Comprehensive analysis of neoantigens derived from structural variation across whole genomes from 2528 tumors von Shi, Yang, Jing, Biyang, Xi, Ruibin

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Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level von Wu, Yingcheng, Yang, Shuaixi, Ma, Jiaqiang, Chen, Zechuan, Song, Guohe, Rao, Dongning, Cheng, Yifei, Huang, Siyuan, Liu, Yifei, Jiang, Shan, Liu, Jinxia, Huang, Xiaowu, Wang, Xiaoying, Qiu, Shuangjian, Xu, Jianmin, Xi, Ruibin, Bai, Fan, Zhou, Jian, Fan, Jia, Zhang, Xiaoming, Gao, Qiang

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Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma von Cui, Yongping, Chen, Hongyan, Xi, Ruibin, Cui, Heyang, Zhao, Yahui, Xu, Enwei, Yan, Ting, Lu, Xiaomei, Huang, Furong, Kong, Pengzhou, Li, Yang, Zhu, Xiaolin, Wang, Jiawei, Zhu, Wenjie, Wang, Jie, Ma, Yanchun, Zhou, Yong, Guo, Shiping, Zhang, Ling, Liu, Yiqian, Wang, Bin, Xi, Yanfeng, Sun, Ruifang, Yu, Xiao, Zhai, Yuanfang, Wang, Fang, Yang, Jian, Yang, Bin, Cheng, Caixia, Liu, Jing, Song, Bin, Li, Hongyi, Wang, Yi, Zhang, Yingchun, Cheng, Xiaolong, Zhan, Qimin, Li, Yanhong, Liu, Zhihua

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Single-cell gene fusion detection by scFusion von Jin, Zijie, Huang, Wenjian, Shen, Ning, Li, Juan, Wang, Xiaochen, Dong, Jiqiao, Park, Peter J., Xi, Ruibin

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Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants von Xi, Ruibin, Lee, Semin, Xia, Yuchao, Kim, Tae-Min, Park, Peter J

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Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression von Song, Guohe, Shi, Yang, Zhang, Meiying, Goswami, Shyamal, Afridi, Saifullah, Meng, Lu, Ma, Jiaqiang, Chen, Yi, Lin, Youpei, Zhang, Juan, Liu, Yuming, Jin, Zijie, Yang, Shuaixi, Rao, Dongning, Zhang, Shu, Ke, Aiwu, Wang, Xiaoying, Cao, Ya, Zhou, Jian, Fan, Jia, Zhang, Xiaoming, Xi, Ruibin, Gao, Qiang

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Single-cell transcriptomic analysis suggests two molecularly subtypes of intrahepatic cholangiocarcinoma von Song, Guohe, Shi, Yang, Meng, Lu, Ma, Jiaqiang, Huang, Siyuan, Zhang, Juan, Wu, Yingcheng, Li, Jiaxin, Lin, Youpei, Yang, Shuaixi, Rao, Dongning, Cheng, Yifei, Lin, Jian, Ji, Shuyi, Liu, Yuming, Jiang, Shan, Wang, Xiaoliang, Zhang, Shu, Ke, Aiwu, Wang, Xiaoying, Cao, Ya, Ji, Yuan, Zhou, Jian, Fan, Jia, Zhang, Xiaoming, Xi, Ruibin, Gao, Qiang

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Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations von Chang, Jiang, Tan, Wenle, Ling, Zhiqiang, Xi, Ruibin, Shao, Mingming, Chen, Mengjie, Luo, Yingying, Zhao, Yanjie, Liu, Yun, Huang, Xiancong, Xia, Yuchao, Hu, Jinlin, Parker, Joel S., Marron, David, Cui, Qionghua, Peng, Linna, Chu, Jiahui, Li, Hongmin, Du, Zhongli, Han, Yaling, Tan, Wen, Liu, Zhihua, Zhan, Qimin, Li, Yun, Mao, Weimin, Wu, Chen, Lin, Dongxin

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Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes von Yang, Lixing, Luquette, Lovelace J., Gehlenborg, Nils, Xi, Ruibin, Haseley, Psalm S., Hsieh, Chih-Heng, Zhang, Chengsheng, Ren, Xiaojia, Protopopov, Alexei, Chin, Lynda, Kucherlapati, Raju, Lee, Charles, Park, Peter J.

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CCL15 Recruits Suppressive Monocytes to Facilitate Immune Escape and Disease Progression in Hepatocellular Carcinoma von Liu, Long‐Zi, Zhang, Zhao, Zheng, Bo‐Hao, Shi, Yang, Duan, Men, Ma, Li‐Jie, Wang, Zhi‐Chao, Dong, Liang‐Qing, Dong, Ping‐Ping, Shi, Jie‐Yi, Zhang, Shu, Ding, Zhen‐Bin, Ke, Ai‐Wu, Cao, Ya, Zhang, Xiao‐Ming, Xi, Ruibin, Zhou, Jian, Fan, Jia, Wang, Xiao‐Ying, Gao, Qiang

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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster von Karpen, Gary H, Park, Peter J, Kharchenko, Peter V, Alekseyenko, Artyom A, Schwartz, Yuri B, Minoda, Aki, Riddle, Nicole C, Ernst, Jason, Sabo, Peter J, Larschan, Erica, Gorchakov, Andrey A, Gu, Tingting, Linder-Basso, Daniela, Plachetka, Annette, Shanower, Gregory, Tolstorukov, Michael Y, Luquette, Lovelace J, Xi, Ruibin, Jung, Youngsook L, Park, Richard W, Bishop, Eric P, Canfield, Theresa P, Sandstrom, Richard, Thurman, Robert E, MacAlpine, David M, Stamatoyannopoulos, John A, Kellis, Manolis, Elgin, Sarah C. R, Kuroda, Mitzi I, Pirrotta, Vincenzo

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Detecting virus integration sites based on multiple related sequencing data by VirTect von Xia, Yuchao, Liu, Yun, Deng, Minghua, Xi, Ruibin

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Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes von Kim, Tae-Min, Xi, Ruibin, Luquette, Lovelace J, Park, Richard W, Johnson, Mark D, Park, Peter J

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TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing von Xia, Yuchao, Jin, Zijie, Zhang, Chengsheng, Ouyang, Linkun, Dong, Yuhao, Li, Juan, Guo, Lvze, Jing, Biyang, Shi, Yang, Miao, Susheng, Xi, Ruibin

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Publisher Correction: Single-cell transcriptomic analysis suggests two molecularly distinct subtypes of intrahepatic cholangiocarcinoma von Song, Guohe, Shi, Yang, Meng, Lu, Ma, Jiaqiang, Huang, Siyuan, Zhang, Juan, Wu, Yingcheng, Li, Jiaxin, Lin, Youpei, Yang, Shuaixi, Rao, Dongning, Cheng, Yifei, Lin, Jian, Ji, Shuyi, Liu, Yuming, Jiang, Shan, Wang, Xiaoliang, Zhang, Shu, Ke, Aiwu, Wang, Xiaoying, Cao, Ya, Ji, Yuan, Zhou, Jian, Fan, Jia, Zhang, Xiaoming, Xi, Ruibin, Gao, Qiang

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Systematic identification of synergistic drug pairs targeting HIV von Tan, Xu, Hu, Long, Luquette, Lovelace J, Gao, Geng, Liu, Yifang, Qu, Hongjing, Xi, Ruibin, Lu, Zhi John, Park, Peter J, Elledge, Stephen J

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Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion von Xi, Ruibin, Hadjipanayis, Angela G, Luquette, Lovelace J, Kim, Tae-Min, Lee, Eunjung, Zhang, Jianhua, Johnson, Mark D, Muzny, Donna M, Wheeler, David A, Gibbs, Richard A, Kucherlapati, Raju, Park, Peter J

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Global impact of somatic structural variation on the DNA methylome of human cancers von Zhang, Yiqun, Yang, Lixing, Kucherlapati, Melanie, Hadjipanayis, Angela, Pantazi, Angeliki, Bristow, Christopher A, Lee, Eunjung Alice, Mahadeshwar, Harshad S, Tang, Jiabin, Zhang, Jianhua, Seth, Sahil, Lee, Semin, Ren, Xiaojia, Song, Xingzhi, Sun, Huandong, Seidman, Jonathan, Luquette, Lovelace J, Xi, Ruibin, Chin, Lynda, Protopopov, Alexei, Park, Peter J, Kucherlapati, Raju, Creighton, Chad J

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Directly selecting cell-type marker genes for single-cell clustering analyses von Chen, Zihao, Wang, Changhu, Huang, Siyuan, Shi, Yang, Xi, Ruibin

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A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases von Zhang, Yiqun, Yang, Lixing, Kucherlapati, Melanie, Chen, Fengju, Hadjipanayis, Angela, Pantazi, Angeliki, Bristow, Christopher A., Lee, Eunjung A., Mahadeshwar, Harshad S., Tang, Jiabin, Zhang, Jianhua, Seth, Sahil, Lee, Semin, Ren, Xiaojia, Song, Xingzhi, Sun, Huandong, Seidman, Jonathan, Luquette, Lovelace J., Xi, Ruibin, Chin, Lynda, Protopopov, Alexei, Li, Wei, Park, Peter J., Kucherlapati, Raju, Creighton, Chad J.

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