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2018 Journal Article Diagnosis of the cause of chronic dyspnoea in primary and tertiary care: characterizing diagnostic confidenceHuang, Yao C., Ferry, Olivia R., McKenzie, Scott C., Bowman, Rayleen, Hamilton, Michael, Masel, Philip J., Fong, Kwun M. and Yang, Ian A. (2018). Diagnosis of the cause of chronic dyspnoea in primary and tertiary care: characterizing diagnostic confidence. Journal of Thoracic Disease, 10 (6), 3745-3756. doi: 10.21037/jtd.2018.05.183 |
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2018 Journal Article Working while unwell: Workplace impairment in people with severe asthmaHiles, S. A., Harvey, E. S., McDonald, V. M., Peters, M., Bardin, P., Reynolds, P. N., Upham, J. W., Baraket, M., Bhikoo, Z., Bowden, J., Brockway, B., Chung, L. P., Cochrane, B., Foxley, G., Garrett, J., Hew, M., Jayaram, L., Jenkins, C., Katelaris, C., Katsoulotos, G., Koh, M. S., Kritikos, V., Lambert, M., Langton, D., Rivero, A. L., Marks, G. B., Middleton, P. G., Nanguzgambo, A., Radhakrishna, N. ... Gibson, P. G. (2018). Working while unwell: Workplace impairment in people with severe asthma. Clinical and Experimental Allergy, 48 (6), 650-662. doi: 10.1111/cea.13153 |
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2018 Journal Article The Immune Landscape of CancerThorsson, Vesteinn, Gibbs, David L., Brown, Scott D., Wolf, Denise, Bortone, Dante S., Yang, Tai-Hsien Ou, Porta-Pardo, Eduard, Gao, Galen F., Plaisier, Christopher L., Eddy, James A., Ziv, Elad, Culhane, Aedin C., Paull, Evan O., Sivakumar, I. K. Ashok, Gentles, Andrew J., Malhotra, Raunaq, Farshidfar, Farshad, Colaprico, Antonio, Parker, Joel S., Mose, Lisle E., Nam Sy Vo,, Liu, Jianfang, Liu, Yuexin, Rader, Janet, Dhankani, Varsha, Reynolds, Sheila M., Bowlby, Reanne, Califano, Andrea, Cherniack, Andrew D. ... Yang, Ian (2018). The Immune Landscape of Cancer. Immunity, 48 (4), 812-830.e14. doi: 10.1016/j.immuni.2018.03.023 |
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2018 Journal Article Comparative Molecular Analysis of Gastrointestinal AdenocarcinomasLiu, Yang, Sethi, Nilay S., Hinoue, Toshinori, Schneider, Barbara G., Cherniack, Andrew D., Sanchez-Vega, Francisco, Seoane, Jose A., Farshidfar, Farshad, Bowlby, Reanne, Islam, Mirazul, Kim, Jaegil, Chatila, Walid, Akbani, Rehan, Kanchi, Rupa S., Rabkin, Charles S., Willis, Joseph E., Wang, Kenneth K., McCall, Shannon J., Mishra, Lopa, Ojesina, Akinyemi I., Bullman, Susan, Pedamallu, Chandra Sekhar, Lazar, Alexander J., Sakai, Ryo, Thorsson, Vesteinn, Bass, Adam J., Laird, Peter W., The Cancer Genome Atlas Research Network and Yang, Ian (2018). Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell, 33 (4), 721-735.e8. doi: 10.1016/j.ccell.2018.03.010 |
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2018 Journal Article Genomic and Functional Approaches to Understanding Cancer AneuploidyTaylor, Alison M., Shih, Juliann, Ha, Gavin, Gao, Galen F., Zhang, Xiaoyang, Berger, Ashton C., Schumacher, Steven E., Wang, Chen, Hu, Hai, Liu, Jianfang, Lazar, Alexander J., Cherniack, Andrew D., Beroukhim, Rameen, Meyerson, Matthew, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell, 33 (4), 676-689.e3. doi: 10.1016/j.ccell.2018.03.007 |
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2018 Journal Article A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast CancersBerger, Ashton C., Korkut, Anil, Kanchi, Rupa S., Hegde, Apurva M., Lenoir, Walter, Liu, Wenbin, Liu, Yuexin, Fan, Huihui, Shen, Hui, Ravikumar, Visweswaran, Rao, Arvind, Schultz, Andre, Li, Xubin, Sumazin, Pavel, Williams, Cecilia, Mestdagh, Pieter, Gunaratne, Preethi H., Yau, Christina, Bowlby, Reanne, Robertson, A. Gordon, Tiezzi, Daniel G., Wang, Chen, Cherniack, Andrew D., Godwin, Andrew K., Kuderer, Nicole M., Rader, Janet S., Zuna, Rosemary E., Sood, Anil K., Lazar, Alexander J. ... Yang, Ian (2018). A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell, 33 (4), 690-705.e9. doi: 10.1016/j.ccell.2018.03.014 |
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2018 Journal Article lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in CancerWang, Zehua, Yang, Bo, Zhang, Min, Guo, Weiwei, Wu, Zhiyuan, Wang, Yue, Jia, Lin, Li, Song, Xie, Wen, Yang, Da, The Cancer Genome Atlas Research Network and Yang, Ian (2018). lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell, 33 (4), 706-720.e9. doi: 10.1016/j.ccell.2018.03.006 |
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2018 Journal Article Pathogenic Germline Variants in 10,389 Adult CancersHuang, Kuan-lin, Mashl, R. Jay, Wu, Yige, Ritter, Deborah I., Wang, Jiayin, Oh, Clara, Paczkowska, Marta, Reynolds, Sheila, Wyczalkowski, Matthew A., Oak, Ninad, Scott, Adam D., Krassowski, Michal, Cherniack, Andrew D., Houlahan, Kathleen E., Jayasinghe, Reyka, Wang, Liang-Bo, Zhou, Daniel Cui, Liu, Di, Cao, Song, Kim, Young Won, Koire, Amanda, McMichael, Joshua F., Hucthagowder, Vishwanathan, Kim, Tae-Beom, Hahn, Abigail, Wang, Chen, McLellan, Michael D., Al-Mulla, Fahd, Johnson, Kimberly J. ... Yang, Ian (2018). Pathogenic Germline Variants in 10,389 Adult Cancers. Cell, 173 (2), 355-370.e14. doi: 10.1016/j.cell.2018.03.039 |
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2018 Journal Article Perspective on Oncogenic Processes at the End of the Beginning of Cancer GenomicsDing, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan-lin, Tokheim, Collin, Cortes-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A. ... Yang, Ian (2018). Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell, 173 (2), 305-320.e10. doi: 10.1016/j.cell.2018.03.033 |
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2018 Journal Article Comprehensive Characterization of Cancer Driver Genes and MutationsBailey, Matthew H., Tokheim, Collin, Porta-Pardo, Eduard, Sengupta, Sohini, Bertrand, Denis, Weerasinghe, Amila, Colaprico, Antonio, Wendl, Michael C., Kim, Jaegil, Reardon, Brendan, Ng, Patrick Kwok-Shing, Jeong, Kang Jin, Cao, Song, Wang, Zixing, Gao, Jianjiong, Gao, Qingsong, Wang, Fang, Liu, Eric Minwei, Mularoni, Loris, Rubio-Perez, Carlota, Nagarajan, Niranjan, Cortes-Ciriano, Isidro, Zhou, Daniel Cui, Liang, Wen-Wei, Hess, Julian M., Yellapantula, Venkata D., Tamborero, David, Gonzalez-Perez, Abel, Suphavilai, Chayaporn ... Yang, Ian (2018). Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell, 173 (2) 385.e1, 371-385.e18. doi: 10.1016/j.cell.2018.02.060 |
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2018 Journal Article A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient SamplesChen, Han, Li, Chunyan, Peng, Xinxin, Zhou, Zhicheng, Weinstein, John N., Liang, Han, The Cancer Genome Atlas Research Network and Yang, Ian (2018). A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell, 173 (2) 399.e1, 386-399.e12. doi: 10.1016/j.cell.2018.03.027 |
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2018 Journal Article Oncogenic Signaling Pathways in The Cancer Genome AtlasSanchez-Vega, Francisco, Mina, Marco, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, La, Konnor C., Dimitriadoy, Sofia, Liu, David L., Kantheti, Havish S., Saghafinia, Sadegh, Chakravarty, Debyani, Daian, Foysal, Gao, Qingsong, Bailey, Matthew H., Liang, Wen-Wei, Foltz, Steven M., Shmulevich, Ilya, Ding, Li, Heins, Zachary, Ochoa, Angelica, Gross, Benjamin, Gao, Jianjiong, Zhang, Hongxin, Kundra, Ritika, Kandoth, Cyriac, Bahceci, Istemi, Dervishi, Leonard, Dogrusoz, Ugur, Zhou, Wanding ... Yang, Ian (2018). Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell, 173 (2), 321-337.e10. doi: 10.1016/j.cell.2018.03.035 |
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2018 Journal Article Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of CancerHoadley, Katherine A., Yau, Christina, Hinoue, Toshinori, Wolf, Denise M., Lazar, Alexander J., Drill, Esther, Shen, Ronglai, Taylor, Alison M., Cherniack, Andrew D., Thorsson, Vesteinn, Akbani, Rehan, Bowlby, Reanne, Wong, Christopher K., Wiznerowicz, Maciej, Sanchez-Vega, Francisco, Robertson, A. Gordon, Schneider, Barbara G., Lawrence, Michael S., Noushmehr, Houtan, Malta, Tathiane M., Stuart, Joshua M., Benz, Christopher C., Laird, Peter W., The Cancer Genome Atlas Network and Yang, Ian (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173 (2), 291-304.e6. doi: 10.1016/j.cell.2018.03.022 |
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2018 Journal Article An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome AnalyticsLiu, Jianfang, Lichtenberg, Tara, Hoadley, Katherine A., Poisson, Laila M., Lazar, Alexander J., Cherniack, Andrew D., Kovatich, Albert J., Benz, Christopher C., Levine, Douglas A., Lee, Adrian V., Omberg, Larsson, Wolf, Denise M., Shriver, Craig D., Thorsson, Vesteinn, Hu, Hai, The Cancer Genome Atlas Research Network and Yang, Ian (2018). An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, 173 (2) 416.e1, 400-416.e11. doi: 10.1016/j.cell.2018.02.052 |
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2018 Journal Article Machine Learning Identifies Stemness Features Associated with Oncogenic DedifferentiationMalta, Tathiane M., Sokolov, Artem, Gentles, Andrew J., Burzykowski, Tomasz, Poisson, Laila, Weinstein, John N., Kaminska, Bozena, Huelsken, Joerg, Omberg, Larsson, Gevaert, Olivier, Colaprico, Antonio, Czerwinska, Patrycja, Mazurek, Sylwia, Mishra, Lopa, Heyn, Holger, Krasnitz, Alex, Godwin, Andrew K., Lazar, Alexander J., Stuart, Joshua M., Hoadley, Katherine A., Laird, Peter W., Noushmehr, Houtan, Wiznerowicz, Maciej, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell, 173 (2), 338-354.e15. doi: 10.1016/j.cell.2018.03.034 |
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2018 Journal Article Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer TypesSeiler, Michael, Peng, Shouyong, Agrawal, Anant A., Palacino, James, Teng, Teng, Zhu, Ping, Smith, Peter G., Buonamici, Silvia, Yu, Lihua, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Reports, 23 (1), 282-296.e4. doi: 10.1016/j.celrep.2018.01.088 |
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2018 Journal Article Driver Fusions and Their Implications in the Development and Treatment of Human CancersGao, Qingsong, Liang, Wen-Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen-Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Chen, Ken, Lazar, Alexander J., Fields, Ryan C., Wendl, Michael C., Van Tine, Brian A., Vij, Ravi, Chen, Feng, Nykter, Matti, Shmulevich, Ilya, Ding, Li, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Reports, 23 (1), 227-238.e3. doi: 10.1016/j.celrep.2018.03.050 |
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2018 Journal Article Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human CancersPeng, Xinxin, Chen, Zhongyuan, Farshidfar, Farshad, Xu, Xiaoyan, Lorenzi, Philip L., Wang, Yumeng, Cheng, Feixiong, Tan, Lin, Mojumdar, Kamalika, Du, Di, Ge, Zhongqi, Li, Jun, Thomas, George V., Birsoy, Kivanc, Liu, Lingxiang, Zhang, Huiwen, Zhao, Zhongming, Marchand, Calena, Weinstein, John N., Bathe, Oliver F., Liang, Han, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Reports, 23 (1), 255-269.e4. doi: 10.1016/j.celrep.2018.03.077 |
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2018 Journal Article Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology ImagesSaltz, Joel, Gupta, Rajarsi, Hou, Le, Kurc, Tahsin, Singh, Pankaj, Nguyen, Vu, Samaras, Dimitris, Shroyer, Kenneth R., Zhao, Tianhao, Batiste, Rebecca, Van Arnam, John, Shmulevich, Ilya, Rao, Arvind U. K., Lazar, Alexander J., Sharma, Ashish, Thorsson, Vesteinn, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Reports, 23 (1), 181-193.e7. doi: 10.1016/j.celrep.2018.03.086 |
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2018 Journal Article Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome AtlasKnijnenburg, Theo A., Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N. ... Yang, Ian (2018). Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Reports, 23 (1), 239-254.e6. doi: 10.1016/j.celrep.2018.03.076 |
