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layout: archive
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title: "Publications"
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title: "Selected Publications"
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permalink: /publications/
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author_profile: true
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## Lab Publications
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### Corresponding Author Studies
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**Single-Cell Precision Medicine and Computational Methods**
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* **Sinha, S.**, Vegesna, R., Mukherjee, S., et al. (2024). PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. **Nature Cancer**, 1-15.
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* Choudhary, M., Liu, L., Yadav, A., ... **Sinha, S.** (2024). ecPath detects ecDNA in tumors from histopathology images. **bioRxiv** doi: 10.1101/2024.11.13.623494 (Under revision in Nature).
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* **Sinha, S.**, Sinha, N. and Ruppin, E., 2022. Deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens. **Biorxiv**, pp.2022-10. (Revision in npj Precision Oncology)
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### Cancer Disparities Research
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* **Sinha, S.**, Mitchell, K.A., Zingone, A., Bowman, E., Sinha, N., Schäffer, A.A., Lee, J.S., Ruppin, E. and Ryan, B.M., 2020. Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans. **Nature Cancer**, 1(1), pp.112-121.
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* Zingone, A., **Sinha, S.**, Ante, M., Nguyen, C., Daujotyte, D., Bowman, E.D., Sinha, N., Mitchell, K.A., et al., 2021. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. **Nature Communications**, 12(1), p.5605.
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* Mitchell, K.A., Nichols, N., Tang, W., Walling, J., Stevenson, H., Pineda, M., Stefanescu, R., Edelman, D.C., Girvin, A.T., Zingone, A. and **Sinha, S.**, 2019. Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans. **Nature Communications**, 10(1), p.5735.
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### Genomic Editing & Cancer Mutations
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* **Sinha, S.**, Barbosa, K., Cheng, K., Leiserson, M.D., Jain, P., Deshpande, A., Wilson III, D.M., Ryan, B.M., Luo, J., Ronai, Z.E.A. and Lee, J.S., 2021. A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing. **Nature Communications**, 12(1), p.6512.
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### Patient Stratification Technologies
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* Lee, J.S., Nair, N.U., Dinstag, G., Chapman, L., Chung, Y., Wang, K., **Sinha, S.**, Cha, H., Kim, D., et al., 2021. Synthetic lethality-mediated precision oncology via the tumor transcriptome. **Cell**, 184(9), pp.2487-2502.
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* Ahmadi, S., Sukprasert, P., Vegesna, R., **Sinha, S.**, Schischlik, F., Artzi, N., Khuller, S., Schäffer, A.A. and Ruppin, E., 2022. The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective. **Nature Communications**, 13(1), p.1613.
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* Hoang, D.T., Dinstag, G., Shulman, E.D., Hermida, L.C., Ben-Zvi, D.S., Elis, E., Caley, K., Sammut, S.J., **Sinha, S.**, Sinha, N. and Dampier, C.H., 2024. A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics. **Nature Cancer**, 5(9), pp.1305-1317.
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### Tumor Mutation Burden & Immunotherapy
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* Sinha, N., **Sinha, S.**, Valero, C., Schäffer, A.A., Aldape, K., Litchfield, K., Chan, T.A., Morris, L.G. and Ruppin, E., 2022. Immune determinants of the association between tumor mutational burden and immunotherapy response across cancer types. **Cancer Research**, 82(11), pp.2076-2083.
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* Sinha, N., **Sinha, S.**, Cheng, K., Madan, S., Erez, A., Ryan, B.M., Schäffer, A.A., Aldape, K. and Ruppin, E., 2021. Using a recently approved tumor mutational burden biomarker to stratify patients for immunotherapy may introduce a sex bias. **JCO Precision Oncology**, 5.
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### Immunotherapy & Liquid Biopsies
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* Cao, Y., Chang, T., Schischlik, F., Wang, K., **Sinha, S.**, Hannenhalli, S., Jiang, P. and Ruppin, E., 2023. Predicting tumor immune microenvironment and checkpoint therapy response of head & neck cancer patients from blood immune single-cell transcriptomics. **bioRxiv**, pp.2023-01.
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* Wu, V.H., Yung, B.S., Faraji, F., Saddawi-Konefka, R., Wang, Z., Wenzel, A.T., Song, M.J., Pagadala, M.S., Clubb, L.M., Chiou, J. and **Sinha, S.**, 2023. The GPCR--Gαs--PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. **Nature Immunology**, pp.1-13.
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For a complete list of publications, please visit [Dr. Sinha's Google Scholar profile](https://scholar.google.com/citations?user=XXXXXXXXXXXX).
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<div class="publication-section">
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<div class="publication-theme">
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<h2>🧬 Precision Medicine & Computational Biology</h2>
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</div>
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<div class="publication-item">
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<div class="publication-title">PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors</div>
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<div><span class="author-highlight">Sinha, S.</span>, Vegesna, R., Mukherjee, S., et al. <span class="journal">Nature Cancer</span> <span class="pub-year">2024</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">ecPath detects ecDNA in tumors from histopathology images</div>
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<div>Choudhary, M., Liu, L., Yadav, A., ... <span class="author-highlight">Sinha, S.</span> <span class="journal">bioRxiv</span> (Under revision in Nature) <span class="pub-year">2024</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">Deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens</div>
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<div><span class="author-highlight">Sinha, S.</span>, Sinha, N. and Ruppin, E. <span class="journal">Biorxiv</span> (Revision in npj Precision Oncology) <span class="pub-year">2022</span></div>
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</div>
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</div>
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<div class="publication-section">
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<div class="publication-theme">
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<h2>🔬 Cancer Disparities Research</h2>
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</div>
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<div class="publication-item">
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<div class="publication-title">Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans</div>
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<div><span class="author-highlight">Sinha, S.</span>, Mitchell, K.A., Zingone, A., et al. <span class="journal">Nature Cancer</span> <span class="pub-year">2020</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients</div>
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<div>Zingone, A., <span class="author-highlight">Sinha, S.</span>, Ante, M., et al. <span class="journal">Nature Communications</span> <span class="pub-year">2021</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans</div>
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<div>Mitchell, K.A., Nichols, N., Tang, W., ... <span class="author-highlight">Sinha, S.</span>, et al. <span class="journal">Nature Communications</span> <span class="pub-year">2019</span></div>
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</div>
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</div>
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<div class="publication-section">
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<div class="publication-theme">
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<h2>🧪 Genomic Editing & Cancer Mutations</h2>
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</div>
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<div class="publication-item">
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<div class="publication-title">A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing</div>
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<div><span class="author-highlight">Sinha, S.</span>, Barbosa, K., Cheng, K., et al. <span class="journal">Nature Communications</span> <span class="pub-year">2021</span></div>
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</div>
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</div>
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<div class="publication-section">
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<div class="publication-theme">
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<h2>👥 Patient Stratification Technologies</h2>
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</div>
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<div class="publication-item">
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<div class="publication-title">Synthetic lethality-mediated precision oncology via the tumor transcriptome</div>
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<div>Lee, J.S., Nair, N.U., Dinstag, G., ... <span class="author-highlight">Sinha, S.</span>, et al. <span class="journal">Cell</span> <span class="pub-year">2021</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective</div>
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<div>Ahmadi, S., Sukprasert, P., Vegesna, R., <span class="author-highlight">Sinha, S.</span>, et al. <span class="journal">Nature Communications</span> <span class="pub-year">2022</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics</div>
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<div>Hoang, D.T., Dinstag, G., Shulman, E.D., ... <span class="author-highlight">Sinha, S.</span>, et al. <span class="journal">Nature Cancer</span> <span class="pub-year">2024</span></div>
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</div>
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</div>
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<div class="publication-section">
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<div class="publication-theme">
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<h2>🔄 Tumor Mutation Burden & Immunotherapy</h2>
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</div>
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<div class="publication-item">
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<div class="publication-title">Immune determinants of the association between tumor mutational burden and immunotherapy response across cancer types</div>
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<div>Sinha, N., <span class="author-highlight">Sinha, S.</span>, Valero, C., et al. <span class="journal">Cancer Research</span> <span class="pub-year">2022</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">Using a recently approved tumor mutational burden biomarker to stratify patients for immunotherapy may introduce a sex bias</div>
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<div>Sinha, N., <span class="author-highlight">Sinha, S.</span>, Cheng, K., et al. <span class="journal">JCO Precision Oncology</span> <span class="pub-year">2021</span></div>
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</div>
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<div class="publication-section">
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<div class="publication-theme">
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<h2>💉 Immunotherapy & Liquid Biopsies</h2>
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</div>
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<div class="publication-item">
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<div class="publication-title">Predicting tumor immune microenvironment and checkpoint therapy response of head & neck cancer patients from blood immune single-cell transcriptomics</div>
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<div>Cao, Y., Chang, T., Schischlik, F., ... <span class="author-highlight">Sinha, S.</span>, et al. <span class="journal">bioRxiv</span> <span class="pub-year">2023</span></div>
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</div>
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<div class="publication-item">
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<div class="publication-title">The GPCR--Gαs--PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure</div>
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<div>Wu, V.H., Yung, B.S., Faraji, F., ... <span class="author-highlight">Sinha, S.</span>, et al. <span class="journal">Nature Immunology</span> <span class="pub-year">2023</span></div>
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<div class="scholar-link">
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<a href="https://scholar.google.com/citations?user=XXXXXXXXXXXX" target="_blank">View Complete Publication List on Google Scholar</a>
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