2026

Robinett RA, Madejski S, Ruark K, Riesenfeld SJ^#, Orecchia L^#. “Atlas-based Manifold Representations for Interpretable Riemannian Machine Learning.” Proc. 29th Ann. Conf. on Artificial Intelligence and Statistics (AISTATS) (2026) ‡ [Accepted; in press] Earlier version available as a preprint (2025) from arXiv: https://arxiv.org/abs/2510.17772

2025

Hieromnimon HH, Dolezal J, Doytcheva K, Howard FM, Kochanny S, Zhang Z, Grossman RL, Tanager K, Wang C, Kather JK, 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) 17(87). In Collection “AI applications in cancer discovery and care”. https://doi.org/10.1186/s13073-025-01502-z

Hieromnimon HH, Trzcinska A, Wen F, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte J, 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, Chin J, 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 (2025) 163:107207. https://doi.org/10.1016/j.oraloncology.2025.107207

Lisicka W*, Earley ZM*, Sifakis JJ, Erickson SA, Mattingly JR, Wu-Woods NJ, Krishnamurthy SR, Belkaid Y, Ismagilov RF, Riesenfeld SJ, Cyster JG, Bendelac A^#, Jabri B^#. “Immunoglobulin A controls intestinalvirus colonization to preserve immune homeostasis.” Cell Host & Microbe (2025) 33(4):498-511.e10. https://doi.org/10.1016/j.chom.2025.03.004

2024

Gao FC, Vaikuntanathan S^#, Riesenfeld SJ^#. “Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems.” Proc. Nat. Academy of Sciences of the USA (PNAS) (2024) 121(18):e2306901121. https://doi.org/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.” Nature Immunology (2024) 25:1172–1182. https://doi.org/10.1038/s41590-024-01861-6

Ramesh S, Tomesh T, Riesenfeld SJ, Chong FT^#, Pearson AT^#. “Quantum Computing for Oncology.” Nature Cancer (2024) 5:811–816. https://doi.org/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 attract and activate a subset of late-stage activated M1-like macrophages that are critical for therapeutic efficacy.” Cancer Cell (2024) 42(6):1032–1050.e10. https://doi.org/10.1016/j.ccell.2024.04.011

2023

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) 56(1):43–57.e10. https://doi.org/10.1016/j.immuni.2022.12.009

Yang D*, Jacobson A*, Meerschaert KA, Sifakis JJ, Wu M, Chen X, Yang T, Zhou Y, Anekal PV, Rucker RA, Sharma D, Sontheimer-Phelps A, Wu GS, Deng L, Anderson MD, Choi S, Neel D, Lee N, Kasper DL, Jabri B, Huh JR, Johansson M, Thiagarajah JR, Riesenfeld SJ^#, Chiu IM^#. “Nociceptor neurons direct goblet cells via a CGRP-RAMP1 axis to drive mucus production and gut barrier protection.” Cell (2022) 185(22):4190–4205.e25. https://doi.org/10.1016/j.cell.2022.09.024