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Genomic and immune profiling of pre-invasive lung adenocarcinoma.
Chen H, Carrot-Zhang J, Zhao Y, Hu H, Freeman SS, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, Zhang J, Ramachandran A, Zheng Q, Pan Y, Zheng D, Zheng S, Cheng C, Kuang M, Zhou X, Zhang Y, Li H, Ye T, Ma Y, Gao Z, Tao X, Han H, Shang J, Yu Y, Bao D, Huang Y, Li X, Zhang Y, Xiang J, Sun Y, Li Y, Cherniack AD, Campbell JD, Shi L, Meyerson M. Chen H, et al. Among authors: cheng c. Nat Commun. 2019 Nov 29;10(1):5472. doi: 10.1038/s41467-019-13460-3. Nat Commun. 2019. PMID: 31784532 Free PMC article.
A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks.
Yuan C, Chen H, Tu S, Huang HY, Pan Y, Gui X, Kuang M, Shen X, Zheng Q, Zhang Y, Cheng C, Hong H, Tao X, Peng Y, Yao X, Meng F, Ji H, Shao Z, Sun Y. Yuan C, et al. Among authors: cheng c. Genome Biol. 2021 May 17;22(1):156. doi: 10.1186/s13059-021-02376-1. Genome Biol. 2021. PMID: 34001209 Free PMC article.
Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer.
Chen M, Chen R, Jin Y, Li J, Hu X, Zhang J, Fujimoto J, Hubert SM, Gay CM, Zhu B, Tian Y, McGranahan N, Lee WC, George J, Hu X, Chen Y, Wu M, Behrens C, Chow CW, Pham HHN, Fukuoka J, Wu J, Parra ER, Little LD, Gumbs C, Song X, Wu CJ, Diao L, Wang Q, Cardnell R, Zhang J, Wang J, Le X, Gibbons DL, Heymach JV, Jack Lee J, William WN Jr, Cheng C, Glisson B, Wistuba I, Andrew Futreal P, Thomas RK, Reuben A, Byers LA, Zhang J. Chen M, et al. Among authors: cheng c. Nat Commun. 2021 Nov 17;12(1):6655. doi: 10.1038/s41467-021-26821-8. Nat Commun. 2021. PMID: 34789716 Free PMC article.
The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics.
Tang M, Abbas HA, Negrao MV, Ramineni M, Hu X, Hubert SM, Fujimoto J, Reuben A, Varghese S, Zhang J, Li J, Chow CW, Mao X, Song X, Lee WC, Wu J, Little L, Gumbs C, Behrens C, Moran C, Weissferdt A, Lee JJ, Sepesi B, Swisher S, Cheng C, Kurie J, Gibbons D, Heymach JV, Wistuba II, Futreal PA, Kalhor N, Zhang J. Tang M, et al. Among authors: cheng c. Nat Commun. 2021 Dec 6;12(1):7081. doi: 10.1038/s41467-021-27341-1. Nat Commun. 2021. PMID: 34873156 Free PMC article.
Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy.
Xie F, Zhang J, Wang J, Reuben A, Xu W, Yi X, Varn FS, Ye Y, Cheng J, Yu M, Wang Y, Liu Y, Xie M, Du P, Ma K, Ma X, Zhou P, Yang S, Chen Y, Wang G, Xia X, Liao Z, Heymach JV, Wistuba II, Futreal PA, Ye K, Cheng C, Xia T. Xie F, et al. Among authors: cheng j, cheng c. Clin Cancer Res. 2020 Jun 15;26(12):2908-2920. doi: 10.1158/1078-0432.CCR-19-1744. Epub 2020 Jan 7. Clin Cancer Res. 2020. PMID: 31911545 Free PMC article.
An integrative ENCODE resource for cancer genomics.
Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. Zhang J, et al. Among authors: cheng c. Nat Commun. 2020 Jul 29;11(1):3696. doi: 10.1038/s41467-020-14743-w. Nat Commun. 2020. PMID: 32728046 Free PMC article.
9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy.
Han G, Yang G, Hao D, Lu Y, Thein K, Simpson BS, Chen J, Sun R, Alhalabi O, Wang R, Dang M, Dai E, Zhang S, Nie F, Zhao S, Guo C, Hamza A, Czerniak B, Cheng C, Siefker-Radtke A, Bhat K, Futreal A, Peng G, Wargo J, Peng W, Kadara H, Ajani J, Swanton C, Litchfield K, Ahnert JR, Gao J, Wang L. Han G, et al. Among authors: cheng c. Nat Commun. 2021 Sep 23;12(1):5606. doi: 10.1038/s41467-021-25894-9. Nat Commun. 2021. PMID: 34556668 Free PMC article.
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