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.; Zien, A.; Zeller, G.; Behr, J.; Dieterich, C.; Ong, C.; Philips, P.; De Bona, F.; Hartmann, L.; Bohlen, A. et al.; Krüger, N.; 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.; Schölkopf, B.: Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning. PLoS Computational Biology 3 (2 ), e20, 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)

Müller, K.-R.; Rätsch, G.; Sonnenburg, S.; Mika, S.; Grimm, M.; Heinrich, N.: Classifying "drug-likeness" with kernel-based learning methods. Journal of Chemical Information and Modeling 45 (2), pp. 249 - 253 (2005)

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)

Zien, A.; Krämer, N.; Sonnenburg, S.; Rätsch, G.: The Feature Importance Ranking Measure. In: Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD 2009, Bled, Slovenia, September 7-11, 2009, Proceedings, Part II, pp. 694 - 709 (Eds. Buntine, W.; Grobelnik, M.; Mladenić, D.; Shawe-Taylor, J.). 16th European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2009), Bled, Slovenia, September 07, 2009 - September 11, 2009. Springer, Berlin, Germany (2009)

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), S7, (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)

Rätsch, G.; Sonnenburg, S.; Schäfer, C.: Learning interpretable SVMs for biological sequence classification. NIPS Workshop on New Problems and Methods in Computational Biology, Whistler, Canada, December 08, 2004. BMC Bioinformatics 7 (Supplement 1), S9, (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)

Sonnenburg, S.; Rätsch, G.; Schäfer, C.: Learning interpretable SVMs for biological sequence classification. In: Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, pp. 389 - 407 (Eds. Miyano, S.; Mesirov, J.; Kasif, S.; Istrail, S.; Pevzner, P. et al.). 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, MA, USA, May 14, 2005 - May 18, 2005. Springer, Berlin, Germany (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)

Sonnenburg, S.; De Bona, F.; Rätsch, G.: SHOGUN: A Large Scale Machine Learning Toolbox. In The R User Conference 2006: 2nd International R User Conference, p. 154. 2nd International R User Conference (useR! 2006), Wien, Austria, June 15, 2006 - June 17, 2006. (2006)

Jean, G.; Raetsch, G.; Kahles, A.; Sonnenburg, S.; Schneeberger, K.; Hagmann, J.; De Bona, F.; Weigel, D.: Fast and Accurate RNA-Seq alignments with PALMapper. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB ECCB 2011), Wien, Austria (2011)