Zobrazeno 1 - 10
of 537
pro vyhledávání: '"Tsherniak A"'
Autor:
Pan, Joshua, Kwon, Jason J., Talamas, Jessica A., Borah, Ashir A., Vazquez, Francisca, Boehm, Jesse S., Tsherniak, Aviad, Zitnik, Marinka, McFarland, James M., Hahn, William C.
In high-throughput functional genomic screens, each gene product is commonly assumed to exhibit a singular biological function within a defined protein complex or pathway. In practice, a single gene perturbation may induce multiple cascading function
Externí odkaz:
http://arxiv.org/abs/2111.06247
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:
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:
Allison Warren, Yejia Chen, Andrew Jones, Tsukasa Shibue, William C. Hahn, Jesse S. Boehm, Francisca Vazquez, Aviad Tsherniak, James M. McFarland
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)
The determination of whether cancer cell lines recapitulate the molecular features of corresponding patient tumours remains essential for the selection of appropriate cell line models for preclinical studies. The method developed here, Celligner, int
Externí odkaz:
https://doaj.org/article/3fba48e4d01a443c98e860de08f9d7ef
Autor:
James M. McFarland, Brenton R. Paolella, Allison Warren, Kathryn Geiger-Schuller, Tsukasa Shibue, Michael Rothberg, Olena Kuksenko, William N. Colgan, Andrew Jones, Emily Chambers, Danielle Dionne, Samantha Bender, Brian M. Wolpin, Mahmoud Ghandi, Itay Tirosh, Orit Rozenblatt-Rosen, Jennifer A. Roth, Todd R. Golub, Aviv Regev, Andrew J. Aguirre, Francisca Vazquez, Aviad Tsherniak
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-15 (2020)
Large-scale screens of chemical and genetic vulnerabilities in cancer are typically limited to simple readouts of cell viability. Here, the authors develop a method for profiling post-perturbation transcriptional responses across large pools of cance
Externí odkaz:
https://doaj.org/article/464481c452404d5080918310ac391162
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:
Jasper E. Neggers, Brenton R. Paolella, Adhana Asfaw, Michael V. Rothberg, Thomas A. Skipper, Annan Yang, Radha L. Kalekar, John M. Krill-Burger, Neekesh V. Dharia, Guillaume Kugener, Jérémie Kalfon, Chen Yuan, Nancy Dumont, Alfredo Gonzalez, Mai Abdusamad, Yvonne Y. Li, Liam F. Spurr, Westley W. Wu, Adam D. Durbin, Brian M. Wolpin, Federica Piccioni, David E. Root, Jesse S. Boehm, Andrew D. Cherniack, Aviad Tsherniak, Andrew L. Hong, William C. Hahn, Kimberly Stegmaier, Todd R. Golub, Francisca Vazquez, Andrew J. Aguirre
Publikováno v:
Cell Reports, Vol 36, Iss 2, Pp 109367- (2021)
Externí odkaz:
https://doaj.org/article/ac506d36e0fc45f58afd5108c6469b14
Autor:
Pratiti Bandopadhayay, Federica Piccioni, Ryan O’Rourke, Patricia Ho, Elizabeth M. Gonzalez, Graham Buchan, Kenin Qian, Gabrielle Gionet, Emily Girard, Margo Coxon, Matthew G. Rees, Lisa Brenan, Frank Dubois, Ofer Shapira, Noah F. Greenwald, Melanie Pages, Amanda Balboni Iniguez, Brenton R. Paolella, Alice Meng, Claire Sinai, Giovanni Roti, Neekesh V. Dharia, Amanda Creech, Benjamin Tanenbaum, Prasidda Khadka, Adam Tracy, Hong L. Tiv, Andrew L. Hong, Shannon Coy, Rumana Rashid, Jia-Ren Lin, Glenn S. Cowley, Fred C. Lam, Amy Goodale, Yenarae Lee, Kathleen Schoolcraft, Francisca Vazquez, William C. Hahn, Aviad Tsherniak, James E. Bradner, Michael B. Yaffe, Till Milde, Stefan M. Pfister, Jun Qi, Monica Schenone, Steven A. Carr, Keith L. Ligon, Mark W. Kieran, Sandro Santagata, James M. Olson, Prafulla C. Gokhale, Jacob D. Jaffe, David E. Root, Kimberly Stegmaier, Cory M. Johannessen, Rameen Beroukhim
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-16 (2019)
BET-bromodomain inhibitors could be used to treat medulloblastoma tumors with Myc amplifications. Here, the authors show that both the response and resistance to BET inhibitors in mice is mediated by bHLH/homeobox transcription factors.
Externí odkaz:
https://doaj.org/article/f1ab52ee34d04a798436204eedf97a8a
Autor:
Hugh S. Gannon, Tao Zou, Michael K. Kiessling, Galen F. Gao, Diana Cai, Peter S. Choi, Alexandru P. Ivan, Ilana Buchumenski, Ashton C. Berger, Jonathan T. Goldstein, Andrew D. Cherniack, Francisca Vazquez, Aviad Tsherniak, Erez Y. Levanon, William C. Hahn, Matthew Meyerson
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)
Specific cancer cell vulnerabilities can provide an opportunity for the development of novel cancer therapeutics. In this study the authors demonstrate that targeting ADAR1 represents a potential therapeutic vulnerability in cancers with activated in
Externí odkaz:
https://doaj.org/article/101c1efd608349f2b4bd50157c1c3989