openBIS: a flexible framework for managing and analyzing complex data in biology research. - Angela Bauch; Izabela Adamczyk; Piotr Buczek; Franz-Josef Elmer; Kaloyan Enimanev; Pawel Glyzewski; Manuel Kohler; Tomasz Pylak; Andreas Quandt; Chandrasekhar Ramakrishnan; Christian Beisel; Lars Malmström; et al. (BMC Bioinform., 2011)

Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing. - Thomas Sakoparnig; Tobias Kockmann; Renato Paro; Christian Beisel; Niko Beerenwinkel (J. Comput. Biol., 2012)

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)

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)

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. - Fabrizio Menardo; Chloé Loiseau; Daniela Brites; Mireia Coscolla; Sebastian M. Gygli; Liliana K. Rutaihwa; Andrej Trauner; Christian Beisel; Sonia Borrell; Sebastien Gagneux (BMC 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)

Statistical tests for intra-tumour clonal co-occurrence and exclusivity. - Jack Kuipers; Ariane L. Moore; Katharina Jahn 001; Peter Schraml; Feng Wang; Kiyomi Morita; P. Andrew Futreal; Koichi Takahashi; Christian Beisel; Holger Moch; Niko Beerenwinkel (PLoS Comput. Biol., 2021)

gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis. - Linda Grob; Anne Bertolini; Matteo Carrara; Ulrike Lischetti; Aizhan Tastanova; Christian Beisel; Mitchell P. Levesque; Daniel J. Stekhoven; Franziska Singer (Bioinform., 2023)