Publications

2026

Chen, A. T., Kelly, M. R., Ideker, T., & Mattson, N. M. (2026). Harmonization and integration of pharmacogenomics screens. Bioinformatics, 42(7), DOI: 10.1093/bioinformatics/btag382 [Link]
Prasad, G., Rajkumar, U., Curtis, E. J., Wong, I. T.-L., Yan, X., Zhang, S., Brückner, L., Turner, K., Wiese, J., Wahl, J., Hemmati, H., Wu, S., Theissen, J., Fischer, M., Chang, H. Y., Henssen, A. G., Mischel, P. S., Bafna, V. (2026). Accurate prediction of ecDNA in interphase cancer cells using deep neural networks. Communications Biology. DOI: 10.1038/s42003-026-09982-4 [Link]
Kong J, Lee I, Boecher D, Singhal A, Kelly MR, Moon J, Ahn CH, Ock C, Pratt D, Kumar T, Sears TJ, Laub D, Wright S, Wall P, Carter H, Wang Z, Ideker T. (2026). A foundation model of cancer genotype enables precise predictions of therapeutic response. Cancer Discovery. Published online May 26, 2026. DOI: 10.1158/2159-8290.CD-25-1735 [Link]
Meyer CT, Dai Y, Pomeroy AE, Twarog NR, Bender A, Rosenfeld SS, Antonarakis ES, Mettetal JT, Huang RS, Quaranta V, Tang J, Shelat AA, Smith MA, Palmer AC. (2026). Rethinking the role of synergy calculations in the next century of drug combination discovery. Med, 7(5):101103. PMID: 42054999. DOI: 10.1016/j.medj.2026.101103 [Link]
Bild AH, Sangar MC, McQuerry JA, Ideker T, Kopetz S, Carey L, Nath A, Marcus D, Regier A, Rashid N, Barzilay R, Winer E, Salgia R, Malhotra J, Gentles A, Buetow K, Mahmood F, Markman DW, Eddy JA, The ADAPT Consortium. (2026). The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapy. Cancer Cell. PMID: 41512871. DOI: 10.1016/j.ccell.2025.12.008 [Link]
Wang X, Nguyen J, Nader K, Miihkinen M, Wall P, Singhal A, Bedard PL, Ideker T, Aittokallio T, Haibe-Kains B. (2026). Discovery of predictive biomarkers for cancer therapy through computational approaches. Nat Rev Clin Oncol. DOI: 10.1038/s41571-025-01109-8 [Link]

2025

Jena S, Kim D, Lee A, Zhang W, Zhan K, Elmorsi RM, Li Y, Dehm S, Huang RS. (2025). Novel mixed cancer-cell models designed to capture inter-patient tumor heterogeneity for accurate evaluation of drug combinations. Int J Mol Sci, 27(1): 413. DOI: 10.3390/ijms27010413 [Link]
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]
Rajkumar U, Prasad G, Curtis EJ, Wong IT, Yan X, Zhang S, Brückner L, Turner K, Wiese J, Wahl J, Wu S, Theissen J, Fischer M, Chang HY, Henssen AG, Mischel PS, Bafna V. Accurate prediction of ecDNA in interphase cancer cells using deep neural networks. bioRxiv [Preprint]. 2025 Jun 27:2025.06.23.661188. DOI: 10.1101/2025.06.23.661188. PMID: 40667255 [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]