Sven Degroeve

Postdoc
(Group member from 2001 until 2004)


+ 32 (0) 9 33 13 695
Personal homepage

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

Research

I'm a last year Phd student with a main interest in data-mining. The topics I've been working on are:

  • benchmarking inductive algorithms on natural language classification tasks
  • vector representations of gene structural elements
  • predicting gene structural elements and percussive sounds using the support vector machine
  • organism specific induction of a gene prediction system
  • selecting relevant features for splice site prediction

My Phd research is about the construction and implementation of an accurate gene structural element prediction system that can be easily adapted to new species and is fast in terms of annotation speed as it will be used to annotated complete eukaryotic genomes.

Google Scholar

An up-to-date list of my publications can be found at Google Scholar.

Papers

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

(15) 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(5793):1596-604. *contributed equally

(14) * 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(31):11647-52. *contributed equally

(13) 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(8):1332-8.

(12) 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.

(11) 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(13):4255-64.

(10) 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.

(9) 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).

(8) 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.

(7) Martens, J.-P., Van Steelant, D., Tanghe, K., Degroeve, S., De Baets, B., Leman, M. (2004) Classification of percussive sounds using support vector machines. Proceedings of Annual Machine Learning Conference of Belgium and the Netherlands, BENELEARN. Brussels, Belgium. (2004) 146-153.

(6) 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.

(5) Van Steelant, D., Degroeve, S., Tanghe, K., De Baets, B., Leman, M., Martens, J.-P. (2004) Support Vector Machines for bass and snare drum recognition. In: 'Classification: The Ubiquitous Challenge' . Editors: Weihs, C and Gauls, W..

(4) Saeys, Y., Degroeve, S., Aeyels, D., Van de Peer, Y., Rouzé, P. (2003) Selecting Relevant Features for Splice Site Prediction by estimation of Distribution Algorithms. Proceedings of the 12th Belgian-Dutch Conference on Machine Learning (Benelearn 2002) 64-70. Utrecht, The Netherlands.

(3) 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:ii179-88.

(2) 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.

(1) Zavrel, J., Degroeve, S., Kool, A., Daelemans, W., Jokinen, K. (2000) Diverse Classifiers for NLP Disambiguation Tasks: Comparison, Optimization, Combination, and Evolution. Proceedings of CEvoLE 2/TWLT 18: "Learing to Behave" 201-221. Ieper, Belgium.











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VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
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+32 (0) 9 33 13809 (fax)

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