Search Results - "Hahn, William C"

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects by Dempster, Joshua M, Boyle, Isabella, Vazquez, Francisca, Root, David E, Boehm, Jesse S, Hahn, William C, Tsherniak, Aviad, McFarland, James M

“…CRISPR loss of function screens are powerful tools to interrogate biology but exhibit a number of biases and artifacts that can confound the results. Here, we…”
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HIF1A Employs CDK8-Mediator to Stimulate RNAPII Elongation in Response to Hypoxia by Galbraith, Matthew D., Allen, Mary A., Bensard, Claire L., Wang, Xiaoxing, Schwinn, Marie K., Qin, Bo, Long, Henry W., Daniels, Danette L., Hahn, William C., Dowell, Robin D., Espinosa, Joaquín M.

“…The transcription factor HIF1A is a key mediator of the cellular response to hypoxia. Despite the importance of HIF1A in homeostasis and various pathologies,…”
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Multiple pathways regulated by the tumor suppressor PP2A in transformation by Westermarck, Jukka, Hahn, William C

“…Reversible protein phosphorylation plays a central role in regulating intracellular signaling. Dysregulation of the mechanisms that regulate phosphorylation…”
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KRAS and YAP1 Converge to Regulate EMT and Tumor Survival by Shao, Diane D., Xue, Wen, Krall, Elsa B., Bhutkar, Arjun, Piccioni, Federica, Wang, Xiaoxing, Schinzel, Anna C., Sood, Sabina, Rosenbluh, Joseph, Kim, Jong W., Zwang, Yaara, Roberts, Thomas M., Root, David E., Jacks, Tyler, Hahn, William C.

“…Cancer cells that express oncogenic alleles of RAS typically require sustained expression of the mutant allele for survival, but the molecular basis of this…”
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Organoid Modeling of the Tumor Immune Microenvironment by Neal, James T., Li, Xingnan, Zhu, Junjie, Giangarra, Valeria, Grzeskowiak, Caitlin L., Ju, Jihang, Liu, Iris H., Chiou, Shin-Heng, Salahudeen, Ameen A., Smith, Amber R., Deutsch, Brian C., Liao, Lillian, Zemek, Allison J., Zhao, Fan, Karlsson, Kasper, Schultz, Liora M., Metzner, Thomas J., Nadauld, Lincoln D., Tseng, Yuen-Yi, Alkhairy, Sahar, Oh, Coyin, Keskula, Paula, Mendoza-Villanueva, Daniel, De La Vega, Francisco M., Kunz, Pamela L., Liao, Joseph C., Leppert, John T., Sunwoo, John B., Sabatti, Chiara, Boehm, Jesse S., Hahn, William C., Zheng, Grace X.Y., Davis, Mark M., Kuo, Calvin J.

“…In vitro cancer cultures, including three-dimensional organoids, typically contain exclusively neoplastic epithelium but require artificial reconstitution to…”
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The landscape of cancer cell line metabolism by Li, Haoxin, Ning, Shaoyang, Ghandi, Mahmoud, Kryukov, Gregory V., Gopal, Shuba, Deik, Amy, Souza, Amanda, Pierce, Kerry, Keskula, Paula, Hernandez, Desiree, Ann, Julie, Shkoza, Dojna, Apfel, Verena, Zou, Yilong, Vazquez, Francisca, Barretina, Jordi, Pagliarini, Raymond A., Galli, Giorgio G., Root, David E., Hahn, William C., Tsherniak, Aviad, Giannakis, Marios, Schreiber, Stuart L., Clish, Clary B., Garraway, Levi A., Sellers, William R.

“…Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism…”
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Making sense of cancer genomic data by Chin, Lynda, Hahn, William C, Getz, Gad, Meyerson, Matthew

“…High-throughput tools for nucleic acid characterization now provide the means to conduct comprehensive analyses of all somatic alterations in the cancer…”
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Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells by Meyers, Robin M, Bryan, Jordan G, McFarland, James M, Weir, Barbara A, Sizemore, Ann E, Xu, Han, Dharia, Neekesh V, Montgomery, Phillip G, Cowley, Glenn S, Pantel, Sasha, Goodale, Amy, Lee, Yenarae, Ali, Levi D, Jiang, Guozhi, Lubonja, Rakela, Harrington, William F, Strickland, Matthew, Wu, Ting, Hawes, Derek C, Zhivich, Victor A, Wyatt, Meghan R, Kalani, Zohra, Chang, Jaime J, Okamoto, Michael, Stegmaier, Kimberly, Golub, Todd R, Boehm, Jesse S, Vazquez, Francisca, Root, David E, Hahn, William C, Tsherniak, Aviad

“…CERES is a new computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for copy number effects and…”
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Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration by McFarland, James M., Ho, Zandra V., Kugener, Guillaume, Dempster, Joshua M., Montgomery, Phillip G., Bryan, Jordan G., Krill-Burger, John M., Green, Thomas M., Vazquez, Francisca, Boehm, Jesse S., Golub, Todd R., Hahn, William C., Root, David E., Tsherniak, Aviad

“…The availability of multiple datasets comprising genome-scale RNAi viability screens in hundreds of diverse cancer cell lines presents new opportunities for…”
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Synthetic Lethal Vulnerabilities in KRAS -Mutant Cancers by Aguirre, Andrew J, Hahn, William C

“…KRAS is the most commonly mutated oncogene in human cancer. Most -mutant cancers depend on sustained expression and signaling of KRAS, thus making it a…”
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β-Catenin-Driven Cancers Require a YAP1 Transcriptional Complex for Survival and Tumorigenesis by Rosenbluh, Joseph, Nijhawan, Deepak, Cox, Andrew G., Li, Xingnan, Neal, James T., Schafer, Eric J., Zack, Travis I., Wang, Xiaoxing, Tsherniak, Aviad, Schinzel, Anna C., Shao, Diane D., Schumacher, Steven E., Weir, Barbara A., Vazquez, Francisca, Cowley, Glenn S., Root, David E., Mesirov, Jill P., Beroukhim, Rameen, Kuo, Calvin J., Goessling, Wolfram, Hahn, William C.

“…Wnt/β-catenin signaling plays a key role in the pathogenesis of colon and other cancers; emerging evidence indicates that oncogenic β-catenin regulates several…”
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Global computational alignment of tumor and cell line transcriptional profiles by Warren, Allison, Chen, Yejia, Jones, Andrew, Shibue, Tsukasa, Hahn, William C., Boehm, Jesse S., Vazquez, Francisca, Tsherniak, Aviad, McFarland, James M.

“…Cell lines are key tools for preclinical cancer research, but it remains unclear how well they represent patient tumor samples. Direct comparisons of tumor and…”
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A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer by Takeda, David Y., Spisák, Sándor, Seo, Ji-Heui, Bell, Connor, O’Connor, Edward, Korthauer, Keegan, Ribli, Dezső, Csabai, István, Solymosi, Norbert, Szállási, Zoltán, Stillman, David R., Cejas, Paloma, Qiu, Xintao, Long, Henry W., Tisza, Viktória, Nuzzo, Pier Vitale, Rohanizadegan, Mersedeh, Pomerantz, Mark M., Hahn, William C., Freedman, Matthew L.

“…Increased androgen receptor (AR) activity drives therapeutic resistance in advanced prostate cancer. The most common resistance mechanism is amplification of…”
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The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis by Pomerantz, Mark M, Li, Fugen, Takeda, David Y, Lenci, Romina, Chonkar, Apurva, Chabot, Matthew, Cejas, Paloma, Vazquez, Francisca, Cook, Jennifer, Shivdasani, Ramesh A, Bowden, Michaela, Lis, Rosina, Hahn, William C, Kantoff, Philip W, Brown, Myles, Loda, Massimo, Long, Henry W, Freedman, Matthew L

“…Matthew Freedman and colleagues show that androgen receptor (AR) binding sites undergo extensive reprogramming during prostate epithelial transformation. They…”
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Mutational processes shape the landscape of TP53 mutations in human cancer by Giacomelli, Andrew O., Yang, Xiaoping, Lintner, Robert E., McFarland, James M., Duby, Marc, Kim, Jaegil, Howard, Thomas P., Takeda, David Y., Ly, Seav Huong, Kim, Eejung, Gannon, Hugh S., Hurhula, Brian, Sharpe, Ted, Goodale, Amy, Fritchman, Briana, Steelman, Scott, Vazquez, Francisca, Tsherniak, Aviad, Aguirre, Andrew J., Doench, John G., Piccioni, Federica, Roberts, Charles W. M., Meyerson, Matthew, Getz, Gad, Johannessen, Cory M., Root, David E., Hahn, William C.

“…Unlike most tumor suppressor genes, the most common genetic alterations in tumor protein p53 (TP53) are missense mutations 1 , 2 . Mutant p53 protein is often…”
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Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling by WAGLE, Nikhil, EMERY, Caroline, MEYERSON, Matthew, GARRAWAY, Levi A, BERGER, Michael F, DAVIS, Matthew J, SAWYER, Allison, POCHANARD, Panisa, KEHOE, Sarah M, JOHANNESSEN, Cory M, MACCONAILL, Laura E, HAHN, William C

“…A detailed understanding of the mechanisms by which tumors acquire resistance to targeted anticancer agents should speed the development of treatment…”
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Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets by Dempster, Joshua M., Pacini, Clare, Pantel, Sasha, Behan, Fiona M., Green, Thomas, Krill-Burger, John, Beaver, Charlotte M., Younger, Scott T., Zhivich, Victor, Najgebauer, Hanna, Allen, Felicity, Gonçalves, Emanuel, Shepherd, Rebecca, Doench, John G., Yusa, Kosuke, Vazquez, Francisca, Parts, Leopold, Boehm, Jesse S., Golub, Todd R., Hahn, William C., Root, David E., Garnett, Mathew J., Tsherniak, Aviad, Iorio, Francesco

“…Genome-scale CRISPR-Cas9 viability screens performed in cancer cell lines provide a systematic approach to identify cancer dependencies and new therapeutic…”
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Loss of ATRX, genome instability, and an altered DNA damage response are hallmarks of the alternative lengthening of telomeres pathway by Lovejoy, Courtney A, Li, Wendi, Reisenweber, Steven, Thongthip, Supawat, Bruno, Joanne, de Lange, Titia, De, Saurav, Petrini, John H J, Sung, Patricia A, Jasin, Maria, Rosenbluh, Joseph, Zwang, Yaara, Weir, Barbara A, Hatton, Charlie, Ivanova, Elena, Macconaill, Laura, Hanna, Megan, Hahn, William C, Lue, Neal F, Reddel, Roger R, Jiao, Yuchen, Kinzler, Kenneth, Vogelstein, Bert, Papadopoulos, Nickolas, Meeker, Alan K

“…The Alternative Lengthening of Telomeres (ALT) pathway is a telomerase-independent pathway for telomere maintenance that is active in a significant subset of…”
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Predicting cell health phenotypes using image-based morphology profiling by Way, Gregory P, Kost-Alimova, Maria, Shibue, Tsukasa, Harrington, William F, Gill, Stanley, Piccioni, Federica, Becker, Tim, Shafqat-Abbasi, Hamdah, Hahn, William C, Carpenter, Anne E, Vazquez, Francisca, Singh, Shantanu

“…Genetic and chemical perturbations impact diverse cellular phenotypes, including multiple indicators of cell health. These readouts reveal toxicity and…”
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Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells by Gannon, Hugh S., Zou, Tao, Kiessling, Michael K., Gao, Galen F., Cai, Diana, Choi, Peter S., Ivan, Alexandru P., Buchumenski, Ilana, Berger, Ashton C., Goldstein, Jonathan T., Cherniack, Andrew D., Vazquez, Francisca, Tsherniak, Aviad, Levanon, Erez Y., Hahn, William C., Meyerson, Matthew

“…Systematic exploration of cancer cell vulnerabilities can inform the development of novel cancer therapeutics. Here, through analysis of genome-scale…”
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