Scientific Publications

Gerstein, M.; Lu, Z.; Van Nostrand, E.; Cheng, C.; Arshinoff, B.; Liu, T.; Yip, K.; Robilotto, R.; Rechtsteiner, A.; Ikegami, K. et al.; Alves, P.; Chateigner, A.; Perry, M.; Morris, M.; Auerbach, R.; Feng, X.; Leng, J.; Vielle, A.; Niu, W.; Rhrissorrakrai, K.; Agarwal, A.; Alexander, R.; Barber, G.; Brdlik, C.; Brennan, J.; Brouillet, J.; Carr, A.; Cheung, M.-S.; Clawson, H.; Contrino, S.; Dannenberg, L.; Dernburg, A.; Desai, A.; Dick, L.; Dosé, A.; Du, J.; Egelhofer, T.; Ercan, S.; Euskirchen, G.; Ewing, B.; Feingold, E.; Gassmann, R.; Good, P.; Green, P.; Gullier, F.; Gutwein, M.; Guyer, M.; Habegger, L.; Han, T.; Henikoff, J.; Henz, S.; Hinrichs, A.; Holster, H.; Hyman, A.; Iniguez, A. L.; Janette, J.; Jensen, M.; Kato, M.; Kent, W. J.; Kephart, E.; Khivansara, V.; Khurana, E.; Kim, J. K.; Kolasinska-Zwierz, P.; Lai, E. C.; Latorre, I.; Leahey, A.; Lewis, S. E.; Lloyd, P.; Lochovsky, L.; Lowdon, R. F.; Lubling, Y.; Lyne, R.; MacCoss, M.; Mackowiak, S. D.; Mangone, M.; McKay, S.; Mecenas, D.; Merrihew, G.; Miller, D. M.; Muroyama, A.; Murray, J. I.; Ooi, S.-L.; Pham, H.; Phippen, T.; Preston, E. A.; Rajewski, N.; Rätsch, G.; Rosenbaum, H.; Rozowksy, J.; Rutherford, K.; Ruzanov, P.; Sarov, M.; Sasidharan, R.; Sboner, A.; Scheid, P.; Segal, E.; Shin, H.; Shou, C.; Slack, F. J.; Slightham, C.; Smith, R.; Spencer, W. C.; Stinson, E. O.; Taing, S.; Takasaki, T.; Vafeados, D.; Voronina, K.; Wang, G.; Washington, N. L.; Whittle, C. M.; Wu, B.; Yang, K.-K.; Zeller, G.; Zha, Z.; Zhong, M.; Zhou, X.; Ahringer, J.; Strome, S.; Gunsalus, K. C.; Micklem, G.; Liu, X. S.; Reinke, V.; Kim, S. K.; Hillier, L. W.; Henikoff, S.; Piano, F.; Snyder, M.; Stein, L.; Lieb, J. D.; Waterston, R. H.: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330 (6012), pp. 1775 - 1787 (2010)

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)

Laubinger, S.; Zeller, G.; Henz, S.; Buechel, S.; Sachsenberg, T.; Wang, J.-W.; Rätsch, G.; Weigel, D.: Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proceedings of the National Academy of Sciences of the United States of America 107 (41), pp. 17466 - 17573 (2010)

Bohnert, R.; Rätsch, G.: rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Research (London) 38, pp. W348 - W351 (2010)

Weir, J.; Bonneau, F.; Hentschel, J.; Conti, E.: Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proceedings of the National Academy of Sciences of the United States of America 107 (27), pp. 12139 - 12144 (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)

Theerthagiri, G.; Eisenhardt, N.; Schwarz, H.; Antonin, W.: The nucleoporin Nup188 controls passage of membrane proteins across the nuclear pore complex. The Journal of Cell Biology: JCB 189 (7), pp. 1129 - 1142 (2010)

Stegle, O.; Drewe, P.; Bohnert, R.; Borgwardt, K.; Rätsch, G.: Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts. Nature Precedings 2010 (2010)

Koch, A.; Hauf, S.: Strategies for the identification of kinase substrates using analog-sensitive kinases. European Journal of Cell Biology: EJCB 89 (2-3), pp. 184 - 193 (2010)

Chan, Y.; Marks, M.; Jones, F.; Villarreal Jr., G.; Shapiro, M.; Brady, S.; Southwick, A.; Absher, D.; Grimwood, J.; Schmutz, J. et al.; Myers, R.; Petrov, D.; Jónsson, B.; Schluter, D.; Bell, M.: Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327 (5963), pp. 302 - 305 (2010)

Schultheiss, S.: Kernel-based identification of regulatory modules. In: Methods in Molecular Biology, Vol. 674. Springer, US (2010)

Toussaint, N.; Widmer, C.; Kohlbacher, O.; Rätsch, G.: Exploiting physico-chemical properties in string kernels. NIPS Workshop on Machine Learning in Computational Biology (MLCB 2019), Whistler, BC, Canada, December 10, 2009 - December 11, 2009. BMC Bioinformatics 11 (Supplement 8), S7, (2010)

Widmer, C.; Toussaint, N.; Altun, Y.; Rätsch, G.: Inferring latent task structure for Multitask Learning by Multiple Kernel Learning. NIPS Workshop on Machine Learning in Computational Biology (MLCB 2019), Whistler, BC, Canada, December 10, 2009 - December 11, 2009. BMC Bioinformatics 11 (Supplement 8), S5, (2010)

Widmer, C.; Toussaint, N.; Altun, Y.; Kohlbacher, O.; Rätsch, G.: Novel Machine Learning Methods for MHC Class I Binding Prediction. In: PRIB 2010: Pattern Recognition in Bioinformatics, pp. 98 - 109 (Eds. Dijkstra, T.; Tsivtsivadze, E.; Marchiori, E.; Heskes, T.). 5th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2010), Nijmegen, The Netherlands, September 22, 2010 - September 24, 2010. Springer, Berlin, Germany (2010)

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)

Widmer, C.; Leiva, J.; Altun, Y.; Rätsch, G.: Leveraging Sequence Classification by Taxonomy-Based Multitask Learning. In: RECOMB 2010: Research in Computational Molecular Biology, pp. 522 - 534 (Ed. Berger, B.). 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisboa, Portugal, April 25, 2010 - April 28, 2010. Springer, Berlin, Germany (2010)

Bohnert, R.; Behr, J.; Kahles, A.; Jean, G.; Raetsch, G.: Oonline transcriptome analysis http://galaxy.tuebingen.mpg.de. In 2010 Meeting on the Biology of Genomes, p. 257. 2010 Meeting on the Biology of Genomes, Cold Spring Harbor, NY, USA, May 11, 2010 - May 15, 2010. (2010)

Bohnert, R.; Behr, J.; Kahles, A.; Jean, G.; Rätsch, G.: Online Quantitative Transcriptome Analysis. 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA (2010)

Drewe, P.; Stegle, O.; Bohnert, R.; Borgwardt, K.; Rätsch, G.: Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts. 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA (2010)