ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. - Evgeniy V. Petrotchenko; Christoph H. Borchers (BMC Bioinform., 2010)

Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation. - Gabriela V. Cohen Freue; Anna Meredith; Derek Smith; Axel Bergman; Mayu Sasaki; Karen K. Y. Lam; Zsuzsanna Hollander; Nina Opushneva; Mandeep Takhar; David Lin; Janet Wilson-McManus; Robert Balshaw; et al. (PLoS Comput. Biol., 2013)

Automatic Peptides Selection for Targeted Proteomics. - Yassene Mohammed; Dominik Domanski; Angela M. Jackson; Derek Smith; André M. Deelder; Magnus Palmblad; Christoph H. Borchers (IWBBIO, 2014)

MRMAssayDB: an integrated resource for validated targeted proteomics assays. - Pallab Bhowmick; Yassene Mohammed; Christoph H. Borchers (Bioinform., 2018)

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. - Nicholas I. Brodie; Konstantin I. Popov; Evgeniy V. Petrotchenko; Nikolay V. Dokholyan; Christoph H. Borchers (PLoS Comput. Biol., 2019)

Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays. - Yassene Mohammed; Pallab Bhowmick; Sarah A. Michaud; Albert Sickmann; Christoph H. Borchers (Bioinform., 2021)