Publications of F De Bona

Jean, G.; Kahles, A.; Sreedharan, V.; De Bona, F.; Rätsch, G.: RNA-Seq read alignments with PALMapper. Current Protocols in Bioinformatics Chapter 11 (Supplement 32), Unit 11.6 (2010)

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)

De Bona, F.; Ossowski, S.; Schneeberger, K.; Rätsch, G.: Optimal spliced alignments of short sequence reads. Bioinformatics 24 (16), pp. i174 - i180 (2008)

De Bona, F.; Riezler, S.; Hall, K.; Ciaramita, M.; Herdagdelen, A.; Holmqvist, M.: Learning Dense Models of Query Similarity from User Click Logs. In: 11th Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL HLT 2010), p. 29. 11th Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL HLT 2010), Los Angeles, CA, June 01, 2010 - June 06, 2010. (2010)

Riezler, S.; De Bona, F.: Simple Risk Bounds for Position-Sensitive Max-Margin Ranking Algorithms. In: NIPS'09 Workshop on "Advances in Ranking". NIPS'09 Workshop on "Advances in Ranking", Vancouver, BC, Canada, December 11, 2009. (2009)

Zien, A.; De Bona, F.; Ong, C.: Training and Approximation of a Primal Multiclass Support Vector Machine. In: XIIth International Conference on Applied Stochastic Models and Data Analysis (ASMDA 2007), 1 (Ed. Skiadas, C.). XIIth International Conference on Applied Stochastic Models and Data Analysis (ASMDA 2007), Chania, Greece, May 29, 2007 - June 01, 2007. (2007)

Bohnert, R.; De Bona, F.; Rätsch, G.: Quantitatively deconvolving alternative RNA secondary structures. In HiTSeq 2011: Conference on High Throughput Sequencing Analysis and Algorithms, pp. 10 - 11. HiTSeq 2011: Conference on High Throughput Sequencing Analysis and Algorithms, Wien, Austria, July 15, 2011 - July 16, 2011. (2011)

Sonnenburg, S.; Rätsch, G.; Henschel, S.; Widmer, C.; Behr, J.; Zien, A.; De Bona, F.; Gehl, C.; Binder, A.; Franc, V.: SHOGUN: A Large Scale Machine Learning Toolbox. In The R User Conference 2010, useR! 2010, p. 154. International R User Conference (useR! 2010), Gaithersburg, MD, USA, July 21, 2010 - July 23, 2010. (2010)

De Bona, F.; Ossowski, S.; Schneeberger, K.; Rätsch, G.: Optimal spliced alignments of short sequence reads. In BMC Bioinformatics, 9 (Supplement 10), O7. Fourth International Society for Computational Biology Student Council Symposium (ISCB 2008) , Toronto, Canada, July 18, 2008. BioMed Central (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)

Schweikert, G.; Zeller, G.; Zien, A.; Ong, C.; De Bona, F.; Sonnenburg, S.; Philips, P.; Rätsch, G.: mGene: A Novel Discriminative Ab-initio Gene Finding System. In Automated Function Prediction: Biosapiens Joint Special Interest Group Meeting, pp. 36 - 37. Automated Function Prediction: Biosapiens Joint Special Interest Group Meeting, Wien, Austria, July 19, 2007 - July 20, 2007. (2007)

Sonnenburg, S.; Rätsch, G.; De Bona, F.: SHOGUN: A Large Scale Machine Learning Toolbox. In 2nd International R User Conference: useR! 2006, p. 155. 2nd International R User Conference: useR! 2006, Wien, Austria, June 15, 2006 - June 17, 2006. (2006)

Schweikert, G.; Zeller, G.; Zien, A.; Ong, C.; De Bona, F.; Sonnenburg, S.; Phillips, 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)

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)

Rätsch, G.; Jean, G.; Kahles, A.; Sonnenburg, S.; De Bona, F.; Schneeberger, K.; Hagmann, J.; Weigel, D.: PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads. 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA (2010)

De Bona, F.; Ossowski, S.; Schneeberger, K.; Rätsch, G.: Optimal spliced alignments of short sequence reads. 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008) , Toronto, Canada (2008)

De Bona, F.; Ong, C.; Zien, A.; Rätsch, G.: RNA secondary structure prediction using large margin methods. 15th Annual International Conference on Intelligent Systems for Molecular Biology & 6th European Conference on Computational Biology (ISMB/ECCB 2007), Wien, Austria (2007)

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)