Publications

 

  • Zhang L, Yu X, Zheng L, Zhang Y, Li Y, Fang Q, Gao R, Kang B, Zhang Q, J Huang, Konno H, Guo X, Ye Y, Gao S, Wang S, Hu X, Ren X, Shen Z, Ouyang W, Zhang Z. (2018). Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature. https://doi.org/10.1038/s41586-018-0694-x.                              
  • 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, Z. Zhang (2018). Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nature medicine, 1546-170X UR.                      
  • Yang, C., Zang, W., Tang, Z., Ji, Y., Xu, R., Yang, Y., Luo, A., Hu, B., Zhang, Z., Liu, Z., et al. (2018). A20/TNFAIP3 Regulates the DNA Damage Response and Mediates Tumor Cell Resistance to DNA-Damaging Therapy. Cancer Research 78, 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, Z. Zhang (2017). Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. Cell, 169(7), 1342–1356.e16.                                                                                             
  • Tang, Z., Li, C., Kang, B., Gao, G., Li, C., & Zhang, Z. (2017). GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic acids research.                                                                                      
  • Fonseca, N.A., He, Y., Greger, L., Brazma, A., and Zhang, Z. (2017). Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer. bioRxiv.
  • Z. Tang, C. Li, K. Zhang, M. Yang, and X. Hu. (2017) GE-mini: a mobile APP for large-scale gene expression visualization. Bioinformatics. 
  • Calabrese, C., Lehmann, K.-V., Urban, L., Liu, F., Erkek, S., Fonseca, N., Kahles, A., Kilpinen-Barrett, L.H., Markowski, J., Waszak, S., et al. (2017). Assessing the Gene Regulatory Landscape in 1,188 Human Tumors. bioRxiv.
  • Ji, Y., Yang, C., Tang, Z., Yang, Y., Tian, Y., Yao, H., Zhu, X., Zhang, Z., Ji, J., and Zheng, X. (2017). Adenylate kinase hCINAP determines self-renewal of colorectal cancer stem cells by facilitating LDHA phosphorylation. Nature Communications 8, 15308.
  • 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. pii: S0016-5085(15)01861-2
  • 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 (* co-corresponding authors)
  • Z. Wang, Z. Shen, Z. Li, J. Duan, S. Fu, Z. Liu, H. Bai, Z. Zhang, J. Zhao, X. Wang, 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, Z. Zhang* (2015) Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics. 16:S5
  • 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
  • L. 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, doi: 10.1038/ncomms4830
  • 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
  • F. Gnad, A. Baucom, K. Mukhyala, G. Manning, and Zhang Z. (2013) Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC Genomics, 14:S7
  • F. 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, and 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, and 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 (* co-corresponding authors)
  • 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 (* co-corresponding authors)
  • H. 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
  • 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
  • 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
  • H. 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, and Z. 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
  • 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  (* first and corresponding author)
  • 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 Discov. 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
  • Y. Zhou, S-M. Luoh, Y. Zhang, C. Watanabe, T. D. Wu, M. Ostland, W. I. Wood, and Z. Zhang. (2003) Genome-wide identification of chromosome regions of increased tumor expression by transcriptome analysis. Cancer Research, 63: 5781-5784
  • K. M. L. Gaensler, Z. Zhang, C. Lin, S. Yang, K. Hardt, and L. Flebbe-Rehwaldt. (2003) Sequences in the Ag – d intergenic regions are not required for stage-specific regulation of the human b-globin gene locus. Proc. Natl. Acad. Sci. USA, 100 (6): 3374-3379
  • Z. Zhang* and W. I. Wood. (2003) A profile hidden Markov model for signal peptides generated by HMMER. Bioinformatics, 19 (2): 307-308  (* first and corresponding author)
  • H. F. Clark, A. L. Gurney, E. Abaya, K. Baker, D. Baldwin, J. Brush, J. Chen, B. Chow, C. Chui, C. Crowley, B. Currell, B. Deuel, P. Dowd, D. Eaton, J. Foster, C. Grimaldi, Q. Gu, P. E. Hass, S. Heldens, A. Huang, H. S. Kim, L. Klimowski, Y. Jin, S. Johnson, J. Lee, L. Lewis, D. Liao, M. Mark, E. Robbie, C. Sanchez, J. Schoenfeld, S. Seshagiri, L. Simmons, J. Singh, V. Smith, J. Stinson, A. Vagts, R. Vandlen, C. Watanabe, D. Wieand, K. Woods, M-H. Xie, D.Yansura, S. Yi, G. Yu, J. Yuan, M. Zhang, Z. Zhang, A. Goddard, W. I. Wood, and P. Godowski. (2003) The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Research, 13: 2265-2270
  • J. LeCouter, R. Lin, G. Frantz, Z. Zhang, K. J. Hillan, and N. Ferrara. (2003) Mouse endocrine gland-derived vascular endothelial growth factor: a distinct expression pattern from its human ortholog suggests different roles as a regulator of organ-specific angiogenesis. Endocrinology, 144 (6): 2606-2616
  • M. Yan, Z. Zhang, J. R. Brady, S. Schilbach, W. J. Fairbrother, and V. M. Dixit. (2002) Identification of a novel death domain-containing adaptor molecule for Ectodysplasin-A receptor that is mutated in crinkled Mice. Current Biology, 12: 409-413
  • J. LeCouter, J. Kowalski, J. Foster, P. Hass, Z. Zhang, L. Dillard-Telm, G. Frantz, L. Rangell, L. DeGuzman, G-A. Keller, F. Peale, A. Gurney, K. J. Hillan, and N. Ferrara. (2001) Identification of an angiogenic mitogen selective for endocrine gland endothelium. Nature, 412: 877-884
  • A. Kishiyama, Z. Zhang, and W. J. Henzel. (2000) Cleavage and identification of proteins, a modified Aspartyl-Prolyl Cleavage. Analytical Chemistry, 72 (21): 5431-5436
  • M-H. Xie, S. Aggarwal, W-H. Ho, J. Foster, Zhang, J. Stinson, W. Wood, A. Goddard, and A. Gurney. (2000) Identification of IL-22, a novel human cytokine that signals through the interferon receptor-related proteins CRF2-4 and IL-22R.  Journal of Biological Chemistry, 275 (40): 31335-31339
  • Z. Zhang* and A. R. Buchman. (1997) Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Molecular and Cellular Biology, 17 (9):5461-5472  (* first and corresponding author)
  • S. Porcu, M. Kitamura, E. Witkowska, Z. Zhang, A. Mutero, C. Lin, J. Chang, and K. L. M. Gaensler. (1997) The human beta globin locus introduced by YAC transfer exhibit a specific and reproducible pattern of developmental regulation in transgenic mice. Blood, 90 (11): 4602-4609