Publications of R Bohnert

Sreedharan, V.; Schultheiss, S.; Jean, G.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics 30 (9), pp. 1300 - 1301 (2014)

Smith, L.; Hartmann, L.; Drewe, P.; Bohnert, R.; Kahles, A.; Lanz, C.; Rätsch, G.: Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. RNA Biology 9 (5), pp. 596 - 609 (2012)

Gan, X.; Stegle, O.; Behr, J.; Steffen, J.; Drewe, P.; Hildebrand, K.; Lyngsoe , R.; Schultheiss, S.; Osborne, E.; Sreedharan, V. et al.; Kahles, A.; Bohnert, R.; Jean, G.; Derwent, P.; Kersey, P.; Belfield, E.; Harberd, N.; Kemen, F.; Toomajian, C.; Kover , P.; Clark, R.; Rätsch, G.; Mott, R.: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477 (7365), pp. 419 - 423 (2011)

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

McNally, K.; Childs, K.; Bohnert, R.; Davidson, R.; Zhao, K.; Ulat, V.; Zeller, G.; Clark, R.; Hoen, T.; Bureau, D. et al.; Stokowski, R.; Ballinger, D.; Frazer, K.; Cox, D.; Padhukasahasram, B.; Bustamante, C.; Weigel, D.; Mackill, D.; Bruskiewich, R.; Rätsch, G.; Buell, C.; Leung, H.; Leach, J.: Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America 106 (30), pp. 12273 - 12278 (2009)

Rätsch, G.; Bohnert, R.: Moderne Methoden zur Rekonstruktion von Transkriptomen: Modern methods for transcriptome reconstruction. Jahrbuch der Max-Planck-Gesellschaft 2008/2009 (2009)

Schultheiss, S.; Jean, G.; Behr, J.; Bohnert, R.; Drewe, P.; Görnitz, N.; Kahles, A.; Mudrakarta, P.; Sreedharan, V.; Zeller, G. et al.; Rätsch, G.: Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. In BMC Bioinformatics, 12 (Supplement 11), A7. Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011, Wien, Austria, July 15, 2011. BioMed Central (2011)

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.; Zeller, G.; Clark, R.; Childs, K.; Ulat, V.; Stokowski, R.; Ballinger , D.; Frazer, K.; Cox, D.; Bruskiewich, R. et al.; Buell, C.; Leach, J.; Leung, H.; McNally, K.; Weigel, D.; Rätsch, G.: Revealing sequence variation patterns in rice with machine learning methods. In BMC Bioinformatics, 9 (Supplement 10), O8. Fourth International Society for Computational Biology Student Council Symposium (ISCB 2008) , Toronto, Canada, July 18, 2008. BioMed Central (2008)

Behr, J.; Bohnert, R.; Kahles, A.; Rätsch, G.: Simultaneous RNA-seq-based Transcript Inference and Quantification Using Mixed Integer Programming. NIPS 2011 Workshop Machine Learning in Computational Biology , Sierra Nevada, Spain (2011)

Drewe, P.; Stegle, O.; Bohnert, R.; Borgwardt, K.: Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Wien, Austria (2011)

Drewe, P.; Stegle, O.; Bohnert, R.; Borgwardt, K.; Rätsch, G.: Statistical tests for detecting differential RNA-transcript expression. 4th Berlin Summer Meeting: “Computational & Experimental Molecular Biology Meet”, Berlin, Germany (2011)

Kahles, A.; Bohnert, R.; Ribeca, P.; Behr, J.; Rätsch, G.: RGASP evaluation of RNA-Seq read alignment algorithms. 4th Berlin Summer Meeting: “Computational & Experimental Molecular Biology Meet”, Berlin, Germany (2011)

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)

Bohnert, R.; Behr, J.; Rätsch, G.: Transcript quantification with RNA-Seq data. Fifth International Society for Computational Biology Student Council Symposium (ISMB/ECCB 2009), Stockholm, Sweden (2009)