A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data

Authors: Alessandro Vinceti, Raffaele M. Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D. Campbell, Francisca Vazquez, Joshua M. Dempster, Francesco Iorio

Source: Genome Biology, Vol 25, Iss 1, Pp 1-25 (2024)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/f283ab13f9214b6087b7f4ee08adc084

Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

Authors: 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

Source: Genome Biology, Vol 24, Iss 1, Pp 1-26 (2023)

Subject Terms: Functional genomics, Cancer genomics, Target identification, RNAi, CRISPR-Cas systems, CRISPR-Cas9 genome editing, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/1c92c0bab42244fc81f9b12dd6f2049f

Author Correction: A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data

Authors: Alessandro Vinceti, Rafaele M. Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D. Campbell, Francisca Vazquez, Joshua M. Dempster, Francesco Iorio

Source: Genome Biology, Vol 25, Iss 1, Pp 1-1 (2024)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/c78f8cbc870743ad97190d6d8b13f963

Mapping the landscape of genetic dependencies in chordoma

Authors: 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

Source: Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/15d1d503cc354ceb925abcc12163767f

Comparative optimization of combinatorial CRISPR screens

Authors: 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

Source: Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/f145c71e8a554f069b81dbb691434bae

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects

Authors: Joshua M. Dempster, Isabella Boyle, Francisca Vazquez, David E. Root, Jesse S. Boehm, William C. Hahn, Aviad Tsherniak, James M. McFarland

Source: Genome Biology, Vol 22, Iss 1, Pp 1-23 (2021)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/ab70c5191afb435eae3c435edff328cd

Integrated cross-study datasets of genetic dependencies in cancer

Authors: 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

Source: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/fdd2ad5966004da891cf74b4446afacf

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

Authors: 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

Source: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/7101cce4933e4a7a88c0656de01f28e5

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

Authors: 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

Source: Nature Communications, Vol 9, Iss 1, Pp 1-13 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d0eb361d0bb14b90ba18bfe3b6bb1fd5

Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers

Authors: 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

Source: Cell Reports, Vol 29, Iss 1, Pp 118-134.e8 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124719311520; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/9a62a78ea0ee4966a7135dceb3c889af