Using high-throughput genomic data, Riesenfeld Group develops approaches to computationally infer the circuits that regulate gene expression and cellular function. By iterating experimental perturbations, data modeling, and targeted validations, they aim to extract from noisy, large-scale data the signals to help answer complex questions about the immune system, such as: What drives tolerant versus inflammatory immune responses? How do immune pathways contribute to or disrupt tissue homeostasis? How can immune responses be manipulated to restore health?
Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine.
Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine. Genome Med. 2025 Aug 07; 17(1):87.
PMID: 40775734
Corrigendum to "Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas". [Oral Oncol. 163 (2025) 107207].
Corrigendum to "Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas". [Oral Oncol. 163 (2025) 107207]. Oral Oncol. 2025 Oct; 169:107510.
PMID: 40721367
Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis.
Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis. Cell Host Microbe. 2025 Apr 09; 33(4):498-511.e10.
PMID: 40154490
Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas.
Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas. Oral Oncol. 2025 Apr; 163:107207.
PMID: 40043423
Epigenetic control of commensal induced Th2 Responses and Intestinal immunopathology.
Epigenetic control of commensal induced Th2 Responses and Intestinal immunopathology. bioRxiv. 2024 Aug 30.
PMID: 39257820
Eomes expression identifies the early bone marrow precursor to classical NK cells.
Eomes expression identifies the early bone marrow precursor to classical NK cells. Nat Immunol. 2024 Jul; 25(7):1172-1182.
PMID: 38871999
Quantum computing for oncology.
Quantum computing for oncology. Nat Cancer. 2024 Jun; 5(6):811-816.
PMID: 38760645
Immunotherapy-activated T cells recruit and skew late-stage activated M1-like macrophages that are critical for therapeutic efficacy.
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.
PMID: 38759656
Dissection and integration of bursty transcriptional dynamics for complex systems.
Dissection and integration of bursty transcriptional dynamics for complex systems. Proc Natl Acad Sci U S A. 2024 Apr 30; 121(18):e2306901121.
PMID: 38669186
Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems.
Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems. bioRxiv. 2023 Jun 13.
PMID: 37398022