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Journal of visualized experiments : JoVE, ISSN 1940-087X, 05/2019, Issue 147
Continuous culture methods enable cells to be grown under quantitatively controlled environmental conditions, and are thus broadly useful for measuring fitness... 
systems biology | experimental evolution | microbial populations | growth selection | eVOLVER | lab automation | fitness landscape | continuous culture
Journal Article
by Zehir, Ahmet and Benayed, Ryma and Shah, Ronak H and Syed, Aijazuddin and Middha, Sumit and Kim, Hyunjae R and Srinivasan, Preethi and Gao, Jianjiong and Chakravarty, Debyani and Devlin, Sean M and Hellmann, Matthew D and Barron, David A and Schram, Alison M and Hameed, Meera and Dogan, Snjezana and Ross, Dara S and Hechtman, Jaclyn F and DeLair, Deborah F and Yao, JinJuan and Mandelker, Diana L and Cheng, Donavan T and Chandramohan, Raghu and Mohanty, Abhinita S and Ptashkin, Ryan N and Jayakumaran, Gowtham and Prasad, Meera and Syed, Mustafa H and Rema, Anoop Balakrishnan and Liu, Zhen Y and Nafa, Khedoudja and Borsu, Laetitia and Sadowska, Justyna and Casanova, Jacklyn and Bacares, Ruben and Kiecka, Iwona J and Razumova, Anna and Son, Julie B and Stewart, Lisa and Baldi, Tessara and Mullaney, Kerry A and Al-Ahmadie, Hikmat and Vakiani, Efsevia and Abeshouse, Adam A and Penson, Alexander V and Jonsson, Philip and Camacho, Niedzica and Chang, Matthew T and Won, Helen H and Gross, Benjamin E and Kundra, Ritika and Heins, Zachary J and Chen, Hsiao-Wei and Phillips, Sarah and Zhang, Hongxin and Wang, Jiaojiao and Ochoa, Angelica and Wills, Jonathan and Eubank, Michael and Thomas, Stacy B and Gardos, Stuart M and Reales, Dalicia N and Galle, Jesse and Durany, Robert and Cambria, Roy and Abida, Wassim and Cercek, Andrea and Feldman, Darren R and Gounder, Mrinal M and Hakimi, A. Ari and Harding, James J and Iyer, Gopa and Janjigian, Yelena Y and Jordan, Emmet J and Kelly, Ciara M and Lowery, Maeve A and Morris, Luc G. T and Omuro, Antonio M and Raj, Nitya and Razavi, Pedram and Shoushtari, Alexander N and Shukla, Neerav and Soumerai, Tara E and Varghese, Anna M and Yaeger, Rona and Coleman, Jonathan and Bochner, Bernard and Riely, Gregory J and Saltz, Leonard B and Scher, Howard I and Sabbatini, Paul J and Robson, Mark E and Klimstra, David S and Taylor, Barry S and Baselga, Jose and Schultz, Nikolaus and Hyman, David M and Arcila, Maria E and Solit, David B and Ladanyi, Marc and Berger, Michael F
Nature Medicine, ISSN 1078-8956, 06/2017, Volume 23, Issue 6, pp. 703 - 713
Journal Article
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 | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
Journal Article
by Sanchez-Vega, Francisco and Mina, Marco and Armenia, Joshua and Chatila, Walid K and Luna, Augustin and La, Konnor and La, Konnor C and Dimitriadoy, Sofia and Liu, Jia and Liu, Yuexin and Liu, David L and Liu, Wenbin and Liu, Xiuping and Kantheti, Havish S and Saghafinia, Sadegh and Chakravarty, Debyani and Daian, Foysal and Gao, Qingsong and Gao, Galen F and Gao, Jianjiong and Bailey, Matthew H and Bailey, Matthew and Liang, Wen-Wei and Liang, Han and Foltz, Steven M and Shmulevich, Ilya and Ding, Li and Heins, Zachary and Heins, Zachary J and Ochoa, Angelica and Gross, Benjamin E and Gross, Benjamin and Zhang, Wei and Zhang, Hongzheng and Zhang, Hailei and Zhang, Hongxin and Zhang, Jiexin and Zhang, Jiashan (Julia) and Zhang, Lizhi and Kundra, Ritika and Kandoth, Cyriac and Bahceci, Istemi and Dervishi, Leonard and Dogrusoz, Ugur and Zhou, Wanding and Shen, Hui and Laird, Peter W and Way, Gregory P and Greene, Casey S and Xiao, Yonghong and Wang, Timothy and Wang, Jioajiao and Wang, Chen and Wang, Zhining and Wang, Linghua and Wang, Jing and Wang, Min and Iavarone, Antonio and Berger, Ashton C and Berger, Alice H and Bivona, Trever G and Lazar, Alexander J and Hammer, Gary D and Giordano, Thomas and Kwong, Lawrence N and McArthur, Grant and Huang, Chenfei and Tward, Aaron D and Frederick, Mitchell J and McCormick, Frank and Meyerson, Matthew 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, Hannah and Yang, Ian and Yang, Ju Dong and Yang, Liming and Zenklusen, Jean C 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 Gehlenborg, Nils and Getz, Gad and Heiman, David I and Kim, Jaegil and Lawrence, Michael S and ... and Cancer Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell, ISSN 0092-8674, 04/2018, Volume 173, Issue 2, pp. 321 - 337.e10
Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent,... 
cancer genome atlas | precision oncology | therapeutics | pan-cancer | signaling pathways | PanCanAtlas | combination therapy | cancer genomics | whole exome sequencing | TCGA | SIGNATURES | COMPREHENSIVE MOLECULAR CHARACTERIZATION | LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENES | MUTATIONS | EXPRESSION | CELL BIOLOGY
Journal Article
by Bailey, Matthew and Bailey, Matthew H and Tokheim, Collin and Porta-Pardo, Eduard and Sengupta, Sohini and Bertrand, Denis and Weerasinghe, Amila and Colaprico, Antonio and Wendl, Michael C and Kim, Jaegil and Reardon, Brendan and Ng, Kwok-Shing and Ng, Patrick Kwok-Shing and Jeong, Kang Jin and Cao, Song and Wang, Jioajiao and Wang, Timothy and Wang, Zhining and Wang, Zixing and Wang, Fang and Wang, Linghua and Wang, Jing and Wang, Min and Gao, Qingsong and Gao, Jianjiong and Gao, Galen F and Liu, Xiuping and Liu, Jia and Liu, Wenbin and Liu, Yuexin and Liu, Eric Minwei and Mularoni, Loris and Rubio-Perez, Carlota and Nagarajan, Niranjan and Cortés-Ciriano, Isidro and Zhou, Wanding and Zhou, Daniel Cui and Liang, Wen-Wei and Liang, Han and Hess, Julian M and Hess, Julian and Yellapantula, Venkata D and Tamborero, David and Gonzalez-Perez, Abel and Suphavilai, Chayaporn and Ko, Jia Yu and Khurana, Ekta and Park, Joong-Won and Park, Peter J and Van Allen, Eliezer M 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, Ju Dong and Yang, Hannah and Yang, Ian and Yang, Liming and Zenklusen, Jean C and Zhang, Wei and Zhang, Hongzheng and Zhang, Hailei and Zhang, Hongxin and Zhang, Jiexin and Zhang, Jiashan (Julia) and Zhang, Lizhi 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 Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Miller, Michael and Miller, Christopher A and Miller, Judy and Reynolds, Sheila and ... and Canc Genome Atlas Res Network and MC3 Working Grp and MC3 Working Group and Cancer Genome Atlas Research Network
Cell, ISSN 0092-8674, 04/2018, Volume 173, Issue 2, pp. 371 - 385.e18
Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to... 
structure analysis | mutations of clinical relevance | oncology | driver gene discovery | MELANOMA | VARIANTS | SIGNATURES | LANDSCAPE | MICROSATELLITE INSTABILITY | PD-1 BLOCKADE | BIOCHEMISTRY & MOLECULAR BIOLOGY | PATTERNS | OPEN-LABEL | SOMATIC MUTATIONS | DISCOVERY | CELL BIOLOGY | Oncology | driver discovery
Journal Article