Publications

2025

• Paulson A, Elmorsi R, Lee A, Huang RS. (2025). Combined XPO1 Inhibition and Parthenolide Treatment Can Be Efficacious in Treating Triple-Negative Breast Cancer. International Journal of Medical Science (IJMS), 26(20); 10243. PMID: 41155531. DOI: 10.3390/ijms262010243 [Link]
• Medina EF, Farmaki E, Griffiths JI, Bild AH, Nath A. (2025). System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells. Cell Reports Medicine, 6(11); 102425. PMID: 41260207. DOI: 10.1016/j.xcrm.2025.102425 [Link]
• Schaffer LV, Jain M, Nasser R, Sharan R, Ideker T. (2025). Unifying proteomic technologies with ProteinProjector. Bioinformatics Advances, vbaf266. DOI: 10.1093/bioadv/vbaf266 [Link]
• Kim C, Gadgil SU, and Lee, SI. (2025). Transparency of medical artificial intelligence systems. Nat Rev Bioeng. [Link]
• Baron M, Tagore M, Wall P, Zheng F, Barkley D, Yanai I, Yang J, Kiuru M, White RM, Ideker T. (2025). Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation. Nat Genet. PMID: 40240879. DOI: 10.1038/s41588-025-02163-9 [Link]
• Schaffer LV, Hu M, Qian G, Moon K-M, Pal A, Soni N, Latham AP, Vaites LP, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg E, Ideker T. (2025). Multimodal cell maps as a foundation for structural and functional genomics. Nature. PMID: 40205054. DOI: 10.1038/s41586-025-08878-3 [Link]
• Lu M, Lin C, Kim C, Lee SI. (2025). An efficient framework for crediting data contributors of diffusion models. International Conference on Learning Representations (ICLR). Published online: January 22, 2025. [Link]
• Singhal A, Zhao X, Wall P, So E, Calderini G, Partin A, Koussa N, Vasanthakumari P, Narykov O, Zhu Y, Jones SE, Abbas-Aghababazadeh F, Nair SK, Belisle-Pipon J-C, Jayaram A, Parker BA, Yeung KT, Griffiths JI, Weil R, Nath A, Haibe-Kains B, Ideker T (2025). The hallmarks of predictive oncology. Cancer Discovery, 15(2): 271–285. PMID: 39760657. DOI: 10.1158/2159-8290.CD-24-0760 [Link]