Publications of S Sonnenburg

Sonnenburg, S.; Rätsch, G.; Henschel, S.; Widmer, C.; Behr, J.; Zien, A.; De Bona, F.; Binder, A.; Gehl, C.; Franc, V.: The SHOGUN Machine Learning Toolbox. Journal of Machine Learning Research 11, pp. 1799 - 1802 (2010)

Schweikert, G.; Zeller, G.; Behr, J.; Dieterich, C.; Ong, C.; Philips, P.; De Bona, F.; Hartmann, L.; Bohlen, A.; Krüger, N. et al.; Sonnenburg, S.; Rätsch, G.: mGene: Accurate SVM-based gene finding with an application to nematode genomes. Genome Research 19 (11), pp. 2133 - 2143 (2009)

Schweikert, G.; Behr, J.; Zien, A.; Zeller, G.; Ong, C.; Sonnenburg, S.; Rätsch, G.: mGene.web: a web service for accurate computational gene finding. Nucleic Acids Research (London) 37 (Supplement 2), pp. W312 - W316 (2009)

Ben-Hur, A.; Ong, C.; Sonnenburg, S.; Schölkopf, B.; Rätsch, G.: Support Vector Machines and Kernels for Computational Biology. PLoS Computational Biology 4 (10), e1000173 (2008)

Sonnenburg, S.; Braun, M.; Ong, C.; Bengio, S.; Bottou, L.; Holmes , G.; LeCun, Y.; Müller, K.-R.; Pereira, F.; Rasmussen, C. et al.; Rätsch, G.; Schölkopf, B.; Smola, A.; Vincent, P.; Weston, J.; Williamson, R.: The Need for Open Source Software in Machine Learning. The Journal of Machine Learning Research 8, pp. 2443 - 2466 (2007)

Rätsch, G.; Sonnenburg, S.; Srinivasan, J.; Witte, H.; Müller, K.-R.; Sommer, R.-J.; Schölkopf, B.: Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning. PLoS Computational Biology 3 (2 ), pp. 0313 - 0322 (2007)

Sonnenburg, S.; Rätsch, G.; Schäfer, C.; Schölkopf, B.: Large Scale Multiple Kernel Learning. The Journal of Machine Learning Research 7, pp. 1531 - 1565 (2006)

Tsuda, K.; Kawanabe, M.; Rätsch, G.; Sonnenburg, S.; Müller, K.: A New Discriminative Kernel from Probabilistic Models. Neural computation 14 (10), pp. 2397 - 2414 (2002)

Sonnenburg, S.; Zien, A.; Philips , P.; Rätsch, G.: POIMs: positional oligomer importance matrices: understanding support vector machine-based signal detectors. 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July 19, 2008 - July 23, 2008. Bioinformatics 24 (13), pp. i6 - i14 (2008)

Sonnenburg, S.; Schweikert, G.; Philips , P.; Behr, J.; Rätsch, G.: Accurate Splice site Prediction Using Support Vector Machines. NIPS 2006 Workshop on New Problems and Methods in Computational Biology, Whistler, Canada, December 08, 2006. BMC Bioinformatics 8 (Supplement 10), pp. 1 - 16 (2007)

Sonnenburg, S.; Zien, A.; Rätsch, G.: ARTS: Accurate Recognition of Transcription Starts in Human. 14th International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, August 06, 2006 - August 10, 2006. Bioinformatics 22 (14), H-56, pp. e472 - e480 (2006)

Sonnenburg, S.; Rätsch, G.; Schölkopf, B.: Large Scale Genomic Sequence SVM Classifiers. In: ICML '05: the 22nd international conference on Machine learning, pp. 848 - 855 (Eds. Dzeroski, S.; de Raedt, L.; Wrobel, S.). 22nd International Conference on Machine Learning (ICML 2005), Bonn, Germany, August 07, 2005 - August 11, 2005. ACM Press, New York, NY, USA (2005)

Rätsch, G.; Sonnenburg, S.; Schölkopf, B.: RASE: recognition of alternatively spliced exons in C.elegans. Thirteenth International Conference on Intelligent Systems for Molecular Biology (ISBM 2005), Detroit, MI, USA, June 25, 2005 - June 29, 2005. Bioinformatics 21 (Supplement 1), pp. i369 - i377 (2005)

Rätsch, G.; Sonnenburg, S.; Ong, C.: Support Vector Machines and Kernels for Computational Biology. In 17th Annual International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology (ISMB/ECCB 2009), AM3. 17th Annual International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology (ISMB/ECCB 2009), Stockholm, Sweden, June 27, 2009 - July 02, 2009. (2009)

Schweikert, G.; Zeller , G.; Zien, A.; Behr, J.; Sonnenburg, S.; Philips , P.; Ong, C.; Rätsch, G.: mGene: A Novel Discriminative Gene Finder. In 2008 Topics Meeting: Worm Genomics and Systems Biology. 2008 Topics Meeting: Worm Genomics and Systems Biology, Cambridge, MA, USA, July 24, 2008 - July 25, 2008. (2008)

Schweikert, G.; Zeller, G.; Behr, J.; Zien, A.; Ong, C.; De Bona, F.; Sonnenburg, S.; Philips, P.; Rätsch, G.; Widmer, C.: mGene: A Novel Discriminative Gene Finding System. In 4th ISCB Student Council Symposium at the 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), p. 20. 4th ISCB Student Council Symposium at the 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July 19, 2008 - July 23, 2008. (2008)

Sonnenburg, S.; Zien, A.; Philips, P.; Rätsch, G.: Positional Oligomer Importance Matrices. NIPS 2007 Workshop on Machine Learning in Computational Biology (MLCB 2007), Whistler, BC, Canada (2007)

Schweikert, G.; Zeller, G.; Zien, A.; Ong, C.; De Bona, F.; Sonnenburg, S.; Philips, P.; Rätsch, G.: Ab-initio gene finding using machine learning. NIPS 2006 Workshop on New Problems and Methods in Computational Biology (MLCB 2006), Vancouver, BC, Canada (2006)

Rätsch, G.; Sonnenburg, S.; Ong, C.; Schölkopf, B.: Accurate prediction of alternative splicing events. NIPS Workshop on Computational Biology and the Analysis of Heterogeneous Data (MLCB 2005), Whistler, BC, Canada (2005)

Schweikert, G.; Zien, A.; Zeller, G.; Ong, C.; De Bona, F.; Sonnenburg, S.; Philips, P.; Rätsch, G.: mGene: A Novel Discriminative Gene Finding System. 15th Annual International Conference on Intelligent Systems for Molecular Biology, 6th Annual European Conference on Computational Biology (ISMB/ECCB 2007), Wien, Austria (2007)