Selected Publications

Precision Medicine & Computational Biology

1. Sinha, S., Vegesna, R., Mukherjee, S., et al. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. Nature Cancer, 2024.
2. Choudhary, M., Liu, L., Yadav, A., ... Sinha, S. ecPath detects ecDNA in tumors from histopathology images. bioRxiv (Under revision in Nature), 2024.
3. Sinha, S., Sinha, N. and Ruppin, E. Deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens. Biorxiv (Revision in npj Precision Oncology), 2022.

Genomic Editing & Cancer Mutations

4. Sinha, S., Barbosa, K., Cheng, K., et al. A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing. Nature Communications, 2021.

Patient Stratification Technologies

5. Lee, J.S., Nair, N.U., Dinstag, G., ... Sinha, S., et al. Synthetic lethality-mediated precision oncology via the tumor transcriptome. Cell, 2021.
6. Ahmadi, S., Sukprasert, P., Vegesna, R., Sinha, S., et al. The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective. Nature Communications, 2022.
7. Hoang, D.T., Dinstag, G., Shulman, E.D., ... Sinha, S., et al. A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics. Nature Cancer, 2024.

Tumor Mutation Burden & Immunotherapy

8. Sinha, N., Sinha, S., Valero, C., et al. Immune determinants of the association between tumor mutational burden and immunotherapy response across cancer types. Cancer Research, 2022.
9. Sinha, N., Sinha, S., Cheng, K., et al. Using a recently approved tumor mutational burden biomarker to stratify patients for immunotherapy may introduce a sex bias. JCO Precision Oncology, 2021.

Immunotherapy & Liquid Biopsies

10. Cao, Y., Chang, T., Schischlik, F., ... Sinha, S., et al. Predicting tumor immune microenvironment and checkpoint therapy response of head & neck cancer patients from blood immune single-cell transcriptomics. bioRxiv, 2023.
11. Wu, V.H., Yung, B.S., Faraji, F., ... Sinha, S., et al. The GPCR--Gαs--PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Nature Immunology, 2023.

Cancer Disparities Research

12. Sinha, S., Mitchell, K.A., Zingone, A., et al. Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans. Nature Cancer, 2020.
13. Zingone, A., Sinha, S., Ante, M., et al. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nature Communications, 2021.
14. Mitchell, K.A., Nichols, N., Tang, W., ... Sinha, S., et al. Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans. Nature Communications, 2019.