Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics. - Joshua E. Elias; Steven P. Gygi (Proteome Bioinformatics, 2010)

Assigning spectrum-specific P-values to protein identifications by mass spectrometry. - Victor Spirin; Alexander Shpunt; Jan Seebacher; Marc Gentzel; Andrej Shevchenko; Steven Gygi; Shamil R. Sunyaev (Bioinform., 2011)

Network-based inference from complex proteomic mixtures using SNIPE. - David P. Nusinow; Adam Kiezun; Daniel J. O'Connell; Joel M. Chick; Yingzi Yue; Richard L. Maas; Steven Gygi; Shamil R. Sunyaev (Bioinform., 2012)

DAGBagM: learning directed acyclic graphs of mixed variables with an application to identify protein biomarkers for treatment response in ovarian cancer. - Shrabanti Chowdhury; Ru Wang; Qing Yu; Catherine J. Huntoon; Larry M. Karnitz; Scott H. Kaufmann; Steven P. Gygi; Michael J. Birrer; Amanda G. Paulovich; Jie Peng; Pei Wang (BMC Bioinform., 2022)