Select Publications

  • R. Xue, Q. Zhang, Q. Cao, R. Kong, X. Xiang, H. Liu, M. Feng, F. Wang, J. Cheng, Z. Li, Q. Zhan, M. Deng, J. Zhu, Z. Zhang, N. Zhang. (2022) Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Nature, doi.org/10.1038/s41586-022-05400-x
  • B. Liu, Y. Zhang, D. Wang, X. Hu, and Z. Zhang. (2022) Single-cell meta-analyses reveal responses of tumor-reactive CXCL13+ T cells to immune-checkpoint blockade. Nature Cancer, 3:1123-1136
  • Z. Liu and Z. Zhang. (2022) Mapping cell types across human tissues. Science, 376(6594):695-696
  • Y. Liu, Q. Zhang, B. Xing, N. Luo, R. Gao, K. Yu, X. Hu, Z. Bu, J. Peng, X. Ren, Z. Zhang. (2022) Immune phenotypic linkage between colorectal cancer and liver metastasis. Cancer Cell, 40:424-437
  • B. Liu, X. Hu, K. Feng, R. Gao, Z. Xue, S. Zhang, Y. Zhang, E. Corse, Y. Hu, W. Han, and Z. Zhang. (2022) Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer. Nature Cancer, 3:108-121
  • C. Caldas, M. Rescigno, S. Turajlic, A. Madabhushi, Z. Zhang, P. Lito, C. E. Brown, K. Pantel, J. Haanen, N. Duma. (2022) With one eye on the future. Cancer Cell, 40(3):221-225.
  • J. Ai, J. Guo, H. Zhang, Y. Zhang, H. Yang, K. Lin, J. Song, Z. Fu, M. Fan, Q. Zhang, H. Wang, Y. Zhao, Z. He, A. Cui, Y. Zhou, J. Wu, M. Zhou, G. Yuan, B. Kang, N. Zhao, Y. Xu, M. Zhu, Y. Wang, Z. Zhang, N. Jiang, C. Qiu, C. Xu, and W. Zhang. (2022) Cellular basis of enhanced humoral immunity to SARS-CoV-2 upon homologous or heterologous booster vaccination analyzed by single-cell immune profiling. Cell Discovery, 8, 114. doi.org/10.1038/s41421-022-00480-5
  • B. Yang, Z. Zhang, X. Chen, X. Wang, S. Qin, L. Du, C. Yang, L. Zhu, W. Sun, Y. Zhu, Q. Zheng, S. Zhao, Q. Wang, L. Zhao, Y. Lin, J. Huang, F. Wu, L. Lu, F. Wang, W. Zheng, X. Zhou, X. Zhao, Z. Wang, X. Sun, Y. Ye, S. Wang, Z. Li, H. Qi, Z. Zhang, D. Kuang, L. Zhang, Z. Shen, W. Liu. (2022) An Asian-specific variant in human IgG1 represses colorectal tumorigenesis by shaping the tumor microenvironment. Journal of Clinical Investigation. e153454. doi: 10.1172/JCI153454
  • C. Zhang, J. Li, Y. Cheng, F. Meng, JW. Song, X. Fan, H. Fan, J. Li, Y.L. Fu, M.J. Zhou, W. Hu, S.Y. Wang, Y.J. Fu, J.Y. Zhang, R.N. Xu, M. Shi, X. Hu, Z. Zhang, X. Ren, and F. S. Wang. (2022) Single-cell RNA sequencing reveals intrahepatic and peripheral immune characteristics related to disease phases in HBV-infected patients. Gut. https://doi.org/10.1136/gutjnl-2021-325915
  • L. Guo, X. Yi, L. Chen, T. Zhang, H. Guo, Z. Chen, J. Cheng, Q. Cao, H. Liu, C. Hou, L. Qi, Z. Zhu, Y. Liu, R. Kong, C. Zhang, X. Zhou, Z. Zhang, T. Song, R. Xue, and N. Zhang. (2022) Single-Cell DNA Sequencing Reveals Punctuated and Gradual Clonal Evolution in Hepatocellular Carcinoma. Gastroenterology. 162(1):238-252
  • L. Zheng, S. Qin, W. Si, A. Wang, B. Xing, R. Gao, X. Ren, L. Wang, X. Wu, J. Zhang, N. Wu, N. Zhang, H. Zheng, H. Ouyang, K. Chen, Z. Bu, X. Hu, J. Ji, and Zhang. (2021) Pan-cancer single cell landscape of tumor-infiltrating T cells. Science, 374(6574):abe6474
  • Y. Zhang, H. Chen, H. Mo, X. Hu, R. Gao, Y. Zhao, B. Liu, L. Niu, X. Sun, X. Yu, Y. Wang, Q. Chang, T. Gong, X. Guan, T. Hu, T. Qian, B. Xu, F. Ma, Z. Zhang, and Z. Liu. (2021) Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer. Cancer Cell. 39(12):1578-1593.
  • S. Cheng, Z. Li, R. Gao, B. Xing, Y. Gao, Y. Yang, S. Qin, L. Zhang, H. Ouyang, P. Du, L. Jiang, B. Zhang, Y. Yang, X. Wang, X. Ren, J. Bei, X. Hu, Z. Bu, J. Ji, and Z. Zhang. (2021) A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells. Cell, 184(3):792-809
  • M. O. Li, N. Wolf, D. H. Raulet, L. Akkari, M. J. Pittet, P. C. Rodriguez, R. N. Kaplan, A. Munitz, Z. Zhang, S. Cheng, and N. Bhardwaj. (2021) Innate immune cells in the tumor microenvironment. Cancer Cell, 39(6):725-729
  • Q. Lu, J. Liu, S. Zhao, M. F. G. Castro, M. Laurent-Rolle, J. Dong, X. Ran, P. Damani-Yokota, H. Tang, T. Karakousi, J. Son, M. E. Kaczmarek, Z. Zhang, S. T. Yeung, B. T. McCune, R. E. Chen, F. Tang, X. Ren, X. Chen, J. C.C. Hsu, M. Teplova, B. Huang, H. Deng, Z. Long, T. Mudianto, S. Jin, P. Lin, J. Du, R. Zang, T. T. Su, A. Herrera, M. Zhou, R. Yan, J. Cui, J. Zhu, Q. Zhou, T. Wang, J. Ma, S. B. Koralov, Zhang, I. Aifantis, L. N. Segal, M. S. Diamond, K. M. Khanna, K. A. Stapleford, P. Cresswell, Y. Liu, S. Ding, Q.Xie, and J. Wang. (2021) SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through C-type lectin receptors and Tweety family member 2. Immunity, 54(6): 1304–1319
  • S. Mizuno, R. Yamaguchi, T. Hasegawa, S. Hayashi, M. Fujita, F. Zhang, Y. Koh, S-Y Lee, S-S Yoon, E. Shimizu, M. Komura, A. Fujimoto, M. Nagai, M. Kato, H. Liang, S. Miyano, Z. Zhang, H. Nakagawa and S. Imoto (2021) Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories. Scientific Reports, 11: 15713
  • D. Wang, S. Hou, L. Zhang, X. Wang, B. Liu, and Z. Zhang. (2021) iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks. Genome Biology, 22:63
  • X. Ren, L. Zhang, Y. Zhang, Z. Li, N. Siemers, and Z. Zhang. (2021) Insights gained from single-cell analysis of immune cells in the tumor microenvironment. Annual Review of Immunology, 15:583-609
  • L. Zheng and Zhang. (2021) Decoding the genetic basis of anti-tumor immunity. Immunity, 54:199-201
  • X. Ren, W. Wen, X. Fan, W. Hou, B. Su, P.i Cai, J. Li, Y. Liu, F. Tang, F. Zhang, Y. Yang, J. He, W. Ma, J. He, P. Wang, … P. Zhou, Q. Jiang, Z. Huang, J-X Bei, L. Wei, X-W Bian, X. Liu, T Cheng, X. Li, P. Zhao, F-S Wang, H. Wang, B. Su, Z. Zhang, K. Qu, X. Wang, J. Chen, R. Jin, and Zhang, (2021) COVID-19 immune features revealed by a large-scale single cell transcriptome atlas, Cell, 184:1895-1913
  • Y. Liu, S. He, X-L Wang, W. Peng, Q-Y Chen, D-M Chi, J-R Chen, B-W Han, G-W Lin, Y-Q Li, Q-Y Wang, R-J Peng, P-P Wei, X Guo, B. Li, X. Xia, H-Q Mai, X-D Hu, Z. Zhang, Y-X Zeng, and J-X Bei. (2021) Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution. Nature Communications. 12(1):741.
  • D. Bhatt, B. Kang, D. Sawant, L. Zheng, K. Perez, Z. Huang, L. Sekirov, D. Wolak, J. Y. Huang, X. Liu, J. DeVoss, P. S. Manzanillo, N. Pierce, Z. Zhang, A. Symons, W. Ouyang. (2021) STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets. Journal of Experimental Medicine, 218(6):e20201329
  • F. Zhang, H. Bai, R. Gao, K. Fei, J. Duan, Z. Zhang, J. Wang, and X. Hu. (2021) Dynamics of peripheral T cell clones during PD-1 blockade in non-small cell lung cancer. Cancer Immunology, Immunotherapy. 69(12):2599-2611
  • M. Rao, X. Wang, G. Guo, L. Wang, S. Chen, P. Yin, K. Chen, L. Chen, Z. Zhang, X. Chen, X. Hu, S. Hu, and J. Song. (2021) Resolving the intertwining of inflammation and fibrosis in human heart failure at single-cell level. Basic Research Cardiology. 116(1):55.
  • X. Wang, Y. He, Q. Zhang, X. Ren, and Z. Zhang. (2021) Direct comparative analysis of 10X Genomics Chromium and Smart-seq2. Genome, Proteome and Bioinformatics, 19:253-266
  • J. Li, H. Y. Comeau, Z. Zhang, and X. Ren. (2020) Landscape of transcript isoforms in single T cells infiltrating in non-small cell lung cancer, Journal of Genetics and Genomics, 47, 373–388
  • B. Liu, C. Li, Z. Li, D. Wang, X. Ren, and Z. Zhang. (2020) An entropy-based metric for assessing the purity of single cell populations, Nature Communications, 11:3155
  • X. Ren, G. Zhong, Q. Zhang, L. Zhang, Y. Sun, and Z. Zhang. (2020) Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly, Cell Research, 30:763-778
  • Q. Zhang and Z. Zhang. (2020) Stepwise immune alterations in multiple myeloma progression. Nature Cancer, 1:477-479
  • L. Zhang, Z. Li, K. M. Skrzypczynska, Q. Fang, W. Zhang, S. A. O’Brien, Y. He, L. Wang, Q. Zhang, A. Kim, R. Gao, J. Orf, T. Wang, D. Sawant, J. Kang, D. Bhatt, D. Lu, C-M Li, A. Rapaport, K. Perez, Y. Ye, S. Wang, X. Hu, X. Ren, W. Ouyang, Z. Shen, J. G. Egen, Z Zhang, and X. Yu. (2020) Single-cell analyses inform mechanisms of myeloid-targeted therapies in colon cancer. Cell, 181:442-459
  • C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, C. Chen, X. Ren, and Z. Zhang. (2020) SciBet as a portable and fast single cell type identifier. Nature Communications, 11:1818
  • PCAWG Transcriptome Core Group, C. Calabrese, N. R. Davidson, D. Demircioğlu, N. A. Fonseca, Y. He, A. Kahles, K-V Lehmann, F. Liu, Y. Shiraishi, C. M. Soulette, L. Urban, L. Greger, S. Li, D. Liu, M. D. Perry, Q. Xiang, F. Zhang, J. Zhang, P. Bailey, S. Erkek, K. A. Hoadley, Y. Hou, M. R. Huska, H. Kilpinen, J. O. Korbel, M. G. Marin, J. Markowski, T. Nandi, Q. Pan-Hammarström, C. S. Pedamallu, R. Siebert, S. G. Stark, H. Su, P. Tan, S. M. Waszak, C. Yung, S. Zhu, P. Awadalla, C. J. Creighton, M. Meyerson, B. F. Ouellette, K. Wu, H. Yang, PCAWG Transcriptome Working Group, A. Brazma, A. N. Brooks, J. Göke, G. Rätsch, R. F. Schwarz, O. Stegle, Zhang & PCAWG Consortium. (2020) Genomic basis for RNA alterations in cancer. Nature, 578:129-136
  • The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature, 578:82–93
  • Y. Zhang, F. Chen, N. A. Fonseca, Y. He, M. Fujita, H. Nakagawa, Z. Zhang, A. Brazma; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, C. J. Creighton; PCAWG Consortium. (2020) High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature Communications, 11:736
  • R. Bernards, E. Jaffee, J. A. Joyce, S. W. Lowe, E. R. Mardis, S. J. Morrison, K. Polyak, C. L. Sears, K. H. Vousden, and Z. Zhang. (2020) A roadmap for the next decade in cancer research. Nature Cancer, 1:12-17
  • R. Yang, S. Cheng, N. Luo, R. Gao, K. Yu, B. Kang, L. Wang, Q. Zhang, Q. Fang, L. Zhang, C. Li, A. He, X. Hu, J. Peng, X. Ren, and Zhang. (2020) Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis. Genome Biology, 21:2
  • Y. Zhang and Z. Zhang. (2020) The history and advances in cancer immunotherapy: understanding the characteristics of tumor-infiltrating immune cells and their therapeutic implications. Cellular & Molecular Immunology, 17(8):807-821
  • L. Che, W. Chi, Y. Qiao, J. Zhang, X. Song, Y. Liu, L. Li, J. Jia, M. G. Pilo, J. Wang, A. Cigliano, Z. Ma, W. Kuang, Z. Tang, Z. Zhang, G. Shui, S. Ribback, F. Dombrowski, M. Evert, R. M. Pascale, C. Cossu, G. M. Pes, T. F. Osborne, D. F. Calvisi, X. Chen, and L. Chen. (2020) Cholesterol biosynthesis supports the growth of hepatocarcinoma lesions depleted of fatty acid synthase in mice and humans. Gut, 69:177-186
  • F. Liu, Y. Zhang, L. Zhang, Z. Li, Q. Fang, R. Gao, and Z. Zhang. (2019) Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data. Genome Biology, 20:242
  • Q. Zhang, Y. He, N. Luo, S. J. Patel, Y. Han, R. Gao, M. Modak, S. Carotta, C. Haslinger, D. Kind, G. W. Peet, G. Zhong, S. Lu, W. Zhu, Y. Mao, M. Xiao, M. Bergmann, X. Hu, S. P. Kerkar, A. B. Vogt, S. Pflanz, K. Liu, J. Peng, X. Ren, and Z. Zhang (2019) Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell, 179:829-845.
  • H. Yang, L. Xia, J. Chen, S. Zhang, V. Martin, Q. Li, S. Lin, J. Chen, J. Calmette, M. Lu, L. Fu, J. Yang, Z. Pan, K. Yu, J. He, E.Morand, G. Schlecht-Louf, R. Krzysiek, L. Zitvogel, B. Kang, Z. Zhang, A. Leader, P. Zhou, L. Lanfumey, M. Shi, G. Kroemer, and Y. Ma. (2019) Stress–glucocorticoid–TSC22D3 axis compromises therapy-induced antitumor immunity. Nature Medicine, 26:1428-1441.
  • X. Ren and Z. Zhang. (2019) Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing. Advances in Immunology, 144:217-245
  • Z. Tang, B. Kang, C. Li, T. Chen, and Z. Zhang. (2019) Identification of transcriptional isoforms associated with survival in cancer patients. Journal of Genetics and Genomics, 46: 413-421.
  • R. Xu, S. Yu, D. Zhu, X. Huang, Y. Xu, Y. Lao, Y. Tian, J. Zhang, Z. Tang, Z. Zhang, J. Yi, H. Zhu, and X. Zheng. (2019) hCINAP regulates the DNA-damage response and mediates the resistance of acute myelocytic leukemia cells to therapy. Nature Communications, 10: 3812.
  • Y. Zhang, L. Zheng, L. Zhang, X. Hu, X. Ren, and Z. Zhang (2019) Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients. Scientific Data, 6:131.
  • Kim, C-J Han, I. Driver, A. Olow, A. K. Sewell, Zhang, W. Ouyang, J. G. Egen, and X. Yu. (2019) LILRB1 blockade enhances bispecific T cell engager antibody-induced tumor cell killing by effector CD8+ T cells. The Journal of Immunology, 203:1076-1087
  • Z. Tang, B. Kang, C. Li, T. Chen, and Z. Zhang. (2019) GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Research, 47:W556-W560
  • L. Zhang and Z. Zhang. (2019) Recharacterizing tumor-infiltrating lymphocytes by single-cell RNA sequencing. Cancer Immunology Research, 7:1040-1046.
  • R. Xue, L. Chen, C. Zhang, M. Fujita, R. Li, S.-M. Yan, C. K. Ong, X. Liao, Q. Gao, S. Sasagawa, Y. Li, J. Wang, H. Guo, Q.-T. Huang, Q. Zhong, J. Tan, L. Qi, W. Gong, Z. Hong, M. Li, J. Zhao, T. Peng, Y. Lu, K. H. T. Lim, A. Boot, A. Ono, K. Chayama, Z. Zhang, S. G. Rozen, B. T. Teh, X. W. Wang, H. Nakagawa, M.-S. Zeng, F. Bai, and N. Zhang. (2019) Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes. Cancer cell, 35:932-947
  • X. Ren, L. Zheng, and Z. Zhang. (2019) SSCC: a computational framework for rapid and accurate clustering of large-scale single cell RNA-seq data. Genome, Proteome and Bioinformatics, 17:201-210
  • L. Zhang, X. Yu, L. Zheng, Y. Zhang, Y. Li, Q. Fang, R. Gao, B. Kang, Q. Zhang, J.Y. Huang, H. Konno, X. Guo, Y. Ye, S. Gao, S. Wang, X. Hu, X. Ren, Z. Shen, W. Ouyang, and Zhang. (2018) Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature, 564:268-272
  • X. Guo, Y. Zhang, L. Zheng, C. Zheng, J. Song, Q. Zhang, B. Kang, Z. Liu, L. Jin,R. Xing, R. Gao, L. Zhang, M. Dong, X. Hu, X. Ren, D. Kirchhoff, H. G. Roider, T. Yan, and Z. Zhang. (2018) Global characterization of T cells in non-small cell lung cancer by single-cell sequencing. Nature Medicine, 24:978-985
  • X. Ren, B. Kang, and Z. Zhang. (2018) Understanding tumor ecosystems by single-cell sequencing: promises and limitations. Genome Biology, 19:211
  • Z. Wang, J. Zhao, G. Wang, F. Zhang, Z. Zhang, F. Zhang, Y. Zhang, H. Dong, X. Zhao, J. Duan, H. Bai, Y. Tian, R. Wan, M. Han, Y. Cao, L. Xiong, L. Liu, S. Wang, S. Cai, T.S.K. Mok, and J. Wang. (2018) Comutations in DNA damage response pathways serve as potential biomarkers for immune checkpoint blockade. Cancer Research, 78(22):6486-6496
  • C. Yang, W. Zang, Z. Tang, Y. Ji, A. Luo, B. Hu, Zhang, Z. Liu, and X. Zheng. (2018) A20/TNFAIP3 regulates the DNA damage response and mediates tumor cell resistance to DNA-damaging therapy. Cancer Research, 78(4):1069-1082
  • C. Zheng, L. Zheng, J.-K. Yoo, H. Guo, Y. Zhang, X. Guo, B. Kang, R. Hu, J. Y. Huang, Q. Zhang, Z. Liu, M. Dong, X. Hu, W. Ouyang, J. Peng, and Zhang. (2017) Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell, 169(7), 1342–1356
  • Z. Tang, C. Li, B. Kang, G. Gao, C. Li, and Z. Zhang. (2017) GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Research, 45(W1):W98-W102
  • N. A. Fonseca, Y. He, L. Greger, A. Brazma, and Z. Zhang. (2017) Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer. bioRxiv, doi:https://doi.org/10.1101/148684
  • Y. Ji, C. Yang, Z. Tang, Y. Yang, Y. Tian, H. Yao, X. Zhu, Z. Zhang, J. Ji, and X. Zheng. (2017) Adenylate kinase hCINAP determines self-renewal of colorectal cancer stem cells by facilitating LDHA phosphorylation. Nature Communications, 8:15308, doi: 10.1038/ncomms15308
  • X. Hu and Z. Zhang. (2016) Understanding the genetic mechanisms of cancer drug resistance using genomic approaches. Trends in Genetics, 32(2):127-37
  • R. Xue, R. Li, H. Guo, L. Guo, Z. Su, X. Ni, L. Qi, T. Zhang, Q. Li, Z. Zhang, X.S. Xie, F. Bai, and N. Zhang. (2016) Variable extent of intra-tumor heterogeneity revealed by genomic sequencing of multiple lesions in patients with hepatocellular carcinoma. Gastroenterology, 150(4):998-1008
  • Z. Wang, Z. Shen, Z. Li, J. Duan, S. Fu, Z. Liu, H. Bai, Z. Zhang, J. Zhao, X. Wang, and J. Wang (2015) Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations. Proc Natl Acad Sci U S A. 112:9990-5
  • F. Gnad, S. Doll, G. Manning, D. Arnott, and Z. Zhang (2015) Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics, 16:S5
  • C. Klijn, S. Durinck, E. Stawiski, P. M. Haverty, Z. Jiang, H. Liu, J. Degenhardt, O. Mayba, F. Gnad, J. Liu, G. Pau, J. Reeder, Y. Cao, K. Mukhyala, S. K. Selvaraj, M. Yu, G. J. Zynda, M. J. Brauer, T. D. Wu, R. C. Gentleman, G. Manning, R. L. Yauch, R. Bourgon, D. Stokoe, Z. Modrusan, R. M. Neve, F. J. de Sauvage, J. Settleman, S. Seshagiri, and Zhang (2015) A comprehensive transcriptional portrait of human cancer cell lines. Nature Biotechnology, 33:305-315
  • S. Jhunjhunwala, Z. Jiang, E. W. Stawiski, F. Gnad, J. Liu, O. Mayba, P. Du, J. Diao, C. Santos, K-F Wong, Z. Gao, Y. Li, S. Johnson, H. M. Stern, T. D. Wu, S. B. Kapadia, Z. Modrusan, J. M. Luk, D. M. French, S. Seshagiri, and Z. Zhang (2014) Diverse modes of genomic alterations in hepatocellular carcinoma. Genome Biology, 15:436
  • J. Liu, M. McCleland, E. Stawiski, F. Gnad, P. M. Haverty, S. Durinck, Y-J. Chen, C. Klijn, O. Mayba, S. Jhunjhunwala, M. Lawrence, H. Liu, Y. Wan, V. Chopra, W. Yuan, C. Ha, H. Gilbert, J. Reeder, G. Pau, J. Stinson, H. Stern, G. Manning, T. D. Wu, R. Neve, F. J. de Sauvage, Z. Modrusan, S. Seshagiri, R. Firestein, and Z. Zhang (2014), Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer. Nature Communications, 5:3830
  • O. Mayba, H. N. Gilbert, J. Liu, P. M. Haverty, S. Jhunjhunwala, Z. Jiang, C. Watanabe, and Zhang (2014) Allele specific expression detection in cancer tissues and cell lines by MBASED. Genome Biology, 15:405
  • G. Lee, P. M. Haverty, L. Li, N. Kljavin, R. Bourgon, J. Lee, H. M. Stern, Z. Modrusan, S. Seshagiri, Z. Zhang, D. Davis, D. Stokoe, J. Settleman, F. J. de Sauvage, and R. M. Neve (2014) Comparative oncogenomics identifies PSMB4 and SHMT2 as potential cancer driver genes. Cancer Research, 74:3114-26
  • A. Adler, V. Chopra, M.L. McCleland, S. Hussain, G. Quinones, Z. Modrusan, S. Seshagiri, E. Torres, B. Haley, Zhang, E.M. Blackwood, M. Singh, M. Junttila, J. Stephan, E. Fearson, Z. Jiang, and R. Firestein. (2014) An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Genes and Development, 28:1068-84
  • O. Mayba, F. Gnad, F. Zhang, K. Walter, P. Du, M. A. Huntley, Z. Jiang, J. Liu, P. M. Haverty, R. Li, M. Peyton, J. D. Minna, Y. Li, D. S. Shames, and Zhang (2014) Integrative analysis of two cell lines derived from a non-small-lung cancer patient – a panomics approach. Pac Symp Biocomput. 2014:75-86
  • W. Yuan, E. Stawiski, V. Janakiraman, E. Chan, S. Durinck, K. Edgar, N. M. Kljavin, C. S. Rivers, F. Gnad, M. Roose-Girma, P. M. Haverty, G. Fedorowicz, S. Heldens, R.H. Soriano, Z. Zhang, J. Wallin, L. Johnson, M. Merchant, Z. Modrusan, H. Stern, and S. Seshagiri (2013) Conditional activation of PIK3CA (H1047R) in a knock-in mouse promotes mammary tumorigenesis and emergence of mutations. Oncogene, 32:318-326
  • Gnad F, Baucom A, Mukhyala K, Manning G, and Zhang Z (2013) Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC Genomics, 14:S7.
  • T. Hwang, G. Atluri, R. Kuang, V. Humar, T. Starr, K.AT.Siverstein, P.M. Haverty, Z. Zhang, and J. Liu (2013), Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers. BMC Genomics, 14:440
  • Z. Zhang (2012), Genomic landscape of liver cancer. Nature Genetics, 44: 1075-1077
  • J. Liu, W. Lee, Z. Chen, Z. Jiang, S. Jhunjhunwala, P. M Haverty, F. Gnad, Y. Guan, H. Gilbert, J. Stinson, C. Klijn, J. Guillory, D. Bhatt, S. Vartanian, K. Walter, J. Chan, P. Dijkgraaf, S. Johnson, J. Koeman, J. Minna, A. Gazdar, H. M. Stern, K. P. Hoeflich, T. D. Wu, F. J. de Sauvage, R. C. Gentleman, R. M. Neve, D. Stokoe, Z. Modrusan, S. Seshagiri, D. S. Shames, Z. Zhang (2012) Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research, 22:2315-2327
  • M. Rudin, S. Durinck, E. W. Stawiski, J. T. Poirier, Z. Modrusan, D. Shames, E. A. Bergbower, Y. Guan, J. Shin, J. Guillory, C. S. Rivers, C. Foo, D. Bhatt, J. Stinson, F. Gnad, P. M. Haverty, R. Gentleman, S. Chaudhuri, V. Janakiraman, B. S. Jaiswal, C. Parikh, W. Yuan, Z. Zhang, H. Koeppen, T. D. Wu, H. M Stern, R. L. Yauch, K. E. Huffman, D. D. Paskulin, P. B. Illei, M. Varella-Garcia, A. F. Gazdar, F. J. de Sauvage, R. Bourgon, J. D. Minna, M. V. Brock and S. Seshagiri (2012) Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small cell lung cancer. Nature Genetics, 44: 1111-1116
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