Supplementary Data

2008

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.

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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.

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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.

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2007

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.

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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.

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Saeys, Y., Inza, I., Larrañaga, P. (2007) A review of feature selection techniques in bioinformatics. Bioinformatics 23, 2507-17.

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2006

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 Biology 7, R13.

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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 Biology 7, R43.

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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.

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

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* 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., Jabbari, K., Bowler, C., 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

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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., Napoli, C., 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

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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.

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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.

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

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* 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

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

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2004

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.

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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.

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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.

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* 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

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

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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.

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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.

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2003

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

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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.

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

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* 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

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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.

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2002

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

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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.

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2001

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.

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1999

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.

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