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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
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X. Hu and Z. Zhang. (2016) Understanding the genetic mechanisms of cancer drug resistance using genomic approaches. Trends in Genetics, 32(2):127-37
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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
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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
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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
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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
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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
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K. M. L. Gaensler, Z. Zhang, C. Lin, S. Yang, K. Hardt, and L. Flebbe-Rehwaldt. (2003) Sequences in the Aγ–δ intergenic region are not required for stage-specific regulation of the human β-globin gene locus. Proc. Natl. Acad. Sci. USA, 100 (6): 3374-3379
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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
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