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 AT#. 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

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

Sangani KA, Parker ME, Anderson HD, Chen L, Pandey SP, Pierre JF, Meisel M, Riesenfeld SJ, Hinterleitner R, Jabri B. Epigenetic control of commensal induced Th2 Responses and Intestinal immunopathology. bioRxiv [Preprint]. 2024 Aug 30:2024.08.30.610485. doi: 10.1101/2024.08.30.610485

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

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