SplicingCompass: differential splicing detection using RNA-Seq data. - Moritz Aschoff; Agnes Hotz-Wagenblatt; Karl-Heinz Glatting; Matthias Fischer 003; Roland Eils; Rainer König (Bioinform., 2013)

Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes. - Sven-Eric Schelhorn; Matthias Fischer 003; Laura Tolosi; Janine Altmüller; Peter Nürnberg; Herbert Pfister; Thomas Lengauer; Frank Berthold (PLoS Comput. Biol., 2013)

CoNCoS: Copy number estimation in cancer with controlled support. - Ali T. Abdallah; Matthias Fischer 003; Peter Nürnberg; Michael Nothnagel; Peter Frommolt (J. Bioinform. Comput. Biol., 2015)