Yvan Saeys

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Papers in refereed journals
  1. Abeel, T., Helleputte, T., Van de Peer, Y., Dupont, P., Saeys, Y. (2009) Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics, In press.

  2. Abeel, T., Van de Peer, Y., Saeys, Y. (2009) Java-ML: a machine learning library. Journal of Machine Learning Research, 10, 931-934.

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

  4. 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.

  5. Van Bel, M.Saeys, Y., and Van de Peer, Y. (2008) FunSip: a modular and extensible classifier for the prediction of functional sites in DNA. Bioinformatics, 24(13), 1532-1533.

  6. Abeel, T.,Saeys, Y., Rouzé, P. and Van de Peer, Y. (2008) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 24(13), i24-i31.

  7. Abeel, T.,Saeys, Y., Bonnet, E., Rouzé, P. and Van de Peer, Y. (2008) Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 18, 310-323.

  8. Saeys, Y., Inza, I. and Larrañaga, P. (2007) A review of feature selection techniques in bioinformatics. Bioinformatics, 23(19), 2507-2517.

  9. Saeys, Y., Abeel, T., Degroeve, S. and Van de Peer, Y. (2007) Translation initiation site prediction on a genomic scale: beauty in simplicity. Bioinformatics, 23(13), i418-i423.

  10. Michoel, T., Maere, S., Bonnet, E., Joshi, A., Saeys, Y., , Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K. and Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data BMC Bioinformatics 8(Suppl 2): S5.

  11. Saeys, Y., , Rouzé, P. and Van de Peer, Y. (2007) In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi, and protists. Bioinformatics 23(4), 414-420.

  12. 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. and Moreau, H. (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl. Acad. Sci. USA 103(31), 11647-11652.

  13. Florquin,K., Saeys, Y., Degroeve, S.,Rouzé, P. and Van de Peer, Y. (2005) Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Research. 33(13), 4255-4264.

  14. Degroeve, S., Saeys, Y., , De Baets, B., Rouzé, P. and Van de Peer, Y. (2005) SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinformatics. 21(8), 1332-1338.

  15. Simillion, C., Vandepoele, K., Saeys, Y., and Van de Peer, Y. (2004) Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 14, 1095-1106.

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

  17. Saeys, Y., , Degroeve, S., Aeyels, D., Van de Peer, Y., and Rouze, P. (2003) Fast feature selection using a simple Estimation of Distribution Algorithm: A case study on splice site prediction. Bioinformatics. 19-2, ii179-ii188.

  18. 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, 117-129.

  19. Vandepoele, K., Saeys, Y., , Simillion, C., Raes, J., Van de Peer, Y. (2002) A new tool for the Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12, 1792-1801.