multiplierz: an extensible API based desktop environment for proteomics data analysis. - Jignesh R. Parikh; Manor Askenazi; Scott B. Ficarro; Tanya Cashorali; James T. Webber; Nathaniel C. Blank; Yi Zhang; Jarrod A. Marto (BMC Bioinform., 2009)

Discovering causal signaling pathways through gene-expression patterns. - Jignesh R. Parikh; Bertram Klinger; Yu Xia 002; Jarrod A. Marto; Nils Blüthgen (Nucleic Acids Res., 2010)

Viral Perturbations of Host Networks Reflect Disease Etiology. - Natali Gulbahce; Han Yan; Amélie Dricot; Megha Padi; Danielle Byrdsong; Rachel Franchi; Deok-Sun Lee; Orit Rozenblatt-Rosen; Jessica Cara Mar; Michael A. Calderwood; Amy Baldwin; Bo Zhao; et al. (PLoS Comput. Biol., 2012)

APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control. - Yiling Elaine Chen; Xinzhou Ge; Kyla Woyshner; Meilu McDermott; Antigoni Manousopoulou; Scott B. Ficarro; Jarrod A. Marto; Kexin Li; Leo David Wang; Jingyi Jessica Li (Genom. Proteom. Bioinform., 2024)