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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 |
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2018 Journal Article Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer TypesGe, Zhongqi, Leighton, Jake S., Wang, Yumeng, Peng, Xinxin, Chen, Zhongyuan, Chen, Hu, Sun, Yutong, Yao, Fan, Li, Jun, Zhang, Huiwen, Liu, Jianfang, Shriver, Craig D., Hu, Hai, Piwnica-Worms, Helen, Ma, Li, Liang, Han, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Reports, 23 (1), 213-226.e3. doi: 10.1016/j.celrep.2018.03.047 |
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2018 Journal Article Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome AtlasWay, Gregory P., Sanchez-Vega, Francisco, La, Konnor, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, Sander, Chris, Cherniack, Andrew D., Mina, Marco, Ciriello, Giovanni, Schultz, Nikolaus, Sanchez, Yolanda, Greene, Casey S., The Cancer Genome Atlas Research Network and Yang, Ian (2018). Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Reports, 23 (1), 172-180.e3. doi: 10.1016/j.celrep.2018.03.046 |
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2018 Journal Article Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor ContextChiu, Hua-Sheng, Somvanshi, Sonal, Patel, Ektaben, Chen, Ting-Wen, Singh, Vivek P., Zorman, Barry, Patil, Sagar L., Pan, Yinghong, Chatterjee, Sujash S., Sood, Anil K., Gunaratne, Preethi H., Sumazin, Pavel, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Reports, 23 (1), 297-312.e12. doi: 10.1016/j.celrep.2018.03.064 |
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2018 Journal Article Systematic Analysis of Splice-Site-Creating Mutations in CancerJayasinghe, Reyka G., Cao, Song, Gao, Qingsong, Wendl, Michael C., Vo, Nam Sy, Reynolds, Sheila M., Zhao, Yanyan, Climente-Gonzalez, Hector, Chai, Shengjie, Wang, Fang, Varghese, Rajees, Huang, Mo, Liang, Wen-Wei, Wyczalkowski, Matthew A., Sengupta, Sohini, Li, Zhi, Payne, Samuel H., Fenyo, David, Miner, Jeffrey H., Walter, Matthew J., Vincent, Benjamin, Eyras, Eduardo, Chen, Ken, Shmulevich, Ilya, Chen, Feng, Ding, Li, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Reports, 23 (1), 270-281.e3. doi: 10.1016/j.celrep.2018.03.052 |
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2018 Journal Article Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous CarcinomasCampbell, Joshua D., Yau, Christina, Bowlby, Reanne, Liu, Yuexin, Brennan, Kevin, Fan, Huihui, Taylor, Alison M., Wang, Chen, Walter, Vonn, Akbani, Rehan, Byers, Lauren Averett, Creighton, Chad J., Coarfa, Cristian, Shih, Juliann, Cherniack, Andrew D., Gevaert, Olivier, Prunello, Marcos, Shen, Hui, Anur, Pavana, Chen, Jianhong, Cheng, Hui, Hayes, D. Neil, Bullman, Susan, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Sadeghi, Sara, Mungall, Karen L., Robertson, A. Gordon, Benz, Christopher ... Yang, Ian (2018). Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Reports, 23 (1), 194-212.e6. doi: 10.1016/j.celrep.2018.03.063 |
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2018 Journal Article The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell CarcinomaRicketts, Christopher J., de Cubas, Aguirre A., Fan, Huihui, Smith, Christof C., Lang, Martin, Reznik, Ed, Bowlby, Reanne, Gibb, Ewan A., Akbani, Rehan, Beroukhim, Rameen, Bottaro, Donald P., Choueiri, Toni K., Gibbs, Richard A., Godwin, Andrew K., Haake, Scott, Hakimi, A. Ari, Henske, Elizabeth P., Hsieh, James J., Ho, Thai H., Kanchi, Rupa S., Krishnan, Bhavani, Kwaitkowski, David J., Lui, Wembin, Merino, Maria J., Mills, Gordon B., Myers, Jerome, Nickerson, Michael L., Reuter, Victor E., Schmidt, Laura S. ... Yang, Ian (2018). The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Reports, 23 (1), 313-326.e5. doi: 10.1016/j.celrep.2018.03.075 |
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2018 Journal Article Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic PipelinesEllrott, Kyle, Bailey, Matthew H., Saksena, Gordon, Covington, Kyle R., Kandoth, Cyriac, Stewart, Chip, Hess, Julian, Ma, Singer, Chiotti, Kami E., McLellan, Michael, Sofia, Heidi J., Hutter, Carolyn, Getz, Gad, Wheeler, David, Ding, Li, The Cancer Genome Atlas Research Network and Yang, Ian (2018). Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Systems, 6 (3), 271-281.e7. doi: 10.1016/j.cels.2018.03.002 |
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2018 Journal Article Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome AtlasSchaub, Franz X., Dhankani, Varsha, Berger, Ashton C., Trivedi, Mihir, Richardson, Anne B., Shaw, Reid, Zhao, Wei, Zhang, Xiaoyang, Ventura, Andrea, Liu, Yuexin, Ayer, Donald E., Hurlin, Peter J., Cherniack, Andrew D., Eisenman, Robert N., Bernard, Brady, Grandori, Carla, The Cancer Genome Atlas Network and Yang, Ian (2018). Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Systems, 6 (3), 282-300.e2. doi: 10.1016/j.cels.2018.03.003 |
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2018 Journal Article Editorial on PanCan studyMarshall, Henry M., Yang, Ian A., Bowman, Rayleen V. and Fong, Kwun M. (2018). Editorial on PanCan study. Translational Lung Cancer Research, 7 (Suppl 1), S57-S59. doi: 10.21037/tlcr.2018.01.17 |
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2018 Journal Article The contribution of respiratory microbiome analysis to a treatable traits model of careTaylor, Steven L., O'Farrell, Hannah E., Simpson, Jodie L., Yang, Ian A. and Rogers, Geraint B. (2018). The contribution of respiratory microbiome analysis to a treatable traits model of care. Respirology, 24 (1), 19-28. doi: 10.1111/resp.13411 |
