Publikationen von 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), S. 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), S. 1185 - 1191 (2013)

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), S. 1177 - 1184 (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), S. 2529 - 2538 (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), S. 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), S. 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), S. 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)

Goernitz, N.; Widmer, C.; Zeller, G.; Kahles, A.; Rätsch, G.; Sonnenburg, S.: Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation. In: Advances in Neural Information Processing Systems 24, S. 2690 - 2698 (Hg. Shawe-Taylor, J.; Zemel, R.; Bartlett, P.; Pereira , F.; Weinberger, K.). 25th Annual Conference on Neural Information Processing Systems (NIPS 2011), Granada, Spain, 12. Dezember 2011 - 14. Dezember 2011. Curran, Red Hook, NY, USA (2012)

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, 19. Juli 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, 25. Juli 2012 - 27. Juli 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, 15. Juli 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, S. 257. 2010 Meeting on the Biology of Genomes, Cold Spring Harbor, NY, USA, 11. Mai 2010 - 15. Mai 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)

Görnitz, N.; Zeller, G.; Behr, J.; Kahles, A.; Mudrakarta, P.; Sonnenburg, S.; Rätsch, G.: mTIM: A Margin-based Transcript Identification Method. Ninth International Society for Computational Biology (ISCB) Student Council Symposium 2013, Berlin, Germany (2014)

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)

Rätsch, G.; Gan, X.; Stegle, O.; Behr, J.; Drewe, P.; Drewe, P.; Steffen, J.; Clark, R.; Osborne, E.; Schultheiss, S. et al.; Sreedharan, V.; Kahles, A.; Bohnert, R.; Jean, G.; Hildebrand, K.; Toomajian, C.; Lyngsoe, R.; Derwent, P.; Kersey, P.; Belfield, E.; Harberd, N.; Kemen, E.; Kover, P.: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012), Long Beach, CA, USA (2012)

Behr, J.; Bohnert, R.; Kahles, A.; Schweikert, G.; Zeller, G.; Hartmann, L.; Rätsch, G.: Accurate RNA-seq based de novo annotation using mGene.ngs. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Wien, Austria (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)