Search Results - "Doench, John"

Am I ready for CRISPR? A user's guide to genetic screens by Doench, John G.

“…Key Points Pooled screens are a cost-effective approach to investigating phenotypes at the genome scale and build on technological innovations with lentivirus,…”
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Design and analysis of CRISPR–Cas experiments by Hanna, Ruth E., Doench, John G.

“…A large and ever-expanding set of CRISPR–Cas systems now enables the rapid and flexible manipulation of genomes in both targeted and large-scale experiments…”
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CRISPR screens for functional interrogation of immunity by Shi, Hao, Doench, John G., Chi, Hongbo

“…CRISPR-based technologies represent a major breakthrough in biomedical science as they offer a powerful platform for unbiased screening and functional genomics…”
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Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation by Doench, John G, Hartenian, Ella, Graham, Daniel B, Tothova, Zuzana, Hegde, Mudra, Smith, Ian, Sullender, Meagan, Ebert, Benjamin L, Xavier, Ramnik J, Root, David E

“…Analysis of the genome editing activity of more than 1800 sgRNAs in mouse and human cells yields rules to facilitate design of highly active RNA guides for…”
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Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities by Sanson, Kendall R., Hanna, Ruth E., Hegde, Mudra, Donovan, Katherine F., Strand, Christine, Sullender, Meagan E., Vaimberg, Emma W., Goodale, Amy, Root, David E., Piccioni, Federica, Doench, John G.

“…The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation…”
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Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map by Smith, Ian, Greenside, Peyton G, Natoli, Ted, Lahr, David L, Wadden, David, Tirosh, Itay, Narayan, Rajiv, Root, David E, Golub, Todd R, Subramanian, Aravind, Doench, John G

“…The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes…”
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Control of gasdermin D oligomerization and pyroptosis by the Ragulator-Rag-mTORC1 pathway by Evavold, Charles L., Hafner-Bratkovič, Iva, Devant, Pascal, D’Andrea, Jasmin M., Ngwa, Elsy M., Boršić, Elvira, Doench, John G., LaFleur, Martin W., Sharpe, Arlene H., Thiagarajah, Jay R., Kagan, Jonathan C.

“…The process of pyroptosis is mediated by inflammasomes and a downstream effector known as gasdermin D (GSDMD). Upon cleavage by inflammasome-associated…”
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Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma by Chapuy, Bjoern, McKeown, Michael R., Lin, Charles Y., Monti, Stefano, Roemer, Margaretha G.M., Qi, Jun, Rahl, Peter B., Sun, Heather H., Yeda, Kelly T., Doench, John G., Reichert, Elaine, Kung, Andrew L., Rodig, Scott J., Young, Richard A., Shipp, Margaret A., Bradner, James E.

“…Diffuse large B cell lymphoma (DLBCL) is a biologically heterogeneous and clinically aggressive disease. Here, we explore the role of bromodomain and…”
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DYNLL1 binds to MRE11 to limit DNA end resection in BRCA1-deficient cells by He, Yizhou Joseph, Meghani, Khyati, Caron, Marie-Christine, Yang, Chunyu, Ronato, Daryl A., Bian, Jie, Sharma, Anchal, Moore, Jessica, Niraj, Joshi, Detappe, Alexandre, Doench, John G., Legube, Gaelle, Root, David E., D’Andrea, Alan D., Drané, Pascal, De, Subhajyoti, Konstantinopoulos, Panagiotis A., Masson, Jean-Yves, Chowdhury, Dipanjan

“…Limited DNA end resection is the key to impaired homologous recombination in BRCA1 -mutant cancer cells. Here, using a loss-of-function CRISPR screen, we…”
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Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells by Shalem, Ophir, Sanjana, Neville E., Hartenian, Ella, Shi, Xi, Scott, David A., Mikkelsen, Tarjei S., Heckl, Dirk, Ebert, Benjamin L., Root, David E., Doench, John G., Zhang, Feng

“…The simplicity of programming the CRISPR (clustered regularly interspaced short palindromic repeats)–associated nuclease Cas9 to modify specific genomic loci…”
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Genetic screens and functional genomics using CRISPR/Cas9 technology by Hartenian, Ella, Doench, John G

“…Functional genomics attempts to understand the genome by perturbing the flow of information from DNA to RNA to protein, in order to learn how gene dysfunction…”
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Cytochrome P450 oxidoreductase contributes to phospholipid peroxidation in ferroptosis by Zou, Yilong, Li, Haoxin, Graham, Emily T., Deik, Amy A., Eaton, John K., Wang, Wenyu, Sandoval-Gomez, Gerardo, Clish, Clary B., Doench, John G., Schreiber, Stuart L.

“…Ferroptosis is widely involved in degenerative diseases in various tissues including kidney, liver and brain, and is a targetable vulnerability in multiple…”
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A GPX4-dependent cancer cell state underlies the clear-cell morphology and confers sensitivity to ferroptosis by Zou, Yilong, Palte, Michael J., Deik, Amy A., Li, Haoxin, Eaton, John K., Wang, Wenyu, Tseng, Yuen-Yi, Deasy, Rebecca, Kost-Alimova, Maria, Dančík, Vlado, Leshchiner, Elizaveta S., Viswanathan, Vasanthi S., Signoretti, Sabina, Choueiri, Toni K., Boehm, Jesse S., Wagner, Bridget K., Doench, John G., Clish, Clary B., Clemons, Paul A., Schreiber, Stuart L.

“…Clear-cell carcinomas (CCCs) are a histological group of highly aggressive malignancies commonly originating in the kidney and ovary. CCCs are distinguished by…”
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Tumor-suppressor function of Beclin 1 in breast cancer cells requires E-cadherin by Wijshake, Tobias, Zou, Zhongju, Chen, Beibei, Zhong, Lin, Xiao, Guanghua, Xie, Yang, Doench, John G., Bennett, Lynda, Levine, Beth

“…Beclin 1, an autophagy and haploinsufficient tumor-suppressor protein, is frequently monoallelically deleted in breast and ovarian cancers. However, the…”
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A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation by Arroyo, Jason D., Jourdain, Alexis A., Calvo, Sarah E., Ballarano, Carmine A., Doench, John G., Root, David E., Mootha, Vamsi K.

“…Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans. Deficiencies in OXPHOS can arise from mutations in either mitochondrial…”
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Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 by Doench, John G, Fusi, Nicolo, Sullender, Meagan, Hegde, Mudra, Vaimberg, Emma W, Donovan, Katherine F, Smith, Ian, Tothova, Zuzana, Wilen, Craig, Orchard, Robert, Virgin, Herbert W, Listgarten, Jennifer, Root, David E

“…Genome-wide sgRNA libraries based on rules for on-target activity improve results of Cas9-based screens and facilitate a further refinement of on- and…”
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Cas9 activates the p53 pathway and selects for p53-inactivating mutations by Enache, Oana M., Rendo, Veronica, Abdusamad, Mai, Lam, Daniel, Davison, Desiree, Pal, Sangita, Currimjee, Naomi, Hess, Julian, Pantel, Sasha, Nag, Anwesha, Thorner, Aaron R., Doench, John G., Vazquez, Francisca, Beroukhim, Rameen, Golub, Todd R., Ben-David, Uri

“…Cas9 is commonly introduced into cell lines to enable CRISPR–Cas9-mediated genome editing. Here, we studied the genetic and transcriptional consequences of…”
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Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy by Wei, Jun, Long, Lingyun, Zheng, Wenting, Dhungana, Yogesh, Lim, Seon Ah, Guy, Cliff, Wang, Yanyan, Wang, Yong-Dong, Qian, Chenxi, Xu, Beisi, KC, Anil, Saravia, Jordy, Huang, Hongling, Yu, Jiyang, Doench, John G., Geiger, Terrence L., Chi, Hongbo

“…Adoptive cell therapy represents a new paradigm in cancer immunotherapy, but it can be limited by the poor persistence and function of transferred T cells 1 …”
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Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs by Rebendenne, Antoine, Roy, Priyanka, Bonaventure, Boris, Chaves Valadão, Ana Luiza, Desmarets, Lowiese, Arnaud-Arnould, Mary, Rouillé, Yves, Tauziet, Marine, Giovannini, Donatella, Touhami, Jawida, Lee, Yenarae, DeWeirdt, Peter, Hegde, Mudra, Urbach, Serge, Koulali, Khadija El, de Gracia, Francisco Garcia, McKellar, Joe, Dubuisson, Jean, Wencker, Mélanie, Belouzard, Sandrine, Moncorgé, Olivier, Doench, John G., Goujon, Caroline

“…CRISPR knockout (KO) screens have identified host factors regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Here, we…”
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Defective NADPH production in mitochondrial disease complex I causes inflammation and cell death by Balsa, Eduardo, Perry, Elizabeth A., Bennett, Christopher F., Jedrychowski, Mark, Gygi, Steven P., Doench, John G., Puigserver, Pere

“…Electron transport chain (ETC) defects occurring from mitochondrial disease mutations compromise ATP synthesis and render cells vulnerable to nutrient and…”
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