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Cancer Program

Mutations and structural variants arising during double-strand break repair.

Dalin S, Webster S, Sugawara N, et al. Mutations and structural variants arising during double-strand break repair. Proceedings of the National Academy of Sciences of the United States of America. 2026;123(6):e2504584123. doi:10.1073/pnas.2504584123

A context-augmented large language model for accurate precision oncology medicine recommendations.

Jun H, Tanaka Y, Johri S, et al. A context-augmented large language model for accurate precision oncology medicine recommendations. Cancer cell. 2026. doi:10.1016/j.ccell.2025.12.017

Deep learning guided design of protease substrates.

Martin-Alonso C, Alamdari S, Samad TS, Yang KK, Bhatia SN, Amini AP. Deep learning guided design of protease substrates. Nature communications. 2026;17(1):54. doi:10.1038/s41467-025-67226-1

Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity.

Pimenta EM, Garza AE, Camp SY, et al. Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity. Science translational medicine. 2026;18(833):eadw4689. doi:10.1126/scitranslmed.adw4689

Sensitive detection of cancer antigens enabled by user-defined peptide libraries.

Manakongtreecheep K, Ctortecka C, Correa-Medero LO, et al. Sensitive detection of cancer antigens enabled by user-defined peptide libraries. Nature biotechnology. 2026. doi:10.1038/s41587-026-03003-9

Nutrient requirements of organ-specific metastasis in breast cancer.

Abbott KL, Subudhi S, Ferreira R, et al. Nutrient requirements of organ-specific metastasis in breast cancer. Nature. 2026. doi:10.1038/s41586-025-09898-9

Cell-free DNA epigenomic profiling enables noninvasive detection and monitoring of translocation renal cell carcinoma.

Garinet S, Semaan K, Li J, et al. Cell-free DNA epigenomic profiling enables noninvasive detection and monitoring of translocation renal cell carcinoma. The Journal of clinical investigation. 2026;136(3). doi:10.1172/JCI195725

Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss.

di Montesano SC, D’Ascenzo D, Raghavan S, Amini AP, Winter PS, Crawford L. Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss. Nature computational science. 2026. doi:10.1038/s43588-025-00945-z

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

Pilcher WC, Yao L, Gonzalez-Kozlova E, et al. A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma. Nature cancer. 2026. doi:10.1038/s43018-025-01072-4

Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.

Kim PG, Hergott CB, Miller AP, et al. Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis. Cell chemical biology. 2026. doi:10.1016/j.chembiol.2026.01.006