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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
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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
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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
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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
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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.
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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.
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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
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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
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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 Zhang (2015) A comprehensive transcriptional portrait of human cancer cell lines. Nature Biotechnology, 33:305-315
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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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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
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 ( co-correspondence authors)
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, 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
X-D. Wang, B. Wang, R. Soriano, J. Zha, 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, 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
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
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, 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
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