Critical assessment of genome interpretation consortium. CAGI, the critical assessment of genome interpretation, establishes progress and pprospects for computational genetic … S Jain, C Bakolitsa, EB Steven, P Radivojac, J Moult, S Repo, AH Roger, ... Genome Biology 22 (22; 25 (1): 53.), 1-46, 2024 | | 2024 |
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods N Null, S Jain, C Bakolitsa, SE Brenner, P Radivojac, J Moult, S Repo, ... Genome Biology 25 (1), 1-46, 2024 | 3 | 2024 |
Pan-cancer proteogenomics connects oncogenic drivers to functional states Y Li, E Porta-Pardo, C Tokheim, MH Bailey, TM Yaron, V Stathias, ... Cell 186 (18), 3921-3944. e25, 2023 | 25 | 2023 |
Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA L Yang, J Wang, J Altreuter, A Jhaveri, CJ Wong, L Song, J Fu, L Taing, ... Nature Protocols 18 (8), 2404-2414, 2023 | 6 | 2023 |
Discovery of targets for immune–metabolic antitumor drugs identifies estrogen-related receptor alpha A Sahu, X Wang, P Munson, JPG Klomp, X Wang, SS Gu, Y Han, G Qian, ... Cancer discovery 13 (3), 672-701, 2023 | 12 | 2023 |
Machine learning modeling of protein-intrinsic features predicts tractability of targeted protein degradation W Zhang, SS Roy Burman, J Chen, KA Donovan, Y Cao, C Shu, B Zhang, ... Genomics, Proteomics and Bioinformatics 20 (5), 882-898, 2022 | 17 | 2022 |
Charting the spatial landscape of cancer hallmarks M Sibai, S Cervilla, D Grases, E Musulen, A Fortian, M Romeo, A Bernat, ... bioRxiv, 2022 | 1 | 2022 |
Genetic fusions favor tumorigenesis through degron loss in oncogenes J Liu, C Tokheim, JD Lee, W Gan, BJ North, XS Liu, PP Pandolfi, W Wei Nature Communications 12 (1), 6704, 2021 | 18 | 2021 |
In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target X Wang, C Tokheim, SS Gu, B Wang, Q Tang, Y Li, N Traugh, Z Zeng, ... Cell 184 (21), 5357-5374. e22, 2021 | 96 | 2021 |
Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC Network Z Zeng, J Fu, C Cibulskis, A Jhaveri, C Gumbs, B Das, ... Clinical Cancer Research 27 (18), 5049-5061, 2021 | 6 | 2021 |
Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade SS Gu, W Zhang, X Wang, P Jiang, N Traugh, Z Li, C Meyer, B Stewig, ... Cancer discovery 11 (6), 1524-1541, 2021 | 116 | 2021 |
Systematic characterization of mutations altering protein degradation in human cancers C Tokheim, X Wang, RT Timms, B Zhang, EL Mena, B Wang, C Chen, ... Molecular cell 81 (6), 1292-1308. e11, 2021 | 44 | 2021 |
The genetic evolution of treatment-resistant cutaneous, acral, and uveal melanomas AP Makohon-Moore, EJ Lipson, JE Hooper, A Zucker, J Hong, CM Bielski, ... Clinical Cancer Research 27 (5), 1516-1525, 2021 | 8 | 2021 |
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade SS Gu, X Wang, X Hu, P Jiang, Z Li, N Traugh, X Bu, Q Tang, C Wang, ... Genome biology 21, 1-28, 2020 | 17 | 2020 |
Determinants of transcription factor regulatory range CH Chen, R Zheng, C Tokheim, X Dong, J Fan, C Wan, Q Tang, M Brown, ... Nature communications 11 (1), 2472, 2020 | 47 | 2020 |
Integrated informatics analysis of cancer-related variants KA Pagel, R Kim, K Moad, B Busby, L Zheng, C Tokheim, M Ryan, ... JCO clinical cancer informatics 4, 310-317, 2020 | 77 | 2020 |
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 | 124 | 2020 |
CHASMplus reveals the scope of somatic missense mutations driving human cancers C Tokheim, R Karchin Cell systems 9 (1), 9-23. e8, 2019 | 98 | 2019 |
A pan-cancer analysis reveals high-frequency genetic alterations in mediators of signaling by the TGF-β superfamily A Korkut, S Zaidi, RS Kanchi, S Rao, NR Gough, A Schultz, X Li, ... Cell systems 7 (4), 422-437. e7, 2018 | 145 | 2018 |
Minimal functional driver gene heterogeneity among untreated metastases JG Reiter, AP Makohon-Moore, JM Gerold, A Heyde, MA Attiyeh, ... Science 361 (6406), 1033-1037, 2018 | 279 | 2018 |