Personal profile
Research interests
My research interests focus on advancing precision medicine by leveraging bioinformatics, data science and interdisciplinary collaboration. My work aims to bridge computational approaches with clinical insights to address the complexities of tumor heterogeneity, particularly through multi-omics integration and predictive modeling.
Specifically, I focus on:
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Biomarker Discovery and Validation: Developing and validating molecular biomarkers that can reliably predict cancer onset, progression, and response to therapies.
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Understanding Cancer Heterogeneity: Utilizing single-cell and bulk omics data to elucidate the genetic and molecular diversity within tumors and across patient populations.
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Integrative Data Approaches for Treatment Prediction: Employing machine learning and AI to integrate multi-omics and clinical data, building models that predict treatment efficacy and resistance mechanisms.
We collaborate with researchers and clinicians to design studies, analyze data, and develop data-driven products. We work on a variety of projects, including:
- Collaborate with researchers to perform in-depth genomics and clinical data analysis, offer support in preparing manuscripts and grant applications.
- Partner with clinicians to design studies and analyze data, develop data-driven products, and validate hypotheses using real-world evidence gathered from diverse consortium organizations, such as labs, hospitals, and literature mining.
- Provide insightful data science consultation to pharmaceutical and biotech companies on new drug development, leveraging both short-reads and long-reads sequencing data analysis, and utilizing structured and unstructured patient's data for clinical research.
Education/Academic qualification
PhD, Electrical Engineering and Computer Science, Washington State University Pullman
Sep 2007 → Jul 2012
Award Date: Jul 1 2012
Master, Electrical Engineering, Nanjing University
Sep 2004 → Jul 2007
Award Date: Jul 1 2007
Bachelor, Electrical Engineering, Nanjing University
Sep 2000 → Jul 2004
Award Date: Jul 1 2004
External positions
Senior Scientist, The Children's Hospital of Philadelphia
Aug 2019 → Jan 2023
Assistant Professor, University of Mississippi Medical Center
Jul 2016 → Jul 2019
Computational Biologist II, UT Southwestern Medical Center
Nov 2012 → Jul 2016
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Collaborations and top research areas from the last five years
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CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer
Li, Q., Ren, Z., Cao, K., Li, M. M., Wang, K. & Zhou, Y., May 6 2022, In: Science Advances. 8, 18, p. eabj1624 eabj1624.Research output: Contribution to journal › Article › peer-review
Open Access49 Scopus citations -
Outcomes in patients treated with frontline immune checkpoint inhibition (ICI) for advanced NSCLC with KRAS mutations and STK11/KEAP1 comutations across PD-L1 levels
Sun, L., Handorf, E. A., Zhou, Y., Borghaei, H., Aggarwal, C. & Bauman, J., Apr 2024, In: Lung Cancer. 190, p. 107510 107510.Research output: Contribution to journal › Article › peer-review
Open Access25 Scopus citations -
Aspirin Treatment Effect and Association with PIK3CA Mutation in Breast Cancer: A Biomarker Analysis
Zhou, Y., Simmons, J., Jordan, C. D., Sonbol, M. B., Maihle, N. & Tang, S.-C., Oct 2019, In: Clinical Breast Cancer. 19, 5, p. 354-362.e7Research output: Contribution to journal › Article › peer-review
9 Scopus citations -
Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT
Yang, J., Liu, C., Deng, W., Wu, D., Weng, C., Zhou, Y. & Wang, K., Jan 12 2024, In: Patterns. 5, 1, p. 100887 100887.Research output: Contribution to journal › Article › peer-review
Open Access43 Scopus citations -
DoTT-ML: Condition-aware detection of transcriptional readthrough from RNA-seq with optional ML-based prioritization
Levin, M., Surumbayeva, A., Li, M., Astsaturov, I. & Zhou, Y., Aug 2026, In: Computational Biology and Chemistry. 123, p. 109039 109039.Research output: Contribution to journal › Article › peer-review
Open Access
Press/Media
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New Necroptosis Study Findings Have Been Reported from Fox Chase Cancer Center (Abstract 3102: Spliceosome perturbation enhances immunotherapy in SCLC by triggering ZBP1-driven necroptosis in cancer-associated fibroblasts)
Balachandran, S., Canadas, I. & Zhou, Y.
04/22/26
1 item of Media coverage
Press/Media