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1. Full Text Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy
by Min, Yuanzeng and Roche, Kyle C and Tian, Shaomin and Eblan, Michael J and McKinnon, Karen P and Caster, Joseph M and Chai, Shengjie and Herring, Laura E and Zhang, Longzhen and Zhang, Tian and Desimone, Joseph M and Tepper, Joel E and Vincent, Benjamin G and Serody, Jonathan S and Wang, Andrew Z
Nature Nanotechnology, ISSN 1748-3387, 09/2017, Volume 12, Issue 9, pp. 877 - 882
Immunotherapy holds tremendous promise for improving cancer treatment(1). To administer radiotherapy with immunotherapy has been shown to improve immune... 
RESPONSES | MELANOMA | SAFETY | MATERIALS SCIENCE, MULTIDISCIPLINARY | ANTIBODY | NANOSCIENCE & NANOTECHNOLOGY | NEOANTIGENS | MECHANISMS | RADIOTHERAPY | BLOCKADE | NANOTECHNOLOGY | RADIATION | Formulations | Antigens | Immune response | Immunoregulation | CD8 antigen | Melanoma | Cytotoxicity | Lymphocytes T | T cell receptors | Radiation therapy | CD4 antigen | Nanoparticles | Proteins | Lymphocytes | Cell death | Antigen-presenting cells | Immunotherapy | Surface properties | Nanotechnology | Cancer | Tumors | Apoptosis | Index Medicus
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2. Full Text Molecular subtype-specific immunocompetent models of high-grade urothelial carcinoma reveal differential neoantigen expression and response to immunotherapy
by Saito, Ryoichi and Smith, Christof C and Utsumi, Takanobu and Bixby, Lisa M and Kardos, Jordan and Wobker, Sara E and Stewart, Kyle G and Chai, Shengjie and Manocha, Ujjawal and Byrd, Kevin M and Damrauer, Jeffrey S and Williams, Scott E and Vincent, Benjamin G and Kim, William Y
Cancer Research, ISSN 0008-5472, 07/2018, Volume 78, Issue 14, pp. 3954 - 3968
High-grade urothelial cancer contains intrinsic molecular subtypes that exhibit differences in underlying tumor biology and can be divided into luminal-like... 
BLADDER-CANCER | CELLS | ONCOLOGY | BREAST | BASAL | Urothelial cancer | Animal models | Immunological memory | Memory cells | PD-1 protein | Immunoregulation | CD8 antigen | Bladder | Lymphocytes T | Biology | Bladder cancer | Molecular chains | CD4 antigen | Molecular modelling | Immunogenicity | Lymphocytes | Immunotherapy | Rodents | Urothelial carcinoma | Cancer | Tumors | Index Medicus
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3. Full Text Integrated Molecular Characterization of Testicular Germ Cell Tumors
by Shen, Hui and Shih, Juliann and Hollern, Daniel P and Hollern, Daniel and Wang, Zhining and Wang, Linghua and Bowlby, Reanne and Tickoo, Satish K and Thorsson, Vésteinn and Thorsson, Vesteinn and Mungall, Andrew J and Newton, Yulia and Hegde, Apurva M and Armenia, Joshua and Sánchez-Vega, Francisco and Pluta, John and Pyle, Louise C and Mehra, Rohit and Reuter, Victor E and Godoy, Guilherme and Jones, Jeffrey and Jones, Steven J.M and Jones, Corbin D and Shelley, Carl S and Feldman, Darren and Feldman, Darren R and Vidal, Daniel O and Lessel, Davor and Kulis, Tomislav and Cárcano, Flavio M and Leraas, Kristen M and Lichtenberg, Tara M and Brooks, Denise and Cherniack, Andrew D and Cho, Juok and Heiman, David I and Kasaian, Katayoon and Liu, Jia and Liu, Wenbin and Liu, Minwei and Noble, Michael S and Xi, Liu and Zhang, Jiashan (Julia) and Zhang, Jiashan and Zhang, Hailei and Zhou, Wanding and ZenKlusen, Jean C and Hutter, Carolyn M and Felau, Ina and Schultz, Nikolaus and Getz, Gad and Meyerson, Matthew and Stuart, Joshua M and Wheeler, David A and Wheeler, David and Hughes, Daniel and Covington, Kyle and Jayaseelan, Joy C and Korchina, Viktoriya and Lewis, Lora and Hu, Jianhong and Doddapaneni, HarshaVardhan and Muzny, Donna and Gibbs, Richard and Hoadley, Katherine A and Vincent, Benjamin G and Chai, Shengjie and Smith, Christof C and Auman, J. Todd and Shi, Yan and Meng, Shaowu and Skelly, Tara and Tan, Donghui and Veluvolu, Umadevi and Mieczkowski, Piotr A and Wilkerson, Matthew D and Balu, Saianand and Bodenheimer, Tom and Hoyle, Alan P and Jefferys, Stuart R and Mose, Lisle E and Simons, Janae V and Soloway, Matthew G and Roach, Jeffrey and Parker, Joel S and Hayes, D. Neil and Perou, Amy H and Perou, Charles M and Saksena, Gordon and Cibulskis, Carrie and Schumacher, Steven E and Beroukhim, Rameen and Gabriel, Stacey B and Ally, Adrian and Balasundaram, Miruna and Carlsen, Rebecca and Cheung, Dorothy and Chuah, Eric and Dhalla, Noreen and Holt, Robert A and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell Reports, ISSN 2211-1247, 06/2018, Volume 23, Issue 11, pp. 3392 - 3406
We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These... 
exome sequencing | miR-375 | KIT | DNA methylation | seminoma | nonseminoma | copy number | testicular germ cell tumors | The Cancer Genome Atlas | ENDOGENOUS RETROVIRUSES | KIT GENE | ADOLESCENTS | HIGH-RESOLUTION | MUTATIONS | SEMINOMA | EXPRESSION | HUMAN CANCER | GENOME | CARCINOMA IN-SITU | CELL BIOLOGY | Index Medicus
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4. Full Text HiView: An integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants
by Xu, Zheng and Zhang, Guosheng and Duan, Qing and Chai, Shengjie and Zhang, Baqun and Wu, Cong and Jin, Fulai and Yue, Feng and Li, Yun and Hu, Ming
BMC Research Notes, ISSN 1756-0500, 03/2016, Volume 9, Issue 1, pp. 159 - 159
Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are... 
Integrative genome browser | GWAS variants | Hi-C data | Polymorphism, Single Nucleotide - genetics | Genome-Wide Association Study | Software | Internet | Genome, Human | Humans | Eukaryotes | Usage | Genome-wide association studies | Research | Genomics | Microscope and microscopy | Index Medicus
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5. Full Text Prognostic value of B cells in cutaneous melanoma
by Selitsky, Sara R and Mose, Lisle E and Smith, Christof C and Chai, Shengjie and Hoadley, Katherine A and Dittmer, Dirk P and Moschos, Stergios J and Parker, Joel S and Vincent, Benjamin G
Genome medicine, ISSN 1756-994X, 05/2019, Volume 11, Issue 1, pp. 36 - 36
Measures of the adaptive immune response have prognostic and predictive associations in melanoma and other cancer types. Specifically, intratumoral T cell... 
RNA sequencing | Usage | Immune response | Prognosis | Development and progression | B cells | Research | Cancer | PD-1 protein | Cytotoxicity | Systematic review | Genomes | Lymphocytes T | Metastasis | B-cell receptor | Cell density | Metastases | CTLA-4 protein | Lymphocytes | Immunotherapy | Classification | Antigens | Phenotypes | Cloning | Melanoma | T cell receptors | Ribonucleic acid--RNA | Gene expression | Patients | Multiculturalism & pluralism | Learning algorithms | Lymphocytes B | Medical prognosis | Skin | Mutation | Immunology | Machine learning
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6. Full Text Abstract 4055: Genomic and immune characterization of triple-negative breast cancer brain metastases
by Vincent, Benjamin G and Sambade, Maria and Chai, Shengjie and Siegel, Marni B and Cuaboy, Luz and Hoyle, Alan and Parker, Joel and Perou, Charles M and Anders, Carey K
Cancer Research, ISSN 0008-5472, 07/2018, Volume 78, Issue 13 Supplement, pp. 4055 - 4055
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7. Full Text Abstract 5120: The novel claudin-low molecular subtype of high-grade urothelial bladder cancer is highly immunogenic yet immunosuppressed
by Vincent, Benjamin G and Kim, William and Kardos, Jordan and Chai, Shengjie and Parker, Joel and Mose, Lisle and Selitsky, Sara and Iglesia, Michael and Milowsky, Matthew
Cancer Research, ISSN 0008-5472, 07/2016, Volume 76, Issue 14 Supplement, pp. 5120 - 5120
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8. Full Text Systematic Analysis of Splice-Site-Creating Mutations in Cancer
by Jayasinghe, Reyka G and Cao, Song and Gao, Qingsong and Gao, Jianjiong and Gao, Galen F and Wendl, Michael C and Vo, Nam Sy and Reynolds, Sheila and Reynolds, Sheila M and Zhao, Fengmei and Zhao, Yanyan and Climente-González, Héctor and Chai, Shengjie and Wang, Zhining and Wang, Fang and Wang, Min and Wang, Jing and Wang, Timothy and Wang, Linghua and Wang, Jioajiao and Varghese, Rajees and Huang, Mo and Liang, Wen-Wei and Liang, Han and Wyczalkowski, Matthew A and Sengupta, Sohini and Li, Zhi and Li, Wei and Li, Jun and Payne, Samuel H and Fenyö, David and Miner, Jeffrey H and Walter, Matthew J and Caesar-Johnson, Samantha J and Demchok, John A and Felau, Ina and Kasapi, Melpomeni and Ferguson, Martin L and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Yang, Liming and Yang, Ju Dong and Yang, Ian and Yang, Hannah and Zenklusen, Jean C and Zhang, Hailei and Zhang, Wei and Zhang, Jiashan (Julia) and Zhang, Lizhi and Zhang, Jiexin and Zhang, Hongxin and Zhang, Hongzheng and Chudamani, Sudha and Liu, Wenbin and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Sun, Yichao and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Getz, Gad and Heiman, David I and Kim, Jaegil and Lawrence, Michael S and Lin, Pei and Meier, Sam and Noble, Michael S and Saksena, Gordon and Voet, Doug and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Miller, Michael and Miller, Judy and Miller, Christopher A and Shmulevich, Ilya and Thorsson, Vesteinn and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and Ju, Zhenlin and Kanchi, Rupa S and Korkut, Anil and Ling, Shiyun and Lu, Yiling and Mills, Gordon B and Ng, Kwok-Shing and Rao, Arvind and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 270 - 281.e3
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential.... 
RNA | mutations of clinical relevance | splicing | BREAST-CANCER | INACTIVATION | RETINOBLASTOMA | REPORTER MINIGENE | MESSENGER-RNA | TRANSCRIPTOME | UNCLASSIFIED VARIANTS | GENETIC-VARIANTS | ABERRANT | SYNONYMOUS MUTATIONS | CELL BIOLOGY | GATA3 Transcription Factor - genetics | BRCA1 Protein - genetics | RNA Splice Sites | Neoplasms - genetics | Humans | HEK293 Cells | Mutation | Programmed Cell Death 1 Receptor - genetics | X-linked Nuclear Protein - genetics | Poly (ADP-Ribose) Polymerase-1 - genetics | Tumor Suppressor Protein p53 - genetics | Index Medicus | Splicing | Mutations of clinical relevance | BASIC BIOLOGICAL SCIENCES
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9. Full Text MP88-20 ESTABLISHMENT OF NOVEL MOUSE BLADDER CANCER CELL LINES MIMICKING INTRINSIC SUBTYPE OF HUMAN INVASIVE BLADDER CANCER
by SAITO, RYOICHI and Smith, Christof and Kardos, Jordan and Bixby, Lisa and Chai, Shengjie and Damrauer, Jeffrey and Utsumi, Takanobu and Wobker, Sara and Krishnan, Bhavani and Ogawa, Osamu and Vincent, Benjamin and Kim, William
Journal of Urology, The, ISSN 0022-5347, 2017, Volume 197, Issue 4, pp. e1182 - e1182
Urology | Bladder cancer
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10. Full Text HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data
by Buchkovich, Martin L and Brown, Chad C and Robasky, Kimberly and Chai, Shengjie and Westfall, Sharon and Vincent, Benjamin G and Weimer, Eric T and Powers, Jason G
Genome Medicine, ISSN 1756-994X, 09/2017, Volume 9, Issue 1, pp. 86 - 86
Background: The human leukocyte antigen (HLA) system is a genomic region involved in regulating the human immune system by encoding cell membrane major... 
RNA-sequencing | Transplantation | Immunology | HLA | HSCT | PROJECT | ASSOCIATIONS | GENETICS & HEREDITY | Cell Line | Sequence Analysis, RNA | Humans | Alleles | Molecular Sequence Data | Reference Values | Software | HLA Antigens - genetics | Histocompatibility Testing - methods | Transcription factors | Disease susceptibility | Genetic aspects | Histocompatibility antigens | Health aspects | HLA histocompatibility antigens | Antigens | Typing | Genomics | Genomes | Gene expression | Ribonucleic acid--RNA | Self-recognition | Graft rejection | Datasets | Regeneration | Accuracy | Databases | Major histocompatibility complex | Immunotherapy | Histocompatibility antigen HLA | Tissue typing | Autoimmune diseases | Bioinformatics | Histocompatibility | Deoxyribonucleic acid--DNA | Immune system | Index Medicus
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11. Full Text Tyrosine kinase ETK/BMX is up-regulated in bladder cancer and predicts poor prognosis in patients with cystectomy
by Guo, Shengjie and Sun, Feng and Guo, Zhiyong and Li, Wei and Alfano, Alan and Chen, Hegang and Magyar, Clara E and Huang, Jiaoti and Chai, Toby C and Qiu, Shaopeng and Qiu, Yun
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 3, pp. e17778 - e17778
Deregulation of the non-receptor tyrosine kinase ETK/BMX has been reported in several solid tumors. In this report, we demonstrated that ETK expression is... 
STAT3 ACTIVATION | CELLS | SUPPRESSOR | GENE | SRC | MULTIDISCIPLINARY SCIENCES | EPIDERMAL-GROWTH-FACTOR | PROSTATE-CANCER | FACTOR RECEPTOR | EXPRESSION | CARCINOMA | Mitochondria - enzymology | Multivariate Analysis | Up-Regulation | Prognosis | Cell Survival | Neoplasm Invasiveness | Protein-Tyrosine Kinases - metabolism | Urinary Bladder Neoplasms - diagnosis | Humans | Urinary Bladder Neoplasms - enzymology | Proportional Hazards Models | Urinary Bladder Neoplasms - surgery | Protein Transport | Cystectomy | Survival Analysis | Urinary Bladder Neoplasms - pathology | Cell Line, Tumor | Protein Binding | bcl-X Protein - metabolism | Cell Movement | Immunohistochemistry | Tyrosine | Medical research | Analysis | Mortality | Medicine, Experimental | Phenols | Development and progression | Diagnosis | Bladder cancer | Health aspects | Deregulation | Phosphorylation | Senescence | Leukocyte migration | Bladder | AKT protein | Tissue analysis | Kinases | Urology | Mitochondria | Cell growth | Epidermal growth factor | Bcl-x protein | Urinary bladder | Rodents | Down-regulation | Bmx protein | Protein-tyrosine kinase receptors | Tumorigenesis | Bioindicators | Protein-tyrosine kinase | Etk protein | Enzymes | Cell survival | Cytokines | Stat3 protein | Pharmacology | Patients | Survival | Medicine | Signaling | Medical prognosis | Biomarkers | Solid tumors | Potassium | Cell migration | Tumors | Cancer | Index Medicus
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12. Full Text Abstract 1654: Development of subtype specific mouse models of bladder cancer
by Smith, Christof C and Saito, Ryoichi and Bixby, Lisa M and Utsumi, Takanobu and Kardos, Jordan and Chai, Shengjie and Wobker, Sara E and Krishnan, Bhavani and Damrauer, Jeffrey S and Serody, Jonathan S and Darr, David and Vincent, Benjamin G and Kim, William Y
Cancer Research, ISSN 0008-5472, 07/2017, Volume 77, Issue 13 Supplement, pp. 1654 - 1654
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13. Full Text Molecular and clinical characterization of a claudin (CLDN)-low subtype of gastric cancer (GC)
by Nishijima, TF and Kardos, J and Chai, SJ and Smith, CC and Bortone, DS and Mose, LE and Selitsky, SR and Sanoff, HK and Parker, JS and Lee, MS and Vincent, BG
JOURNAL OF CLINICAL ONCOLOGY, ISSN 0732-183X, 02/2017, Volume 35, Issue 4, pp. 67 - 67
ONCOLOGY
Conference Proceeding
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