2025

Hieromnimon HM, Dolezal J, Doytcheva K, Howard FM, Kochanny S, Zhang Z, Grossman RL, Tanager K, Wang C, Kather JN, Izumchenko E, Cipriani NA, Fertig EJ, Pearson AT, Riesenfeld SJ. Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine. Genome Medicine, (2025). doi: 10.1186/s13073-025-01502-z

Hieromnimon HM, Trzcinska A, Wen FT, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte JJ, Wang C, Chen H, Chin J, Blair E, Agrawal N, Rosenberg A, Vokes E, Katipally R, Juloori A, Izumchenko E, Lingen MW, Cipriani N, Jalaly JB, Basu D, Riesenfeld SJ, Pearson A. Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas. Oral Oncology. 163, 107207 (2025). doi: 10.1016/j.oraloncology.2025.107207

Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and integration of bursty transcriptional dynamics for complex systems. Proc Natl Acad Sci U S A. 2024 Apr 30;121(18):e2306901121. doi: 10.1073/pnas.2306901121

Howard FM, Hieromnimon HM, Ramesh S, Dolezal J, Kochanny S, Zhang Q, Brad Feiger, Peterson J, Fan C, Perou CM, Vickery J, Sullivan M, Cole K, Khramtsova G, Pearson A. Generative adversarial networks accurately reconstruct pan-cancer histology from pathologic, genomic, and radiographic latent features. Sci. Adv.10, eadq0856 (2024). doi: 10.1126/sciadv.adq0856

Liang Z, Anderson HD, Locher V, O'Leary C, Riesenfeld SJ, Jabri B, McDonald BD, Bendelac A. Eomes expression identifies the early bone marrow precursor to classical NK cells. Nat Immunol. 2024 Jul;25(7):1172-1182. doi: 10.1038/s41590-024-01861-6

Ramesh S, Tomesh T, Riesenfeld SJ, Chong FT, Pearson AT. Quantum computing for oncology. Nat Cancer. 2024 Jun;5(6):811-816. doi: 10.1038/s43018-024-00770-9

van Elsas MJ, Middelburg J, Labrie C, Roelands J, Schaap G, Sluijter M, Tonea R, Ovcinnikovs V, Lloyd K, Schuurman J, Riesenfeld SJ, Gajewski TF, de Miranda NFCC, van Hall T, van der Burg SH. Immunotherapy-activated T cells recruit and skew late-stage activated M1-like macrophages that are critical for therapeutic efficacy. Cancer Cell. 2024 Jun 10;42(6):1032-1050.e10. doi: 10.1016/j.ccell.2024.04.011

Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity. 2023 Jan 10;56(1):43-57.e10. doi: 10.1016/j.immuni.2022.12.009

Chaudagar K, Hieromnimon HM, Kelley A, Labadie B, Shafran J, Rameshbabu S, Drovetsky C, Bynoe K, Solanki A, Markiewicz E, Fan X, Loda M, Patnaik A. Suppression of tumor cell lactate-generating signaling pathways eradicates murine PTEN/p53-deficient aggressive-variant prostate cancer via macrophage phagocytosis. Clin Cancer Res. (2023). doi: 10.1158/1078-0432.CCR-23-1441

Dolezal JM, Wolk R, Hieromnimon HM, Howard FM, Srisuwananukorn A, Karpeyev D, Ramesh S, Kochanny S, Kwon JW, Agni M, Simon RC, Desai C, Kherallah R, Nguyen TD, Schulte JJ, Cole K, Khramtsova G, Garassino MC, Husain AN, Li H, Grossman R, Cipriani NA, Pearson AT. Deep learning generates synthetic cancer histology for explainability and education. npj Precis. Onc. 7, 49 (2023). doi: 10.1038/s41698-023-00399-4

Hieromnimon HM, Dolezal J, Doytcheva K, Howard FM, Kochanny S, Zhang Z, Grossman RL, Tanager K, Wang C, Kather JN, Izumchenko E, Cipriani NA, Fertig EJ, Pearson AT, Riesenfeld SJ. Latent transcriptional programs reveal histology-encoded tumor features spanning tissue origins. bioRxiv (2023). doi: 10.1101/2023.03.22.533810