Lambda: the local aligner for massive biological data. - Hannes Hauswedell; Jochen Singer; Knut Reinert (Bioinform., 2014)

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)

SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. - Jochen Singer; Jack Kuipers; Katharina Jahn 001; Niko Beerenwinkel (RECOMB, 2018)

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. - Jochen Singer; Hans-Joachim Ruscheweyh; Ariane L. Hofmann; Thomas Thurnherr; Franziska Singer; Nora C. Toussaint; Charlotte K. Y. Ng; Salvatore Piscuoglio; Christian Beisel; Gerhard Christofori; Reinhard Dummer; Michael N. Hall; et al. (Bioinform., 2018)

SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. - Franziska Singer; Anja Irmisch; Nora C. Toussaint; Linda Grob; Jochen Singer; Thomas Thurnherr; Niko Beerenwinkel; Mitchell P. Levesque; Reinhard Dummer; Luca Quagliata; Sacha I. Rothschild; Andreas Wicki; et al. (BMC Medical Informatics Decis. Mak., 2018)

Bioinformatics for precision oncology. - Jochen Singer; Anja Irmisch; Hans-Joachim Ruscheweyh; Franziska Singer; Nora C. Toussaint; Mitchell P. Levesque; Daniel J. Stekhoven; Niko Beerenwinkel (Briefings Bioinform., 2019)

Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. - Jack Kuipers; Jochen Singer; Niko Beerenwinkel (Bioinform., 2022)