Tinyi Chu, PhD
Assistant Professor, Genome Sciences
3rd Floor, MSB 3238
Charlottesville, VA 22903
Bio & Overview
My lab develops statistical learning, deep learning, and AI methods to decode single‑cell and spatial omics data. We hope to use these tools to extract mechanistic insights into how cells sense and respond to perturbations and how they interact with their microenvironment across space and time. Leveraging large‑scale training datasets, our long‑term goal is to design and optimize in silico perturbations that can be translated into interventions for inflammation, cellular senescence, and cancer.
A second major focus is liquid biopsy. We develop rigorous machine‑learning methods and integrate experimental innovation to analyze circulating nucleic acids in human biofluids, enabling noninvasive early detection, disease monitoring, and prediction of treatment outcomes. Across both areas, we emphasize collaborative science to deliver tools that are robust and translatable.
Academic Information
- Department
- Genome Sciences
Primary Education
- Ph.D., Computational Biology, Cornell University, 2019
- Postdoc, Computational Biology, Memorial Sloan-Kettering Cancer Center, 2023
- Postdoc, Biostatistics, Yale University, 2026
Research Interests
Research Disciplines
- Biomedical Engineering
- Cancer Biology
- Computational Biology
- Computer Science
- Data Science in Medicine
- Statistics
- Translational Science
Research Opportunities
- Bioinformatics & Genomics
- Biotechnology
- Computational Biology
- Epigenetics
- Immunology
PhD Programs
- Computational Biology
Selected Publications
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Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, et al. Chromatin run‑on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nature Genetics. 2018;50(11):1553–1564.
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Chu T, Wang Z, Pe’er D, Danko CG. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single‑cell RNA sequencing in oncology. Nature Cancer. 2022;3(4):505–517.
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Niec RE*, Chu T*, Schernthanner M, Gur‑Cohen S, Hidalgo L, Pasolli HA, et al. Lymphatics act as a signaling hub to regulate intestinal stem cell activity. Cell Stem Cell. 2022;29(7):1067–1082.e18.
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Romero R, Chu T, González Robles TJ, Smith P, Xie Y, Kaur H, et al. The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1. Nature Cancer. 2024;5(11):1641–1659.
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Loy C, Agun G, Cheng MP, Gonzalez‑Bocco IH, Lenz J, Belcher E, et al. Plasma Cell‑Free RNA Captures Immune Dynamics and Predicts GVHD after Hematopoietic Stem Cell Transplantation. medRxiv. 2025;:2024.05.15.24307448. (preprint)
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Liu T, Chu T, Luo X, Zhao H. Building a unified model for drug synergy analysis powered by large language models. Nature Communications. 2025;16(1):4537.
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Liu T, Huang T, Jin W, Chu T, Ying R, Zhao H. spRefine denoises and imputes spatial transcriptomics with a reference‑free framework powered by genomic language model. Genome Research. 2026;:gr.281001.125.