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)

Steijger, T.; Abril, J.; Engström, P.; Kokocinski, F.; Akerman, M.; Alioto, T.; Ambrosini, G.; Antonarakis, S.; Behr, J.; Bohnert, R. et al.; Bucher, P.; Cloonan, N.; Derrien, T.; Djebali, S.; Du, J.; Dudoit, S.; Gerstein, M.; Gingeras, T.; Gonzalez, D.; Grimmond, S.; Habegger, L.; Iseli, C.; Jean, G.; Kahles, A.; Kokocinski, F.; Lagarde, J.; Leng, J.; Lefebvre, G.; Lewis, S.; Mortazavi, A.; Niermann, P.; Rätsch, G.; Reymond, A.; Ribeca, P.; Richard, H.; Rougemont, J.; Rozowsky, J.; Sammeth, M.; Sboner, A.; Schulz, M.; Searle, S.; Solorzano, N.; Solovyev, V.; Stanke, M.; Steijger, T.; Stevenson, B.; Stockinger, H.; Valsesia, A.; Weese, D.; White, S.; Wold, B.; Wu, J.; Wu, T.; Zeller, G.; Zerbino, D.; Zhang, M.; Hubbard, T.; Guigó, R.; Harrow, J.; Bertone, P.: Assessment of Transcript Reconstruction Methods for RNA-seq. Nature Methods 10 (12), pp. 1177 - 1184 (2013)

Drewe, P.; Stegle, O.; Hartmann, L.; Kahles, A.; Bohnert, R.; Wachter, A.; Borgwardt, K.; Rätsch, G.: Accurate detection of differential RNA processing. Nucleic Acids Research 41 (10), pp. 5189 - 5198 (2013)

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)

Ong, C.; Hartmann, L.; Bohnert, R.; Krüger , N.; Bohlen, A.; Rätsch, G.: Bootstrapping the alternative splicing annotation of newly sequenced genomes. In: Alternative Splicing: Special Interest Group Meeting (AS-SIG) at ISMB 2007, pp. 33 - 35. Alternative Splicing: Special Interest Group Meeting (AS-SIG) at ISMB 2007, Wien, Austria, July 19, 2007 - July 20, 2007. (2007)

Sreedharan, V.; Schultheiss, S.; Jean, G.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Oqtans: a multifunctional workbench for RNA-seq data analysis. In BMC Bioinformatics, 15 (Supplement 13), A7. Ninth International Society for Computational Biology (ISCB) Student Council Symposium 2013, Berlin, Germany, July 19, 2013. BioMed Central (2014)

Schultheiss, S.; Jean, G.; Sreedharan, V.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Easier Workflows & Tool Comparison with Oqtans+. In Galaxy Community Conference 2012 (GCC 2012). Galaxy Community Conference 2012 (GCC 2012), Chacago, IL, USA, July 25, 2012 - July 27, 2012. (2012)

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 at ISMB/ECCB 2011, Wien, Austria, July 15, 2011. BioMed Central (2011)

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)

Behr, J.; Bohnert, R.; Zeller, G.; Schweikert, G.; Hartmann, L.; Rätsch, G.: Next generation genome annotation with mGene.ngs. In BMC Bioinformatics, 11 (Supplement 10), O8. Sixth International Society for Computational Biology Student Council Symposium (ISCB 2010) , Boston, MA, USA, July 09, 2010. BioMed Central (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.; 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)

Bohnert, R.; Behr, J.; Rätsch, G.: Quantitative Detection of Alternative Transcripts with RNA-Seq Data. ISMB 2009 Special Interest Group on Short Read Sequencing, Stockholm, Sweden (2009)

Sreedharan, V.; Schultheiss, S.; Jean, G.; Kahles, A.; Bohnert, R.; Drewe, P.; Mudrakarta, P.; Görnitz, N.; Zeller, G.; Rätsch, G.: Oqtans: a multifunctional workbench for RNA-seq data analysis. 14th Annual Bioinformatics Open Source Conference (BOSC 2013), Berlin, Germany (2013)