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1. Full Text The Immune Landscape of Cancer
by Thorsson, Vesteinn and Thorsson, Vésteinn and Gibbs, Richard A and Gibbs, David L and Brown, Scott D and Wolf, Gregory and Wolf, Denise and Bortone, Dante S and Ou Yang, Tai-Hsien and Porta-Pardo, Eduard and Gao, Galen F and Gao, Jianjiong and Plaisier, Christopher L and Eddy, James A and Ziv, Elad and Culhane, Aedin C and Paull, Evan O and Sivakumar, I.K. Ashok and Gentles, Andrew J and Malhotra, Raunaq and Farshidfar, Farshad and Colaprico, Antonio and Parker, Joel S and Mose, Lisle E and Vo, Nam Sy and Liu, Wenbin and Liu, Jianfang and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Rader, Janet and Dhankani, Varsha and Reynolds, Sheila and Reynolds, Sheila M and Bowlby, Reanne and Califano, Andrea and Cherniack, Andrew D and Anastassiou, Dimitris and Bedognetti, Davide and Mokrab, Younes and Newman, Aaron M and Rao, Arvind and Chen, Amy and Chen, Chu and Chen, Ken and Krasnitz, Alexander and Hu, Jianhong and Hu, Hai and Malta, Tathiane M and Noushmehr, Houtan and Pedamallu, Chandra Sekhar and Bullman, Susan and Ojesina, Akinyemi I and Lamb, Andrew and Zhou, Wanding and Shen, Hui and Choueiri, Toni K and Weinstein, John N and Guinney, Justin and Saltz, Joel and Holt, Robert and Holt, Robert A and Rabkin, Charles S 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 Wang, Jioajiao and Wang, Min and Wang, Linghua and Wang, Zhining and Wang, Timothy and Wang, Jing and Yang, Ju Dong and Yang, Hannah and Yang, Liming and Yang, Ian and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Zhang, Jiexin and Zhang, Lizhi and Zhang, Wei and Zhang, Hongzheng and Zhang, Hailei and Zhang, Hongxin and Chudamani, Sudha and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Yichao and Sun, Qiang and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Immunity, ISSN 1074-7613, 04/2018, Volume 48, Issue 4, pp. 812 - 830.e14
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across... 
tumor immunology | immunotherapy | cancer genomics | integrative network analysis | immuno-oncology | tumor microenvironment | immune subtypes | immunomodulatory | GENOMIC ANALYSES | INFORMATION | T-CELL-RECEPTOR | REGULATORY NETWORK | CLASSIFICATION | IMMUNOLOGY | SEQUENCING DATA | SOMATIC MUTATIONS | COMPREHENSIVE ANALYSIS | PREDICTION | REVEALS | Transforming Growth Factor beta - immunology | Prognosis | Humans | Middle Aged | Th1-Th2 Balance - physiology | Male | Neoplasms - classification | Wound Healing - immunology | Young Adult | Transforming Growth Factor beta - genetics | Neoplasms - genetics | Neoplasms - immunology | Interferon-gamma - immunology | Adolescent | Aged, 80 and over | Adult | Female | Aged | Interferon-gamma - genetics | Wound Healing - genetics | Genomics - methods | Child | Macrophages - immunology | Cell proliferation | Cluster analysis | Transcription | Copy number | p53 Protein | Lung cancer | Genomics | Aneuploidy | Lymphocytes T | Genomes | Cell interactions | Macrophages | Immunotherapy | DNA methylation | Deoxyribonucleic acid--DNA | Immune system | Medical research | Wound healing | Immunomodulation | MiRNA | Stockholders | Inflammation | T cell receptors | Communications networks | Gene expression | White blood cells | Inventors | Medical prognosis | γ-Interferon | Mutation | Cancer | Tumors | Index Medicus | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
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2. Full Text The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima
by Chipman, Ariel D and Ferrier, David E K and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S T and Schröder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C and Alonso, Claudio R and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C J and Blankenburg, Kerstin P and Brites, Daniela and Capella-Gutiérrez, Salvador and Coyle, Marcus and Dearden, Peter K and Du Pasquier, Louis and Duncan, Elizabeth J and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D and Extavour, Cassana G and Francisco, Liezl and Gabaldón, Toni and Gillis, William J and Goodwin-Horn, Elizabeth A and Green, Jack E and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J P and Gubbala, Sai and Guigó, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H L and Hunn, Julia P and Hunnekuhl, Vera S and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N and Jiggins, Francis M and Jones, Tamsin E and Kaiser, Tobias S and Kalra, Divya and Kenny, Nathan J and Korchina, Viktoriya and Kovar, Christie L and Kraus, F Bernhard and Lapraz, François and Lee, Sana L and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J and Patil, Shobha and Patraquim, Peo and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C and Robertson, Helen E and Robertson, Hugh M and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sánchez-Gracia, Alejano and Scherer, Steven E and Schurko, Anew M and Siggens, Kenneth W and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M and Willis, Judith H and Wu, Yuanqing and Zou, Xiaoyan and ...
PLoS Biology, ISSN 1544-9173, 11/2014, Volume 12, Issue 11, pp. e1002005 - e1002005
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but... 
PHYLOGENY | EVOLUTION | PROTEIN | DNA METHYLATION | SEGMENT FORMATION | JUVENILE-HORMONE SYNTHESIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | OLFACTORY RECEPTORS | BIOLOGY | DROSOPHILA | ODORANT-BINDING | FAMILY | Multigene Family | Protein Kinases - genetics | Arthropods - genetics | Selenoproteins - genetics | Circadian Rhythm Signaling Peptides and Proteins - genetics | Synteny | Male | Phylogeny | Sex Chromosomes | Transcription Factors - genetics | RNA, Untranslated - genetics | Hormones - genetics | Polymorphism, Genetic | DNA Methylation | Animals | Receptors, Odorant - genetics | Female | Genome, Mitochondrial | Genome | Evolution, Molecular | Index Medicus | Genètica evolutiva | Genètica animal | Proteins | Scholarships & fellowships | Insects | Genes | Genomics | Project management | Colleges & universities | Phylogenetics | Genomes
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3. Full Text Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
by Knijnenburg, Theo and Knijnenburg, Theo A and Wang, Chen and Wang, Linghua and Wang, Jing and Wang, Jioajiao and Wang, Min and Wang, Zhining and Wang, Timothy and Zimmermann, Michael T and Chambwe, Nyasha and Gao, Jianjiong and Gao, Galen F and Cherniack, Andrew D and Fan, Huihui and Fan, Cheng and Shen, Yang and Shen, Hui and Way, Gregory P and Greene, Casey S and Liu, Wenbin and Liu, Jianfang and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Akbani, Rehan and Feng, Bin and Donehower, Lawrence A and Miller, Christopher A and Miller, Chase and Miller, Judy and Miller, Michael and Karimi, Mostafa and Chen, Haoran and Chen, Amy and Chen, Chu and Kim, Jaegil and Kim, Pora and Jia, Peilin and Shinbrot, Eve and Zhang, Hongxin and Zhang, Wei and Zhang, Hailei and Zhang, Jiashan (Julia) and Zhang, Lizhi and Zhang, Jiexin and Zhang, Shaojun and Zhang, Hongzheng and Hu, Jianhong and Hu, Hai and Bailey, Matthew H and Bailey, Matthew and Yau, Christina and Wolf, Denise and Wolf, Gregory and Zhao, Fengmei and Zhao, Zhongming and Weinstein, John N and Li, Lei and Li, Jun and Li, Wei and Ding, Li and Mills, Gordon B and Laird, Peter W and Wheeler, David A and Shmulevich, Ilya 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, Ian and Yang, Ju Dong and Yang, Hannah and Yang, Liming and Zenklusen, Jean C and Chudamani, Sudha 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 Lawrence, Michael S and Lin, Pei and Meier, Sam and Noble, Michael S and Saksena, Gordon and Voet, Doug and Bernard, Brady and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 239 - 254.e6
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a... 
somatic mutations | DNA damage repair | protein structure analysis | mutational signatures | somatic copy-number alterations | DNA damage footprints | The Cancer Genome Atlas PanCanAtlas project | epigenetic silencing | integrative statistical analysis | POLYMERASE-EPSILON | HUMAN COLON | INACTIVATION | REPLICATION FORK STABILITY | PROMOTER HYPERMETHYLATION | STRUCTURAL BASIS | MICROSATELLITE INSTABILITY | MUTANT-CELLS | MUTATIONS | PREDICTS RESPONSE | CELL BIOLOGY | Index Medicus
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4. 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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