Accurate splice site prediction using support vector machines. - Sören Sonnenburg; Gabriele Beate Schweikert; Petra Philips; Jonas Behr; Gunnar Rätsch (BMC Bioinform., 2007)

Transcript quantification with RNA-Seq data. - Regina Bohnert; Jonas Behr; Gunnar Rätsch (BMC Bioinform., 2009)

mGene.web: a web service for accurate computational gene finding. - Gabriele Beate Schweikert; Jonas Behr; Alexander Zien; Georg Zeller; Cheng Soon Ong; Sören Sonnenburg; Gunnar Rätsch (Nucleic Acids Res., 2009)

Next generation genome annotation with mGene.ngs. - Jonas Behr; Regina Bohnert; Georg Zeller; Gabriele Beate Schweikert; Lisa Hartmann; Gunnar Rätsch (BMC Bioinform., 2010)

The SHOGUN Machine Learning Toolbox. - Sören Sonnenburg; Gunnar Rätsch; Sebastian Henschel; Christian Widmer; Jonas Behr; Alexander Zien; Fabio De Bona; Alexander Binder; Christian Gehl; Vojtech Franc (J. Mach. Learn. Res., 2010)

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. - Sebastian J. Schultheiß; Géraldine Jean; Jonas Behr; Regina Bohnert; Philipp Drewe; Nico Görnitz; André Kahles; Pramod Mudrakarta; Vipin T. Sreedharan; Georg Zeller; Gunnar Rätsch (BMC Bioinform., 2011)

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. - Jonas Behr; André Kahles; Yi Zhong; Vipin T. Sreedharan; Philipp Drewe; Gunnar Rätsch (Bioinform., 2013)

MMR: a tool for read multi-mapper resolution. - André Kahles; Jonas Behr; Gunnar Rätsch (Bioinform., 2016)

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. - Ariane L. Hofmann; Jonas Behr; Jochen Singer; Jack Kuipers; Christian Beisel; Peter Schraml; Holger Moch; Niko Beerenwinkel (BMC Bioinform., 2017)

Network-based integration of multi-omics data for prioritizing cancer genes. - Christos Dimitrakopoulos; Sravanth Kumar Hindupur; Luca Häfliger; Jonas Behr; Hesam Montazeri; Michael N. Hall; Niko Beerenwinkel (Bioinform., 2018)