Publications

(* correspondence authors)

  • C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, C. Chen, X. Ren*, and Z. Zhang*. SciBet as a portable and fast single cell type identifier. Nature Communication (accepted)
  • 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*, Z. 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 Communication, 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 Z. 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
  • 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 Z. 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
  • 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.
  • 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.
  • A. Kim, C-J Han, I. Driver, A. Olow, A. K. Sewell, Z. 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. 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. (2019) Cholesterol biosynthesis supports the growth of hepatocarcinoma lesions depleted of fatty acid synthase in mice and humans. Gut, doi:10.1136/gutjnl-2018-317581
  • 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
  • C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, X. Ren and Z. Zhang. (2019) SciBet: a fast classifier for cell type identification using single cell RNA sequencing data. bioRxiv, doi: http://dx.doi.org/10.1101/645358
  • 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 Z. 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
  • C. Yang, W. Zang, Z. Tang, Y. Ji, A. Luo, B. Hu,Z. 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
  • S. Mizuno, R. Yamaguchi, T. Hasegawa, S. Hayashi, M.i 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*. (2018) Immuno-genomic Pan-cancer Landscape Reveals Diverse Immune Escape Mechanisms and Immuno-Editing Histories. bioRxiv, doi: https://doi.org/10.1101/285338
  • PCAWG Transcriptome Core Group, C. Calabrese, N. R. Davidson, N. A. Fonseca, Y. He, A.Kahles, K-V Lehmann, F. Liu, Y. Shiraishi, C.M. Soulette, L. Urban, D. Demircioğlu, L. Greger, S. Li, D. Liu, M.D. Perry, L. Xiang, F. Zhang, J. Zhang, P. Bailey, S. Erkek, K.A. Hoadley, Y. Hou, 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, PCAWG Transcriptome Working Group, P. Awadalla, C. Creighton, M.Meyerson, B.F. Ouellette, K. Wu, H. Yang, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, A. Brazma*, A.N. Brooks*, J. Göke*, G. Rätsch*, R.F. Schwarz*, O. Stegle*, and Z. Zhang*. (2018) Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types. bioRxiv, doi: https://doi.org/10.1101/183889
  • 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 Z. Zhang*. (2017) Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell, 169(7), 1342–1356
  • C. Calabrese, K-V Lehmann, L. Urban, F. Liu, S. Erkek, N. Fonseca, A. Kahles, L. H. Kilpinen-Barrett, J. Markowski, PCAWG-3, S. Waszak, J. Korbel, Z. Zhang, A. Brazma*, G. Raetsch*, R. Schwarz*, and O. Stegle*. (2017) Assessing the Gene Regulatory Landscape in 1,188 Human Tumors. bioRxiv, doi: https://doi.org/10.1101/225441
  • 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 Communication, 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 Z. 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 Communication, 5:3830
  • O. Mayba, H. N. Gilbert, J. Liu, P. M. Haverty, S. Jhunjhunwala, Z. Jiang, C. Watanabe, and Z. 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, Z. 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 Z. 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
  • C. 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
  • S. Seshagiri, E. Stawiski, S. Durinck, Z. Modrusan, E. Storm, C. B. Conboy, S. Chaudhuri, Y. Guan, V. Janakiraman, B. S. Jaiswal, J. Guillory, C. Ha, G. J. P. Dijkgraaf, J. Stinson, F. Gnad, M. Huntley, J. D. Degenhardt, P. M. Haverty, R. Bourgon, W. Wang, H. Koeppan, R. Gentleman, T. K. Starr, Z. Zhang, D. A. Largaespada, T. D. Wu and F. J. de Sauvage (2012) Recurrent R-spondin fusions in colon cancer. Nature, 488, 660–664
  • Z. Jiang*, S. Jhunihunwala*, J. Liu, P. Haverty, K. Pant, M. I. Kennemer, P. Carnevali, Y. Guan, J. Stinson, P. Dijkgraaf, J. Rae, S. Johnson, C. Watanabe, J. Diao, S. Kapadia, F. de Sauvage, R. Gentleman, H. Stern, S. Seshagiri, Z. Modrusan, D. Ballinger, Z. Zhang (2012) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Research, 22:593-601 (cover article)
  • W. Lee, Z. Jiang, J. Liu, P. M. Haverty, Y. Guan, J. Stinson, P. Yue, Y. Zhang, K. P. Pant, D. Bhatt, C. Ha, S. Johnson., M. I. Kennemer, S. Mohan, I. Nazarenko, C. Watanabe, A. B. Sparks, D. S. Shames, R. Gentleman, F. J. de Sauvage, H. Stern, A. Pandita, D. G. Ballinger, R. Drmanac, Z. Modrusan, S. Seshagiri, and Z. Zhang (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature, 465:473-477
  • Z. Kan, B. S. Jaiswal, J. Stinson, V. Janakiraman, D. Bhatt, H. M. Stern, P. Yue, P. M. Haverty, R. Bourgon, J. Zheng, M. Moorhead, S. Chaudhuri, L. P. Tomsho, B. A. Peters, K. Pujara, S. Cordes, D. P. Davis, V. E. Carlton, W. Yuan, L. Li, W. Wang, C. Eigenbrot, J. S. Kaminker, D. A. Eberhard, P. Waring, S. C. Schuster, Z. Modrusan, Z. Zhang, D. Stokoe, F. J. de Sauvage, M. Faham and S. Seshagiri. (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature, 466: 869-873
  • P. Yue, J. S. Kaminker, W. F. Forrest, S. Lohr, Z. Zhang and G. Cavet (2010) Inferring the functional effects of mutation through clusters of mutations in homologous proteins. Human Mutation, 31 (3): 264-271
  • W. Lee, Y. Zhang, K. Mukhyala, R. Lazarus and Z. Zhang. (2009) Bi-directional SIFT predicts a subset of activating mutations. PLoS ONE, 4 (12): e8311. doi:10.1371/journal.pone.0008311
  • W. Lee, P. Yue, and Z. Zhang. (2009) Analytical methods for inferring functional effects of single base-pair substitutions in human cancers. Human Genetics, 126:481-498
  • L. S. Hon, Y. Zhang, J. S. Kaminker, and Z. Zhang. (2009) Computational prediction of the functional effects of amino acid substitutions in signal peptides using a model-based approach. Human Mutation, 30 (1): 99-106
  • P. M. Haverty, L. S. Hon, J. S. Kaminker, J. Chant*, and Z. Zhang*. (2009) High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Medical Genomics, 2:21
  • H. Jin, R. Yang, Z. Zheng, M. Romero, J. Ross, H. Bou-Reslan, R. A. D. Carano, I. Kasman, E. Mai, J. Young, J. Zha, Z. Zhang, S. Ross, R. Schwall, G. Colbern, and M. Merchant. (2008) MetMAb, the one-armed 5D5 anti-c-Met antibody, inhibits orthotopic pancreatic tumor growth and improves survival. Cancer Research, 68 (11): 4360-4368
  • J. Liu, Y. Zhang, X. Lei, and Z. Zhang. (2008) Natural selection of protein structural and functional properties: a SNP perspective. Genome Biology, 9(4): R69
  • P. M. Haverty, J. Fridlyand, L. Li, G. Getz, R. Beroukhim, S. Lohr, T. D. Wu, G. Cavet, Z. Zhang*, and J. Chant*. (2008) High-resolution genomic and expression analyses of copy number alterations in breast tumors. Genes, Chromosomes and Cancer, 47: 530-542
  • L. S. Hon, J. S. Kaminker, and Z. Zhang. (2008) Computational approaches for predicting causal missense mutations in cancer genome projects. Current Bioinformatics, 3 (1): 46-55
  • N. Kayagaki, Q. Phung, S. Chan, R. Chaudhari, C. Quan, K. M. O’Rourke, M. Eby, E. Pietras, G. Cheng, J. F. Bazan, Z. Zhang, D. Arnott, and V. M. Dixit. (2007) DUBA: a deubiquitinase that regulates type I interferon production. Science, 318: 1628-1632
  • L. D. Wood, D. W. Parsons, S. Jones, J. Lin, T. Sjöblom, R. J. Leary, D. Shen, S. M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P. A. Wilson, J. S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J. K. V. Willson, S. Sukumar, K. Polyak, B. H. Park, C. L. Pethiyagoda, P. V. K. Pant, D. G. Ballinger, A. B. Sparks, J. Hartigan, D. R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S. D. Markowitz, G. Parmigiani, K. W. Kinzler, V. E. Velculescu, and B. Vogelstein. (2007) The genomic landscapes of human breast and colorectal cancers. Science, 318: 1108-1113
  • L. S. Hon and Z. Zhang. (2007) The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biology, 8 (8): R166
  • J. S. Kaminker, Y. Zhang, C. Watanabe, andZ. Zhang. (2007) CanPredict: A computational tool for predicting missense cancer-associated mutations. Nucleic Acids Research, 35: W595-598
  • Y. Zhang, S-M Luoh, L. S. Hon, R. Baertsch, W. I. Wood and Z. Zhang. (2007) GeneHub-GEPIS: Digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Research, 35: W152-158
  • J. S. Kaminker, Y. Zhang, A. Waugh, P. Haverty, J. Stinson, B. Peters, D. Sebisanovic, W. F. Forrest, J. F. Bazan, S. Seshagiri, and Z. Zhang. (2007) Distinguishing cancer associated missense mutations from common polymorphisms. Cancer Research, 67: 465-473
  • X-D. Wang, B. Wang, R. Soriano, J. Zha, Z. Zhang, Z. Modrusan, G.R. Cunha, and W-Q Gao. (2007) Expression profiling of the mouse prostate after castration and hormone replacement: implication of H-cadherin in prostate tumorigenesis. Differentiation, 75: 219-234
  • D. Gray, A. M. Jubb, D. Hogue, P. Dowd, N. Kljavin, S. Yi, G. Frantz, W. Bai, Z. Zhang, H. Koeppen, F. de Sauvage, and D. Davis. (2005) Maternal Embryonic Leucine Zipper Kinase/Murine Protein Serine-Threonine Kinase 38 is a promising therapeutic target for multiple cancers. Cancer Research, 65: 97511-9761
  • Z. Zhang and W. J. Henzel. (2004) Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Science, 13: 2819-2824
  • Y. Zhang, D. Eberhard, G. D. Frantz, P. Dowd, T. D. Wu, C. Watanabe, Y. Zhou, P. Polakis, K. J. Hillan, W. I. Wood, and Z. Zhang. (2004) GEPIS – Quantitative gene expression profiling in normal and cancer tissues. Bioinformatics, 20: 2390-2398
  • B. Desany and Z. Zhang. (2004) Bioinformatics and cancer target discovery. Drug Discovery Today, 9: 795-802
  • I. E. Wertz, K. M. O’Rourke, Z. Zhang, D. Dornan, D. Arnott, R. J. Deshaies, and V. M. Dixit. (2004) Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. Science, 303: 1371-1374
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