Artigos e Materiais de Revistas Científicas - LIM/14

Artigos e Materiais de Revistas Científicas - LIM/14

 

A coleção de Artigos e Materiais de Revistas Científicas engloba artigos originais, artigos de revisão, artigos de atualização, artigos técnicos, relatos de experiências, resenhas, ensaios, editoriais, cartas ao editor, debates, notas científicas e técnicas, depoimentos, entrevistas e pontos de vista. Consideram-se como artigos científicos originais os trabalhos redigidos para divulgação de informações e resultados sobre determinada pesquisa científica, publicados em periódico científico após avaliação por outros pesquisadores.

Recent Submissions

  • SCHAUB, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers ...
  • ELLROTT, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center ...
  • 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; KWAITKOWSKI, 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 T.; ROBERTSON, A. Gordon; SPELLMAN, Paul T.; RATHMELL, W. Kimryn; LINEHAN, W. Marston (CELL PRESS, CAMBRIDGE, USA, 2018)
    Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three ...
  • CHIU, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors ...
  • SEILER, Michael; PENG, Shouyong; AGRAWAL, Anant A.; PALACINO, James; TENG, Teng; ZHU, Ping; SMITH, Peter G.; BUONAMICI, Silvia; YU, Lihua (CELL PRESS, CAMBRIDGE, USA, 2018)
    Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across ...
  • JAYASINGHE, 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 (CELL PRESS, CAMBRIDGE, USA, 2018)
    For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale ...
  • 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 ...

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