Publications

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2016
Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CSimon, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, A Hakimi A, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 ;14(10):2476-89.
2017
Chen F, Zhang Y, Bossé D, Lalani A-KA, A Hakimi A, Hsieh JJ, Choueiri TK, Gibbons DL, Ittmann M, Creighton CJ. Pan-urologic cancer genomic subtypes that transcend tissue of origin. Nat Commun. 2017 ;8(1):199.
2018
Chen F, Zhang Y, Gibbons DL, Deneen B, Kwiatkowski DJ, Ittmann M, Creighton CJ. Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases. Clin Cancer Res. 2018 ;24(9):2182-2193.
2019
Chen F, Zhang Y, Varambally S, Creighton CJ. Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas. Mol Cancer Res. 2019 ;17(2):476-487.
Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers. Nat Commun. 2019 ;10(1):5679.
2021
Chen F, Zhang Y, Sucgang R, Ramani S, Corry D, Kheradmand F, Creighton CJ. Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. Sci Rep. 2021 ;11(1):2459.
2022
Chen F, Chandrashekar DS, Scheurer ME, Varambally S, Creighton CJ. Global molecular alterations involving recurrence or progression of pediatric brain tumors. Neoplasia. 2022 ;24(1):22-33.
2023
Chen F, Zhang Y, Chandrashekar DS, Varambally S, Creighton CJ. Global impact of somatic structural variation on the cancer proteome. Nat Commun. 2023 ;14(1):5637.
2024
Chen F, Zhang Y, Sedlazeck FJ, Creighton CJ. Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Rep Med. 2024 ;:101446.