Education & Training
- PostDoc.,Memorial Sloan Kettering Cancer Center-2018
- Ph.D., University of Pittsburgh School of Medicine-2012
- MS., University of Pittsbugh-Bioengineering-2009
- MS., Carnegie Mellon University-Electrical and Computer Engineering-2006
- BS., Northeastern University, Computer Engineering-2004
Research Interest Summary
Research Categories
Research Interests
Our projects span across the following areas:
- Cancer Genomics: Leveraging machine learning techniques to analyze genomic data from cancer patients, identifying genetic mutations, biomarkers, and potential therapeutic targets for personalized cancer treatment.
- Single Cell and Spatial Omics: Developing statistical methods for single-cell multi-omics integration, integrating data from different omic layers (such as genomics, proteomics, transcriptomics, epigenomics) to gain a comprehensive understanding of cellular processes and disease mechanisms.
- Epigenetics: Studying how epigenetic modifications influence an individual's response to different drugs and integrating epigenetic data with clinical information.
Our projects are executed through multi-disciplinary collaborations, recognizing that precision medicine requires expertise from various domains. By leveraging machine learning and integrating diverse datasets, our aim is to contribute to the advancement of precision medicine, ultimately leading to more targeted and effective treatments for patients.
Representative Publications
Ma X, Somasundaram A, Qi Z, Hartman DJ, Singh H, Osmanbeyoglu HU. SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators. Nucleic Acids Res. 2021;49(17):9633-47. Epub 2021/09/10. doi: 10.1093/nar/gkab745. PubMed PMID: 34500467; PMCID: PMC8464045
Cascio S, Chandler C, Zhang L, Sinno S, Gao B, Onkar S, Bruno TC, Vignali DAA, Mahdi H, Osmanbeyoglu HU, Vlad AM, Coffman LG, Buckanovich RJ. Cancer-associated MSC drive tumor immune exclusion and resistance to immunotherapy, which can be overcome by Hedgehog inhibition. Sci Adv. 2021;7(46):eabi5790. Epub 2021/11/13. doi: 10.1126/sciadv.abi5790. PubMed PMID: 34767446; PMCID: PMC8589308.
Lee S, Osmanbeyoglu HU. Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas. Breast Cancer Res. 2022;24(1):54. Epub 2022/07/30. doi: 10.1186/s13058-022-01550-y. PubMed PMID: 35906698; PMCID: PMC9338552.
Sugitani N, Vendetti FP, Cipriano AJ, Pandya P, Deppas JJ, Moiseeva TN, Schamus-Haynes S, Wang Y, Palmer D, Osmanbeyoglu HU, Bostwick A, Snyder NW, Gong YN, Aird KM, Delgoffe GM, Beumer JH, Bakkenist CJ. Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-alpha/beta expression. Cell Rep. 2022;40(12):111371. Epub 2022/09/22. doi: 10.1016/j.celrep.2022.111371. PubMed PMID: 36130512; PMCID: PMC9646445.
Tao Y*, Ma X*, Palmer D, Schwartz R, Lu X, Osmanbeyoglu HU. Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers. Nucleic Acids Res. 2022. Epub 2022/10/17. doi: 10.1093/nar/gkac881. PubMed PMID: 36243974.
Osmanbeyoglu HU#, Palmer D, Sagan A, Sementino E, Becich MJ, Testa JR. Isolated BAP1 Genomic Alteration in Malignant Pleural Mesothelioma Predicts Distinct Immunogenicity with Implications for Immunotherapeutic Response. Cancers (Basel). 2022;14. (#corresponding author)
Onkar S, Cui J, Zou J, Cardello C, Cillo AR, Uddin MR, Sagan A, Joy M, Osmanbeyoglu HU, Pogue-Geile KL, McAuliffe PF, Lucas PC, Tseng GC, Lee AV, Bruno TC, Oesterreich S, Vignali DAA. Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment. Nature Cancer. 2023. doi: 10.1038/s43018-023-00527-w.
Ramjattun K*, Ma X*, Singh H, Gao SJ, Osmanbeyoglu HU. COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells. J Med Virol. 2023;95(6):e28887. Epub 2023/06/21. doi: 10.1002/jmv.28887. PubMed PMID: 37341527.