Detecting the impact of sequencing errors on SAGE data. - Jacques Colinge; Georg Feger (Bioinform., 2001)

A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring. - Jacques Colinge; Alexandre Masselot; Jérôme Magnin (WABI, 2003)

Introduction to Computational Proteomics. - Jacques Colinge; Keiryn L. Bennett (PLoS Comput. Biol., 2007)

A Computational Approach to Analyze the Mechanism of Action of the Kinase Inhibitor Bafetinib. - Thomas R. Burkard; Uwe Rix; Florian P. Breitwieser; Giulio Superti-Furga; Jacques Colinge (PLoS Comput. Biol., 2010)

Initial characterization of the human central proteome. - Thomas R. Burkard; Melanie Planyavsky; Ines Kaupe; Florian P. Breitwieser; Tilmann Bürckstümmer; Keiryn L. Bennett; Giulio Superti-Furga; Jacques Colinge (BMC Syst. Biol., 2011)

Systems Biology Analysis of Kinase Inhibitor Protein Target Profiles in Leukemia Treatments. - Jacques Colinge; Uwe Rix; Keiryn L. Bennett; Giulio Superti-Furga (IPCAT, 2012)

CLOUD - CeMM library of unique drugs. - Patrick Markt; Gerhard Dürnberger; Jacques Colinge; Stefan Kubicek (J. Cheminformatics, 2012)

TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens. - Markus K. Muellner; Gerhard Dürnberger; Florian Ganglberger; Claudia Kerzendorfer; Iris Z. Uras; Andreas Schoenegger; Klaudia Bagienski; Jacques Colinge; Sebastian M. B. Nijman (BMC Bioinform., 2014)

Application of modular response analysis to medium- to large-size biological systems. - Meriem Mekedem; Patrice Ravel; Jacques Colinge (PLoS Comput. Biol., 2022)

Modular response analysis reformulated as a multilinear regression problem. - Jean-Pierre Borg; Jacques Colinge; Patrice Ravel (Bioinform., 2023)

Testing and overcoming the limitations of modular response analysis. - Jean-Pierre Borg; Jacques Colinge; Patrice Ravel (Briefings Bioinform., 2025)