| High-throughput prediction of MHC class I and II neoantigens with MHCnuggets XM Shao, R Bhattacharya, J Huang, IKA Sivakumar, C Tokheim, L Zheng, ... Cancer immunology research 8 (3), 396-408, 2020 | 116 | 2020 |
| Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial PM Forde, V Anagnostou, Z Sun, SE Dahlberg, HL Kindler, N Niknafs, ... Nature medicine 27 (11), 1910-1920, 2021 | 74 | 2021 |
| Single‐cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions Y Kuboki, CG Fischer, V Beleva Guthrie, W Huang, J Yu, P Chianchiano, ... The Journal of pathology 247 (3), 347-356, 2019 | 62 | 2019 |
| Integrative tumor and immune cell multi-omic analyses predict response to immune checkpoint blockade in melanoma V Anagnostou, DC Bruhm, N Niknafs, JR White, XM Shao, JW Sidhom, ... Cell Reports Medicine 1 (8), 2020 | 55 | 2020 |
| Persistent mutation burden drives sustained anti-tumor immune responses N Niknafs, A Balan, C Cherry, K Hummelink, K Monkhorst, XM Shao, ... Nature medicine 29 (2), 440-449, 2023 | 49 | 2023 |
| Characterization of genetic subclonal evolution in pancreatic cancer mouse models N Niknafs, Y Zhong, JA Moral, L Zhang, MX Shao, A Lo, ... Nature communications 10 (1), 5435, 2019 | 22 | 2019 |
| HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade XM Shao, J Huang, N Niknafs, A Balan, C Cherry, J White, VE Velculescu, ... Annals of Oncology 33 (7), 728-738, 2022 | 14 | 2022 |
| High-throughput prediction of MHC class I and II neoantigens with MHCnuggets. Cancer Immunol Res.(2020) 8: 396–408. doi: 10.1158/2326-6066 XM Shao, R Bhattacharya, J Huang, IKA Sivakumar, C Tokheim, L Zheng, ... CIR-19-0464, 0 | 10 | |
| Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity BA Albert, Y Yang, XM Shao, D Singh, KN Smith, V Anagnostou, ... Nature machine intelligence 5 (8), 861-872, 2023 | 8 | 2023 |
| Sex-specific differences in immunogenomic features of response to immune checkpoint blockade SC Scott, XM Shao, N Niknafs, A Balan, G Pereira, KA Marrone, VK Lam, ... Frontiers in Oncology 12, 945798, 2022 | 8 | 2022 |
| High-throughput prediction of MHC class I and II neoantigens with MHCnuggets. Cancer Immunol. Res. 8, 396–408 XM Shao, R Bhattacharya, J Huang, IKA Sivakumar, C Tokheim, L Zheng, ... | 7 | 2020 |
| Corrigendum to" HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade":[Annals of Oncology volume 33 (2022) 728-738] XM Shao, J Huang, N Niknafs, A Balan, C Cherry, J White, VE Velculescu, ... Annals of oncology: official journal of the European Society for Medical …, 2023 | | 2023 |
| SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors T Palmer, MD Kessler, XM Shao, A Balan, M Yarchoan, N Zaidi, ... bioRxiv, 2023.05. 26.542165, 2023 | | 2023 |
| Persistent mutation burden drives sustained anti-tumor immune responses in human cancers N Niknafs, A Balan, C Cherry, K Hummelink, K Monkhorst, XM Shao, ... Cancer Research 83 (7_Supplement), 1393-1393, 2023 | | 2023 |
| 10. HLA class II Immunogenic Mutation Burden predicts response to immune checkpoint blockade X Shao, J Huang, N Niknafs, A Balan, C Cherry, J White, V Velculescu, ... Cancer Genetics 268, 4, 2022 | | 2022 |
| Deep Neural Networks Predict MHC-I Epitope Presentation and Transfer Learn Neoepitope Immunogenicity BA Albert, Y Yang, XM Shao, D Singh, KN Smith, V Anagnostou, ... bioRxiv, 2022.08. 29.505690, 2022 | | 2022 |
| Sex-specific genomic determinants of response to immunotherapy SC Scott, XM Shao, N Niknafs, A Balan, M Lanis, J White, P Forde, ... Cancer Research 81 (13_Supplement), 1617-1617, 2021 | | 2021 |
| Abstract A33: High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets XM Shao, R Bhattacharya, J Huang, A Sivakumar, C Tokheim, L Zheng, ... Cancer Immunology Research 8 (3_Supplement), A33-A33, 2020 | | 2020 |
| AB113. P087. Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions Y Kuboki, C Guerra, V Beleva, W Huang, J Yu, P Chianchiano, W Hosoda, ... Annals of Pancreatic Cancer 1 (4), 2018 | | 2018 |
Rachel KarchinProfessor of Biomedical Engineering, Oncology and Computer Science, Johns Hopkins UniversityVerified email at jhu.edu
