. J. Gen. Microbiol. 136, 11-8.

1989

Van den Eynde, H., De Baere, R., Shah, H., Gharbia, S., Fox, G., Michalik, J., Van de Peer, Y., De Wachter, R. (1989) 5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: Evolutionary relationships within these genera and among eubacteria in general. Int. J. Syst. Bacteriol. 39, 78-84.

Hendriks, L., Goris, A., Neefs, J.-M., Van de Peer, Y., Hennebert, G.L., De Wachter, R. (1989) The nucleotide sequence of the small ribosomal subunit RNA of the yeast Candida albicans and the evolutionary position of the fungi among the eukaryotes. Syst. Appl. Microbiol. 12, 223-229..

1988

Hendriks, L., Van Broeckhoven, C., Vandenberghe, A., Van de Peer, Y., De Wachter, R. (1988) Primary and secondary structure of the 18S ribosomal RNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla. Eur. J. Biochem. 177, 15-20.

Van den Eynde, H., Van de Peer, Y., De Wachter, R. (1988) Inferring eubacterial phylogeny from 5S ribosomal RNA structure analysis. in Green Photosynthetic Bacteria pp. 217-221..

Van den Eynde, H., De Baere, R., De Roeck, H., Van de Peer, Y., Vandenberghe, A., Willekens, P., De Wachter, R. (1988) The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast. Implications for the evolution of plastids and cyanobacteria. J. Mol. Evol. 27, 126-32.

Dams, E., Hendriks, L., Van de Peer, Y., Neefs, J.-M., Smits, G., Vandenbempt, I., De Wachter, R. (1988) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 16 Suppl, r87-173.










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