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Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group; Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group; Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. PCAWG Transcriptome Core Group, et al. Among authors: liu f, liu d. Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5. Nature. 2020. PMID: 32025019 Free PMC article.
Frequent alterations in cytoskeleton remodelling genes in primary and metastatic lung adenocarcinomas.
Wu K, Zhang X, Li F, Xiao D, Hou Y, Zhu S, Liu D, Ye X, Ye M, Yang J, Shao L, Pan H, Lu N, Yu Y, Liu L, Li J, Huang L, Tang H, Deng Q, Zheng Y, Peng L, Liu G, Gu X, He P, Gu Y, Lin W, He H, Xie G, Liang H, An N, Wang H, Teixeira M, Vieira J, Liang W, Zhao X, Peng Z, Mu F, Zhang X, Xu X, Yang H, Kristiansen K, Wang J, Zhong N, Wang J, Pan-Hammarström Q, He J. Wu K, et al. Among authors: liu l, liu g, liu d. Nat Commun. 2015 Dec 9;6:10131. doi: 10.1038/ncomms10131. Nat Commun. 2015. PMID: 26647728 Free PMC article.
RED-ML: a novel, effective RNA editing detection method based on machine learning.
Xiong H, Liu D, Li Q, Lei M, Xu L, Wu L, Wang Z, Ren S, Li W, Xia M, Lu L, Lu H, Hou Y, Zhu S, Liu X, Sun Y, Wang J, Yang H, Wu K, Xu X, Lee LJ. Xiong H, et al. Among authors: liu x, liu d. Gigascience. 2017 May 1;6(5):1-8. doi: 10.1093/gigascience/gix012. Gigascience. 2017. PMID: 28328004 Free PMC article.
Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression.
Ren S, Wei GH, Liu D, Wang L, Hou Y, Zhu S, Peng L, Zhang Q, Cheng Y, Su H, Zhou X, Zhang J, Li F, Zheng H, Zhao Z, Yin C, He Z, Gao X, Zhau HE, Chu CY, Wu JB, Collins C, Volik SV, Bell R, Huang J, Wu K, Xu D, Ye D, Yu Y, Zhu L, Qiao M, Lee HM, Yang Y, Zhu Y, Shi X, Chen R, Wang Y, Xu W, Cheng Y, Xu C, Gao X, Zhou T, Yang B, Hou J, Liu L, Zhang Z, Zhu Y, Qin C, Shao P, Pang J, Chung LWK, Xu J, Wu CL, Zhong W, Xu X, Li Y, Zhang X, Wang J, Yang H, Wang J, Huang H, Sun Y. Ren S, et al. Among authors: liu l, liu d. Eur Urol. 2018 Mar;73(3):322-339. doi: 10.1016/j.eururo.2017.08.027. Epub 2017 Sep 18. Eur Urol. 2018. PMID: 28927585
The genomic landscape of Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma.
Hong S, Liu D, Luo S, Fang W, Zhan J, Fu S, Zhang Y, Wu X, Zhou H, Chen X, Chen G, Zhang Z, Zheng Q, Li X, Chen J, Liu X, Lei M, Ye C, Wang J, Yang H, Xu X, Zhu S, Yang Y, Zhao Y, Zhou N, Zhao H, Huang Y, Zhang L, Wu K, Zhang L. Hong S, et al. Among authors: liu x, liu d. Nat Commun. 2019 Jul 16;10(1):3108. doi: 10.1038/s41467-019-10902-w. Nat Commun. 2019. PMID: 31311932 Free PMC article.
Heterogeneous immunogenomic features and distinct escape mechanisms in multifocal hepatocellular carcinoma.
Dong LQ, Peng LH, Ma LJ, Liu DB, Zhang S, Luo SZ, Rao JH, Zhu HW, Yang SX, Xi SJ, Chen M, Xie FF, Li FQ, Li WH, Ye C, Lin LY, Wang YJ, Wang XY, Gao DM, Zhou H, Yang HM, Wang J, Zhu SD, Wang XD, Cao Y, Zhou J, Fan J, Wu K, Gao Q. Dong LQ, et al. J Hepatol. 2020 May;72(5):896-908. doi: 10.1016/j.jhep.2019.12.014. Epub 2019 Dec 27. J Hepatol. 2020. PMID: 31887370
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group; Creighton CJ; PCAWG Consortium. Zhang Y, et al. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w. Nat Commun. 2020. PMID: 32024823 Free PMC article.
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