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by Thorsson, Vésteinn and Gibbs, David L and Brown, Scott D and Wolf, Denise and Bortone, Dante S and Ou Yang, Tai-Hsien and Porta-Pardo, Eduard and Gao, Galen F 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, Jianfang and Liu, Yuexin and Rader, Janet and Dhankani, Varsha 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, Ken and Krasnitz, Alexander 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 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, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang 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 Kim, Jaegil and Lawrence, Michael S and Lin, Pei and Meier, Sam and Noble, Michael S and Saksena, Gordon and Voet, Doug and Zhang, Hailei and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Reynolds, Sheila and Shmulevich, Ilya and Thorsson, Vesteinn and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and ... and The Cancer Genome Atlas Research Network 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 | Immunology | Infectious Diseases | Immunology and Allergy | 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 | miRNA | Deoxyribonucleic acid--DNA | Immune system | Medical research | Wound healing | Immunomodulation | Stockholders | Inflammation | T cell receptors | Communications networks | Gene expression | White blood cells | Inventors | Medical prognosis | γ-Interferon | Mutation | Cancer | Tumors | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
Journal Article
by Saltz, Joel and Gupta, Rajarsi and Hou, Le and Kurc, Tahsin and Singh, Pankaj and Nguyen, Vu and Samaras, Dimitris and Shroyer, Kenneth R and Zhao, Tianhao and Batiste, Rebecca and Van Arnam, John 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, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang 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 Kim, Jaegil and Lawrence, Michael S and Lin, Pei and Meier, Sam and Noble, Michael S and Saksena, Gordon and Voet, Doug and Zhang, Hailei and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Reynolds, Sheila and Shmulevich, Ilya and Thorsson, Vesteinn and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and Ju, Zhenlin and Kanchi, Rupa S and Korkut, Anil and Li, Jun and Liang, Han and Ling, Shiyun and Liu, Wenbin and Lu, Yiling and Mills, Gordon B and Ng, Kwok-Shing and Rao, Arvind and Ryan, Michael and Wang, Jing and Weinstein, John N and Zhang, Jiexin and Abeshouse, Adam and Armenia, Joshua and Chakravarty, Debyani and Chatila, Walid K and de Bruijn, Ino and Gao, Jianjiong and Gross, Benjamin E and Heins, Zachary J and Kundra, Ritika and La, Konnor and Ladanyi, Marc and Luna, Augustin and Nissan, Moriah G and Ochoa, Angelica and Phillips, Sarah M and Reznik, Ed and Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sheridan, Robert and Sumer, S. Onur and Sun, Yichao and Taylor, Barry S and Wang, Jioajiao and Zhang, Hongxin and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 181 - 193.e7
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this... 
deep learning | lymphocytes | digital pathology | bioinformatics | computer vision | tumor-infiltrating lymphocytes | immuno-oncology | tumor microenvironment | machine learning | artificial intelligence | MELANOMA | IMMUNE CONTEXTURE | GENOMIC ANALYSES | SOLID TUMORS | SUBTYPES | SQUAMOUS-CELL CARCINOMA | PROPOSAL | CANCER | STANDARDIZED METHOD | BREAST | CELL BIOLOGY
Journal Article
by Shungin, Dmitry and Winkler, Thomas W and Croteau-Chonka, Damien C and Ferreira, Teresa and Locke, Adam E and Mägi, Reedik and Strawbridge, Rona J and Pers, Tune H and Fischer, Krista and Justice, Anne E and Workalemahu, Tsegaselassie and Wu, Joseph M. W and Buchkovich, Martin L and Heard-Costa, Nancy L and Roman, Tamara S and ng, Alexander W and Song, Ci and Gustafsson, Stefan and Day, Felix R and Esko, Tonu and Fall, Tove and Kutalik, Zoltán and Luan, Jian'an and Randall, Joshua C and Scherag, Ané and Vedantam, Sailaja and Wood, Anew R and Chen, Jin and Fehrmann, Rudolf and Karjalainen, Juha and Kahali, Bratati and Liu, Ching-Ti and Schmidt, Ellen M and Absher, Devin and Amin, Najaf and Anderson, Denise and Beekman, Marian and Bragg-Gresham, Jennifer L and Buyske, Steven and Demirkan, Ayse and Ehret, Georg B and Feitosa, Mary F and Goel, Anuj and Jackson, Anne U and Johnson, Toby and Kleber, Marcus E and Henneman, Peter and Hovingh, G. Kees and Kastelein, John J. P and Chen, Wei and PAGE Consortium and LifeLines Cohort Study and CARDIOGRAMplusC4D Consortium and MuTHER Consortium and ICBP and ADIPOGEN Consortium and CKDGen Consortium and GEFOS Consortium and Int Endogene Consortium and GENIE Consortium and MAGIC Investigators and ReproGen Consortium and GLGC and ADIPOGen Consortium and International Endogene Consortium and The PAGE Consortium and The International Endogene Consortium and The MAGIC Investigators and The ReproGen Consortium and The CKDGen Consortium and The ADIPOGen Consortium and The ICBP and The CARDIOGRAMplusC4D Consortium and The GENIE Consortium and The GLGC and The GEFOS Consortium and The MuTHER Consortium and The LifeLines Cohort Study and Högskolan Dalarna and Akademin Utbildning, hälsa och samhälle and Medicinsk vetenskap
Nature, ISSN 0028-0836, 2015, Volume 518, Issue 7538, pp. 187 - U378
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our... 
ABDOMINAL ADIPOSITY | METAANALYSIS | VARIANTS | MULTIDISCIPLINARY SCIENCES | COMMON SNPS | GLYCEMIC TRAITS | RISK | FALSE DISCOVERY | GENOME-WIDE ASSOCIATION | ADIPOGENIC DIFFERENTIATION | SEXUAL-DIMORPHISM | Body Mass Index | Genome-Wide Association Study | Age Factors | Neovascularization, Physiologic - genetics | Epigenesis, Genetic | Humans | Male | Continental Population Groups - genetics | Sex Characteristics | Obesity - genetics | Europe - ethnology | Genome, Human - genetics | Adipose Tissue - metabolism | Insulin - metabolism | Models, Biological | Adipocytes - metabolism | Insulin Resistance - genetics | Polymorphism, Single Nucleotide - genetics | Female | Body Fat Distribution | Transcription, Genetic - genetics | Adipogenesis - genetics | Waist-Hip Ratio | Quantitative Trait Loci - genetics | Adipose tissues | Quantitative trait loci | Genetic research | Genetic aspects | Research | Metabolism | Health aspects | Studies | Body mass index | Genealogy | Body fat | Insulin resistance | Genetics | Genomes | Abdomen | Meta-analysis | Life Sciences | Adipocytes/metabolism Adipogenesis/genetics Adipose Tissue/metabolism Age Factors Body Fat Distribution Body Mass Index Continental Population Groups/genetics Epigenesis, Genetic Europe/ethnology Female Genome, Human/genetics Genome-Wide Association Study Humans Insulin/metabolism Insulin Resistance/genetics Male Models, Biological Neovascularization, Physiologic/genetics Obesity/genetics Polymorphism, Single Nucleotide/genetics Quantitative Trait Loci/genetics Sex Characteristics Transcription, Genetic/genetics Waist-Hip Ratio | Clinical Medicine | Hälsa och välfärd | Medical and Health Sciences | Klinisk medicin | Medicin och hälsovetenskap | Health and Welfare
Journal Article