Zobrazeno 1 - 10
of 63
pro vyhledávání: '"Joshua M. Dempster"'
Autor:
Alessandro Vinceti, Raffaele M. Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D. Campbell, Francisca Vazquez, Joshua M. Dempster, Francesco Iorio
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-25 (2024)
Abstract Background CRISPR-Cas9 dropout screens are formidable tools for investigating biology with unprecedented precision and scale. However, biases in data lead to potential confounding effects on interpretation and compromise overall quality. The
Externí odkaz:
https://doaj.org/article/f283ab13f9214b6087b7f4ee08adc084
Autor:
Alessandro Vinceti, Rafaele M. Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D. Campbell, Francisca Vazquez, Joshua M. Dempster, Francesco Iorio
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-1 (2024)
Externí odkaz:
https://doaj.org/article/c78f8cbc870743ad97190d6d8b13f963
Autor:
J. Michael Krill-Burger, Joshua M. Dempster, Ashir A. Borah, Brenton R. Paolella, David E. Root, Todd R. Golub, Jesse S. Boehm, William C. Hahn, James M. McFarland, Francisca Vazquez, Aviad Tsherniak
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-26 (2023)
Abstract Background Hundreds of functional genomic screens have been performed across a diverse set of cancer contexts, as part of efforts such as the Cancer Dependency Map, to identify gene dependencies—genes whose loss of function reduces cell vi
Externí odkaz:
https://doaj.org/article/1c92c0bab42244fc81f9b12dd6f2049f
Autor:
Tanaz Sharifnia, Mathias J. Wawer, Amy Goodale, Yenarae Lee, Mariya Kazachkova, Joshua M. Dempster, Sandrine Muller, Joan Levy, Daniel M. Freed, Josh Sommer, Jérémie Kalfon, Francisca Vazquez, William C. Hahn, David E. Root, Paul A. Clemons, Stuart L. Schreiber
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)
Cancer cells possess unique molecular features that can confer an increased dependence on specific genes. Here, the authors use CRISPR-Cas9 screens to identify selectively essential genes and therapeutic targets in chordoma.
Externí odkaz:
https://doaj.org/article/15d1d503cc354ceb925abcc12163767f
Autor:
Ruitong Li, Olaf Klingbeil, Davide Monducci, Michael J. Young, Diego J. Rodriguez, Zaid Bayyat, Joshua M. Dempster, Devishi Kesar, Xiaoping Yang, Mahdi Zamanighomi, Christopher R. Vakoc, Takahiro Ito, William R. Sellers
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)
Combinatorial CRISPR screens can be utilized to identify genetic interactions and functional redundancies of multiple genes. Here, the authors benchmark ten digenic CRISPR technologies and identify novel Cas9 tracrRNA combinations that show superior
Externí odkaz:
https://doaj.org/article/f145c71e8a554f069b81dbb691434bae
Autor:
Joshua M. Dempster, Isabella Boyle, Francisca Vazquez, David E. Root, Jesse S. Boehm, William C. Hahn, Aviad Tsherniak, James M. McFarland
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-23 (2021)
Abstract 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 introduce Chronos, an algorithm for inferring gene knockout fitness effects based
Externí odkaz:
https://doaj.org/article/ab70c5191afb435eae3c435edff328cd
Autor:
Clare Pacini, Joshua M. Dempster, Isabella Boyle, Emanuel Gonçalves, Hanna Najgebauer, Emre Karakoc, Dieudonne van der Meer, Andrew Barthorpe, Howard Lightfoot, Patricia Jaaks, James M. McFarland, Mathew J. Garnett, Aviad Tsherniak, Francesco Iorio
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)
The integration of independent pan-cancer CRISPR-Cas9 datasets allows better representation of genomic heterogeneity across different cancer types. Here, the authors propose a strategy for the integration of two large CRISPR-Cas9 screens and report i
Externí odkaz:
https://doaj.org/article/fdd2ad5966004da891cf74b4446afacf
Autor:
Joshua M. Dempster, Clare Pacini, Sasha Pantel, Fiona M. Behan, Thomas Green, John Krill-Burger, Charlotte M. Beaver, Scott T. Younger, Victor Zhivich, Hanna Najgebauer, Felicity Allen, Emanuel Gonçalves, Rebecca Shepherd, John G. Doench, Kosuke Yusa, Francisca Vazquez, Leopold Parts, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Mathew J. Garnett, Aviad Tsherniak, Francesco Iorio
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Integrating independent large-scale pharmacogenomic screens can enable unprecedented characterization of genetic vulnerabilities in cancers. Here, the authors show that the two largest independent CRISPR-Cas9 gene-dependency screens are concordant, p
Externí odkaz:
https://doaj.org/article/7101cce4933e4a7a88c0656de01f28e5
Autor:
James M. McFarland, Zandra V. Ho, Guillaume Kugener, Joshua M. Dempster, Phillip G. Montgomery, Jordan G. Bryan, John M. Krill-Burger, Thomas M. Green, Francisca Vazquez, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Aviad Tsherniak
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-13 (2018)
Integrated analyses of multiple large-scale screenings can be complicated by batch effects and technical artefacts. McFarland et al. introduce DEMETER2, a hierarchical model coupled with model-based normalization, which allows the assessment of diffe
Externí odkaz:
https://doaj.org/article/d0eb361d0bb14b90ba18bfe3b6bb1fd5
Autor:
Rita Sulahian, Jason J. Kwon, Katherine H. Walsh, Emma Pailler, Timothy L. Bosse, Maneesha Thaker, Diego Almanza, Joshua M. Dempster, Joshua Pan, Federica Piccioni, Nancy Dumont, Alfredo Gonzalez, Jonathan Rennhack, Behnam Nabet, John A. Bachman, Amy Goodale, Yenarae Lee, Mukta Bagul, Rosy Liao, Adrija Navarro, Tina L. Yuan, Raymond W.S. Ng, Srivatsan Raghavan, Nathanael S. Gray, Aviad Tsherniak, Francisca Vazquez, David E. Root, Ari J. Firestone, Jeff Settleman, William C. Hahn, Andrew J. Aguirre
Publikováno v:
Cell Reports, Vol 29, Iss 1, Pp 118-134.e8 (2019)
Summary: The mitogen-activated protein kinase (MAPK) pathway is a critical effector of oncogenic RAS signaling, and MAPK pathway inhibition may be an effective combination treatment strategy. We performed genome-scale loss-of-function CRISPR-Cas9 scr
Externí odkaz:
https://doaj.org/article/9a62a78ea0ee4966a7135dceb3c889af