Publications of A Kahles

Dubin, M.; Zhang, P.; Meng, D.; Remigereau, M.-S.; Osborne, E.; Casale, F.; Drewe, P.; Kahles, A.; Jean, G.; Vilhjálmsson, B. et al.; Jagoda, J.; Irez, S.; Voronin, V.; Song, Q.; Long, Q.; Rätsch, G.; Stegle, O.; Clark, R.; Nordborg, M.: DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 4, e05255 (2015)

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)

Engström, P.; Steijger, T.; Sipos, B.; Grant, G.; Kahles, A.; Rätsch, G.; Goldman, N.; Hubbard, T.; Harrow, J.; Guigó, R. et al.; Bertone, P.; RGASP Consortium: Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods 10 (12), pp. 1185 - 1191 (2013)

Behr, J.; Kahles, A.; Zhong, Y.; Sreedharan, V.; Drewe, P.; Rätsch, G.: MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics 29 (20), pp. 2529 - 2538 (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)

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)

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)

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)

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)

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)