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Artigos e Materiais de Revistas Científicas - IMT: Recent submissions

  • KNIJNENBURG, 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.; LI, Lei; DING, Li; MILLS, Gordon B.; LAIRD, Peter W.; WHEELER, David A.; SHMULEVICH, Ilya; MONNAT JR., Raymond J.; XIAO, Yonghong; WANG, Chen (CELL PRESS, CAMBRIDGE, USA, 2018)
    DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations ...
  • PENG, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression ...
  • GE, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer ...
  • GAO, 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.; TINE, Brian A. Van; VIJ, Ravi; CHEN, Feng; NYKTER, Matti; SHMULEVICH, Ilya; DING, Li (CELL PRESS, CAMBRIDGE, USA, 2018)
    Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 ...
  • CAMPBELL, 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; SCHULTZ, Andre; KANCHI, Rupa S.; GAY, Carl M.; HEGDE, Apurva; DIAO, Lixia; WANG, Jing; MA, Wencai; SUMAZIN, Pavel; CHIU, Hua-Sheng; CHEN, Ting-Wen; GUNARATNE, Preethi; DONEHOWER, Larry; RADER, Janet S.; ZUNA, Rosemary; AL-AHMADIE, Hikmat; LAZAR, Alexander J.; FLORES, Elsa R.; TSAI, Kenneth Y.; ZHOU, Jane H.; RUSTGI, Anil K.; DRILL, Esther; SHEN, Ronglei; WONG, Christopher K.; STUART, Joshua M.; LAIRD, Peter W.; HOADLEY, Katherine A.; WEINSTEIN, John N.; PETO, Myron; PICKERING, Curtis R.; CHEN, Zhong; WAES, Carter Van (CELL PRESS, CAMBRIDGE, USA, 2018)
    This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). ...
  • SALTZ, Joel; GUPTA, Rajarsi; HOU, Le; KURC, Tahsin; SINGH, Pankaj; Vu Nguyen; SAMARAS, Dimitris; SHROYER, Kenneth R.; ZHAO, Tianhao; BATISTE, Rebecca; ARNAM, John Van; SHMULEVICH, Ilya; RAO, Arvind U. K.; LAZAR, Alexander J.; SHARMA, Ashish; THORSSON, Vesteinn (CELL PRESS, CAMBRIDGE, USA, 2018)
    Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) ...
  • WAY, 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. (CELL PRESS, CAMBRIDGE, USA, 2018)
    Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these ""hidden responders'' may reveal responsive molecular states. ...
  • CHEN, Han; LI, Chunyan; PENG, Xinxin; ZHOU, Zhicheng; WEINSTEIN, John N.; LIANG, Han (CELL PRESS, CAMBRIDGE, USA, 2018)
    The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers ...
  • LIU, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical ...
  • HUANG, 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.; LICHTARGE, Olivier; BOUTROS, Paul C.; RAPHAEL, Benjamin; LAZAR, Alexander J.; ZHANG, Wei; WENDL, Michael C.; GOVINDAN, Ramaswamy; JAIN, Sanjay; WHEELER, David; KULKARNI, Shashikant; DIPERSIO, John F.; REIMAND, Juri; MERIC-BERNSTAM, Funda; CHEN, Ken; SHMULEVICH, Ilya; PLON, Sharon E.; CHEN, Feng; DING, Li (CELL PRESS, CAMBRIDGE, USA, 2018)
    We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or ...
  • BAILEY, 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; KO, Jia Yu; KHURANA, Ekta; PARK, Peter J.; ALLEN, Eliezer M. Van; LIANG, Han; LAWRENCE, Michael S.; GODZIK, Adam; LOPEZ-BIGAS, Nuria; STUART, Josh; WHEELER, David; GETZ, Gad; CHEN, Ken; LAZAR, Alexander J.; MILLS, Gordon B.; KARCHIN, Rachel; DING, Li (CELL PRESS, CAMBRIDGE, USA, 2018)
    Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report ...
  • SANCHEZ-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; SHEN, Hui; LAIRD, Peter W.; WAY, Gregory P.; GREENE, Casey S.; LIANG, Han; XIAO, Yonghong; WANG, Chen; IAVARONE, Antonio; BERGER, Alice H.; BIVONA, Trever G.; LAZAR, Alexander J.; HAMMER, Gary D.; GIORDANO, Thomas; KWONG, Lawrence N.; MCARTHUR, Grant; HUANG, Chenfei; TWARD, Aaron D.; FREDERICK, Mitchell J.; MCCORMICK, Frank; MEYERSON, Matthew; ALLEN, Eliezer M. Van; CHERNIACK, Andrew D.; CIRIELLO, Giovanni; SANDER, Chris; SCHULTZ, Nikolaus (CELL PRESS, CAMBRIDGE, USA, 2018)
    Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ ...
  • MALTA, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic ...
  • DING, 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.; WENDL, Michael C.; SHMULEVICH, Llya; LAZAR, Alexander J.; WHEELER, David A.; GETZ, Gad (CELL PRESS, CAMBRIDGE, USA, 2018)
    The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 ...
  • HOADLEY, 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. (CELL PRESS, CAMBRIDGE, USA, 2018)
    We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed ...
  • LIU, 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. (CELL PRESS, CAMBRIDGE, USA, 2018)
    We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct ...
  • WANG, Zehua; YANG, Bo; ZHANG, Min; GUO, Weiwei; WU, Zhiyuan; WANG, Yue; JIA, Lin; LI, Song; XIE, Wen; YANG, Da (CELL PRESS, CAMBRIDGE, USA, 2018)
    We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed ...
  • BERGER, 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.; OJESINA, Akinyemi I.; ADEBAMOWO, Clement; ADEBAMOWO, Sally N.; BAGGERLY, Keith A.; CHEN, Ting-Wen; CHIU, Hua-Sheng; LEFEVER, Steve; LIU, Liang; MACKENZIE, Karen; ORSULIC, Sandra; ROSZIK, Jason; SHELLEY, Carl Simon; SONG, Qianqian; VELLANO, Christopher P.; WENTZENSEN, Nicolas; WEINSTEIN, John N.; MILLS, Gordon B.; LEVINE, Douglas A.; AKBANI, Rehan (CELL PRESS, CAMBRIDGE, USA, 2018)
    We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and ...
  • TAYLOR, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic ...
  • RICKETTS, Christopher J.; CUBAS, Aguirre A. De; 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; KWIATKOWSKI, David J.; LUI, Wembin; MERINO, Maria J.; MILLS, Gordon B.; MYERS, Jerome; NICKERSON, Michael L.; REUTER, Victor E.; SCHMIDT, Laura S.; SHELLEY, C. Simon; SHEN, Hui; SHUCH, Brian; SIGNORETTI, Sabina; SRINIVASAN, Ramaprasad; TAMBOLI, Pheroze; THOMAS, George; VINCENT, Benjamin G.; VOCKE, Cathy D.; WHEELER, David A.; YANG, Lixing; KIM, William Y.; ROBERTSON, A. Gordon; SPELLMAN, Paul T.; RATHMELL, W. Kimryn; LINEHAN, W. Marston (CELL PRESS, CAMBRIDGE, USA, 2018)

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