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Publications

References to publications, sorted by year and author.
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2010 De Bona, F, Hall, K, Riezler, S, Ciaramita, M, Herdagdelen, A, and Holmqvist, M (2010).
Learning Dense Models of Query Similarity from User Click Logs
In: NAACL 2010.
Kloft, M, Brefeld, U, Sonnenburg, S, and Zien, A (2010).
Non-Sparse Regularization and Efficient Training with Multiple Kernels
University of California, Berkeley.
Printable file
Widmer, C, Leiva, J, Altun, Y, and Rätsch, G (2010).
Leveraging Sequence Classification by Taxonomy-based Multitask Learning
In: Proc. RECOMB'10.
2009 Bohnert, R, Behr, J, and Rätsch, G (2009).
Transcript quantification with RNA-Seq data
BMC Bioinformatics, 10(S13):P5.
http://www.biomedcentral.com/1471-2105/10/S13/P5
Printable file
Dietmann, S, Georgii, E, Antonov, A, Tsuda, K, and Mewes, H (2009).
The DICS repository: module-assisted analysis of disease-related gene lists
Bioinformatics, 25(6):830-831.
Printable file
Franc, V and Sonnenburg, S (2009).
Optimized Cutting Plane Algorithm for Large-Scale Risk Minimization
Journal of Machine Learning Research, 10:2157--2192.
Georgii, E, Dietmann, S, Uno, T, Pagel, P, and Tsuda, K (2009).
Enumeration of condition-dependent dense modules in protein interaction networks
Bioinformatics, 25(7):933-940.
Printable file
Georgii, E, Tsuda, K, and Schölkopf, B (2009).
Multi-Way Set Enumeration in Real-Valued Tensors
In: Data Mining using Matrices and Tensors (DMMT'09), ed. by Chris Ding, Tao Li, pp. 32-41, ACM.
Printable file
Jenssen, R, Kloft, M, Zien, A, Sonnenburg, S, and Müller, K (2009).
A Multi-Class Support Vector Machine Based on Scatter Criteria
Technical University Berlin, Technical Report(014-2009).
http://www.eecs.tu-berlin.de/menue/forschung/forschungsberichte/
Printable file
Kloft, M, Brefeld, U, Sonnenburg, S, Laskow, P, Mueller, K, and Zien, A (2009).
Efficient and Accurate Lp-Norm MKL
In: Advances in Neural Information Processing Systems 21, ed. by Y. Bengio and D. Schuurmans and J. Lafferty and C. K. I. Williams and A. Culotta, pp. 997--1005, Cambridge, MA, MIT Press.
McNally, KL, Childs, KL, Bohnert, R, Davidson, RM, Zhao, K, Ulat, VJ, Zeller, G, Clark, RM, Hoen, DR, Bureau, TE, Stokowski, R, Ballinger, DG, Frazer, KA, Cox, DR, Padhukasahasram, B, Bustamante, CD, Weigel, D, Mackill, DJ, Bruskiewich, RM, Rätsch, G, Buell, CR, Leung, H, and Leach, JE (2009).
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
Proceedings of the National Academy of Sciences.
http://www.pnas.org/content/106/30/12273.full
http://www.pnas.org/content/106/30/12273/suppl/DCSupplemental
Printable file
Naouar, N, Vandepoele, K, Lammens, T, Casneuf, T, Zeller, G, van Hummelen, P, Weigel, D, Rätsch, G, Inzé, D, Kuiper, M, De Veylder, L, and Vuylsteke, M (2009).
Quantitative RNA expression analysis with Affymetrix Tiling 1.0R Arrays identifies new E2F target genes
Plant Journal, 57(1):184-194.
Printable file
Plantegenet, S, Weber, J, Goldstein, DR, Zeller, G, Nussbaumer, C, Thomas, J, Weigel, D, Harshmann, K, and Hardtke, CS (2009).
Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance
Molecular Systems Biology, 5:Article 242.
Printable file
Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Rätsch, G (2009).
KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences
Bioinformatics.
Printable file
Schweikert, G, Behr, J, Zien, A, Zeller, G, Ong, CS, Sonnenburg, S, and Rätsch, G (2009).
mGene.web: a web service for accurate computational gene finding
Nucleic Acids Research, Web Server Issue.
http://mgene.org/web
Printable file
Schweikert, G, Zien, A, Zeller, G, Behr, J, Dieterich, C, Ong, CS, Philips, P, De Bona, F, Hartmann, L, Bohlen, A, Krüger, N, Sonnenburg, S, and Rätsch, G (2009).
mGene: Accurate SVM-Based Gene Finding with an Application to Nematode Genomes
Genome Research, 19:2133-2143.
http://mgene.org
http://www.fml.tuebingen.mpg.de/Members/raetsch/papers/Supplement-mGene.pdf
Printable file
Zeller, G, Henz, SR, Widmer, CK, Sachsenberg, T, Rätsch, G, Weigel, D, and Laubinger, S (2009).
Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays
Plant Journal, 58(6):1068-1082.
http://www.weigelworld.org/resources/microarray/at-tax
Printable file
Zien, A, Krämer, N, Sonnenburg, S, and Rätsch, G (2009).
The Feature Importance Ranking Measure
In: Proc. ECML PKDD, ed. by W. Buntine, M. Grobelnik, D. Mladenic, J. Shawe-Taylor, vol. 5782/2009, pp. 694-709, Springer Berlin / Heidelberg, Springer, XXIX ed.. Lecture Notes in Artificial Intelligence.
Printable file
2008 Bartlett, PL, Mendelson, S, and Philips, P (2008).
Optimal sample-based estimates of the expectation of the empirical minimizer
ESAIM: Probability and Statistics (ESAIM: P&S), Accepted.
Behr, J (2008).
Improving Gene Finding Accuracy with Tiling Array and RNA-Seq Data
Diplom Thesis, Jonas Behr.
Ben-Hur, A, Ong, CS, Sonnenburg, S, Schölkopf, B, and Rätsch, G (2008).
Support Vector Machines and Kernels for Computational Biology
PLoS Computational Biology, 4(10):e1000173.
http://svmcompbio.tuebingen.mpg.de
Printable file
Bohnert, R, Zeller, G, Clark, RM, Childs, KL, Ulat, V, Stokowski, R, Ballinger, D, Frazer, K, Cox, D, Bruskiewich, R, Buell, CR, Leach, J, Leung, H, McNally, KL, Weigel, D, and Rätsch, G (2008).
Revealing Sequence Variation Patterns in Rice with Machine Learning Methods
BMC Bioinformatics, 9(S10):O8.
http://www.biomedcentral.com/1471-2105/9/S10/O8
Printable file
Coghlan, A, Fiedler, TJ, McKay, SJ, Flicek, P, Harris, TW, Blasiar, D, nGASP Consortium, LD, and Stein (2008).
nGASP – the nematode genome annotation assessment project
BMC Bioinformatics.
http://www.biomedcentral.com/1471-2105/9/549
Printable file
De Bona, F, Ossowski, S, Schneeberger, K, and Rätsch, G (2008).
QPALMA: Optimal Spliced Alignments of Short Sequence Reads
In: Bioinformatics/Proc. ECCB'08, Oxford University Press.
http://www.fml.tuebingen.mpg.de/raetsch/projects/qpalma
Printable file
De Bona, F, Ossowski, S, Schneeberger, K, and Rätsch, G (2008).
QPALMA:: Optimal Spliced Alignments of Short Sequence Reads
In: BMC Bioinformatics, vol. 9((Suppl 10)), pp. O7, BioMed Central Ltd.
http://www.fml.tuebingen.mpg.de/raetsch/projects/qpalma
Printable file
 
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