Shanye Yin, Ph.D.

My research interests lie at the intersection of single-cell sequencing, spatial transcriptomics, tumor heterogeneity, and computational analysis, with a specific focus on cancers, including head and neck cancer (HNSCC), chronic lymphocytic leukemia (CLL), lung cancer (NSCLC), and adult T-cell leukemia/lymphoma (ATLL).

Tumor heterogeneity is a central theme in my research. I seek to decipher the underlying mechanisms driving this diversity and its implications for disease progression and treatment response. Computational analysis plays a pivotal role in my work, enabling the integration of multi-dimensional data to predict patient outcomes and guide precision medicine approaches. Single-cell sequencing allows for the exploration of cellular diversity within tumors, offering insights into the genetic and phenotypic variations that contribute to tumor heterogeneity. Spatial transcriptomics is another transformative tool that helps us understand how gene expression patterns are distributed within tissues. My interest lies in applying this technique to map the spatial heterogeneity of tumors, shedding light on the microenvironment and interactions between cancer cells and their surroundings in these specific cancer types. I am deeply committed to leveraging this technology to unravel the complexities of different cancers, aiming to identify novel therapeutic targets and personalized treatment strategies.

Ultimately, my professional passion centers on advancing our understanding of these cancers through innovative technologies and computational methodologies, with the ultimate goal of improving patient care and outcomes.

1. An J, Hu E, Shen Q, Zhu J, Zhu J, Liu N, Lin Q, Nunez L, Bello S, Ren Y, Kurt S, Harris K, Kawachi N, Rosenblatt G, Ye R, Segall JE, Ostrer H, Hebert T, Fecher R, Liu Q, Aminu M, Ow TJ, Prystowsky MB, Verma A, Deng W, Yin S#. Spatially defined microenvironmental niches are associated with clinical outcome and tumor ecosystem diversity in head and neck cancer. Med. 2026 Jul 2:101214
2. Liu N, Deng W, Yin S#. Therapeutic Plasma Exchange Rapidly Restores Red Blood Cell Deformability in Waldenström Macroglobulinemia. iMed. 2026, 1(1), 10003
3. Yin S, Cheng L, Hu E, Li J, An J, Nunez L, Kawachi N, Zhu J, Rosenblatt G, Segall JE, Ostrer H, Augustine S, Song EZ, Ow TJ, Smith RV, Prystowsky MB, Verma A, Deng W. Association of Intratumoral Microbiota with Prognosis in Head and Neck Squamous Cell Carcinoma. Clinical Cancer Research. 2026 Feb 27.
4. Segal S, An J, Berkovsky M, Jung G, Stone A, Yau V, Lin J, Smith RV, Yin S#. The Role of Tumor Immune Microenvironment and Clinical Factors in Head and Neck Cancer Prognosis Among African American Men and Women. Cancers. 2026 Jan 31;18(3):481
5. Wu G, Fan X, Cheng L, Yi Y, Liang J, Huang X, Yang N, Yin J, Guo W, Huang Y, Yin S#. Metabolism-driven post-translational modifications and immune regulation. Science Advances. 2025 Sep 12;11(37):eadx6489.
6. Xue M, An J, Hu E, Deng W, Yin S#. SF3B1K700E-driven transcriptional alterations in hematopoietic progenitors underlie blood cancer pathophysiology. Genes & Diseases. 2025 Jul 15, 101775.
7. An J, Hu E, Shi Y, Fang Y, Liu N, Liu Q, Wang Q, Wang Y, He W, Wang A, Song Y, Shan J, Zhang J, Zou Y, Cheng H, Cai W, Verma AK, Sica RA, Deng W, Yin S#. Single-Cell Analysis of Oncolytic Virotherapy in Adult T-Cell Leukemia/Lymphoma. The Journal for ImmunoTherapy of Cancer. 2025 Mar 25:13-3.
8. Hu E, An J, Gersten AJ, Wu N, Kawachi N, Zhu J, Rosenblatt G, Augustine S, Smith RV, Segall JE, Ostrer H, Amelio AL, Chung CH, Prystowsky MB, Ow TJ, Deng W, Yin S#. Virusplot: a web server for viral integration analysis and visualization. Front. Oncol. 2025 Feb 19:15:1539782
9. Huang Y, Cheng L, Bi G, Liang J, Li M, Zhang H, Shan G, Hu Z, Chen Z, Wu G, Lin Z, Jiang W, Wang Q, Xi J, Zhan C, Yin S#. Unveiling neoadjuvant chemotherapy-induced immune landscape remodeling and metabolic reprogramming in lung adenocarcinoma by scRNA-sequencing. Elife. 2024 Dec 27:13:RP95988.
10. Ye R, Wang A, Bu B, Luo P, Deng W, Zhang X, Yin S#. Viral oncogenes, viruses, and cancer: a third-generation sequencing perspective on viral integration into the human genome. Front. Oncol. 2023 Dec 20:13
11. Deng W, Yin S#. Decoding the Pan-Cancer Regulatory Landscape: Insights from Proteogenomics and Post-Translational Modifications. The Innovation Life.2023.100032.
12. Yin S* ,#, Klaeger S, Chea V, Carulli I, Rachimi S, Black K, Filbin M, Hariri L, Knipe R, Carr S, Wu JC#, Kim EY#, and Keskin DB#. Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies. Front. Immunol. 2023 Oct 20:14:1269335
13. Wang Y, Wang S, Chen D, Li M, Mi S, Xiong L, Song W, Wang W, Yin S#, Wang B#. Mitral valve aneurysms: echocardiographic characteristics, formation mechanisms, and patient outcomes. Front Cardiovasc Med. 2023 Aug 25;10:1233926.
14. Ten Hacken E*, Yin S*, Redd R, Hernández Sánchez M, Clement K, Hoffmann GB,Regis FF, Witten E, Li S, Neuberg D, Pinello L, Livak KJ, Wu CJ. Loss-of-function lesions impact B-cell development and fitness but are insufficient todrive CLL in mouse models. Blood Adv. 2023 Aug 22;7(16):4514-4517.
15. Ten Hacken E*, Yin S*, Hoffmann GB, Gruber M, et al. In Vivo Modelingof CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Pathsand Therapeutic Vulnerabilities. Blood Cancer Discov. 2023 Mar 1;4(2):150-169.
16. Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, et al. A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell. 2019 Jan 14;35(2):283-296 [Cover story].
17. Lazarian G*, Yin S*, Hacken E, Sewastianik T, Uduman M, A Font-Tello, et al. A hotspot mutation p.L162R in IKZF3 drives B cell neoplasia via transcriptional dysregulation. Cancer Cell. 2021 Mar 8;39(3):380-393.
18. Yin S, Iocolano A, Yu Y, Gangopadhyay J, Reed R. In Vitro System for Coupling RNAP II Transcription to Primary microRNA Processing and a Three-Way System for RNAP II Transcription/Splicing/microRNA Processing. Methods Mol Biol. 2018;1823:43-50.
19. Yin S, Lopez-Gonzalez R, Kunz RC, Gangopadhyay J, Borufka C, Gygi SP, Gao FB, Reed R. Evidence that C9ORF72 Dipeptide Repeat Proteins Associate with U2 snRNP to Cause Mis-splicing in ALS/FTD Patients. Cell Reports. 2017 Jun 13;19(11):2244-2256.
20. Yin S, Wang P, Deng W, Zheng H, Hu L, Hurst LD, Kong X. Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals. Genome Biology. 2016;10(7):R74.