A5019605726- Monoclonal and Polyclonal Antibodies Research
- Cancer Genomics and Diagnostics
- Protein Structure and Dynamics
- vaccines and immunoinformatics approaches
- Gene Regulatory Network Analysis
- Cancer Immunotherapy and Biomarkers
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- Immune cells in cancer
- Ferroptosis and cancer prognosis
- RNA and protein synthesis mechanisms
Stanford University
2024-2025
Millennium Science Initiative
2024
Millennium Institute for Integrative Biology
2024
National Institute of Genomic Medicine
2022
Abstract Immune checkpoint inhibition (ICI) has fundamentally changed cancer treatment. However, only a minority of patients with metastatic triple negative breast (TNBC) benefit from ICI, and the determinants response remain largely unknown. To better understand factors influencing patient outcome, we assembled longitudinal cohort tissue multiple timepoints, including primary tumor, pre-treatment on-treatment tumor 117 treated ICI (nivolumab) in phase II TONIC trial. We used highly...
The function of a protein is strongly dependent on its structure. During evolution, proteins acquire new functions through mutations in the amino-acid sequence. Given advance deep mutational scanning, recent findings have found functional change to be position dependent, notwithstanding chemical properties mutant and mutated amino acids. This could indicate that structural given are potentially responsible for relevance mutation. Here, we looked at relation between structure positions using...
Tumors with the same diagnosis can have different molecular profiles and response to treatment. It remains unclear when why these differences arise. Somatic genomic aberrations occur within context of a highly variable germline genome. Interrogating 5870 breast cancer lesions, we demonstrated that germline-derived epitopes in recurrently amplified genes influence somatic evolution by mediating immunoediting. Individuals high germline-epitope burden human epidermal growth factor receptor 2...
Breast cancer is a highly heterogeneous disease whose prognosis and treatment as defined by the expression of three receptors—oestrogen receptor (ER), progesterone human epidermal growth factor 2 (HER2; encoded ERBB2)—is insufficient to capture full spectrum clinical outcomes therapeutic vulnerabilities. Previously, we demonstrated that transcriptional genomic profiles define eleven integrative subtypes with distinct outcomes, including four ER+ increased risk relapse decades after...
Abstract The amazing complexity of gene regulatory circuits, and biological systems in general, makes mathematical modeling an essential tool to frame develop our understanding their properties. Here, we present some fundamental considerations analyze a model circuit interest, either representing natural, synthetic, or theoretical system. A allows us effectively evaluate the logical implications hypotheses. Using models systematically perform silico experiments, can then propose specific...