Publications of A Kahles
All genres
Journal Article (9)
1.
Journal Article
4, e05255 (2015)
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 2.
Journal Article
30 (9), pp. 1300 - 1301 (2014)
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics 3.
Journal Article
10 (12), pp. 1185 - 1191 (2013)
Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods 4.
Journal Article
10 (12), pp. 1177 - 1184 (2013)
Assessment of Transcript Reconstruction Methods for RNA-seq. Nature Methods 5.
Journal Article
29 (20), pp. 2529 - 2538 (2013)
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics 6.
Journal Article
41 (10), pp. 5189 - 5198 (2013)
Accurate detection of differential RNA processing. Nucleic Acids Research 7.
Journal Article
9 (5), pp. 596 - 609 (2012)
Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. RNA Biology 8.
Journal Article
477 (7365), pp. 419 - 423 (2011)
Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 9.
Journal Article
Chapter 11 (Supplement 32), Unit 11.6 (2010)
RNA-Seq read alignments with PALMapper. Current Protocols in Bioinformatics Conference Paper (1)
10.
Conference Paper
Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation. In: Advances in Neural Information Processing Systems 24, pp. 2690 - 2698 (Eds. Shawe-Taylor, J.; Zemel, R.; Bartlett, P.; Pereira , F.; Weinberger, K.). 25th Annual Conference on Neural Information Processing Systems (NIPS 2011), Granada, Spain, December 12, 2011 - December 14, 2011. Curran, Red Hook, NY, USA (2012)
Meeting Abstract (4)
11.
Meeting Abstract
15 (Supplement 13), A7. Ninth International Society for Computational Biology (ISCB) Student Council Symposium 2013, Berlin, Germany, July 19, 2013. BioMed Central (2014)
Oqtans: a multifunctional workbench for RNA-seq data analysis. In BMC Bioinformatics, 12.
Meeting Abstract
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)
13.
Meeting Abstract
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)
Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. In BMC Bioinformatics, 14.
Meeting Abstract
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)
Talk (1)
15.
Talk
Simultaneous RNA-seq-based Transcript Inference and Quantification Using Mixed Integer Programming. NIPS 2011 Workshop Machine Learning in Computational Biology
, Sierra Nevada, Spain (2011)
Poster (11)
16.
Poster
mTIM: A Margin-based Transcript Identification Method. Ninth International Society for Computational Biology (ISCB) Student Council Symposium 2013, Berlin, Germany (2014)
17.
Poster
Oqtans: a multifunctional workbench for RNA-seq data analysis. 14th Annual Bioinformatics Open Source Conference (BOSC 2013), Berlin, Germany (2013)
18.
Poster
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)
19.
Poster
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)
20.
Poster
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)