Zobrazeno 1 - 10
of 240
pro vyhledávání: '"Joshua M, Stuart"'
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)
Abstract Inferring gene regulatory networks from single-cell RNA-sequencing trajectories has been an active area of research yet methods are still needed to identify regulators governing cell transitions. We developed DREAMIT (Dynamic Regulation of E
Externí odkaz:
https://doaj.org/article/c61dfb181b57437ebce32fd3a8d7dcec
Publikováno v:
Scientific Reports, Vol 14, Iss 1, Pp 1-6 (2024)
Abstract We present the Manatee variational autoencoder model to predict transcription factor (TF) perturbation-induced transcriptomes. We demonstrate that the Manatee in silico perturbation analysis recapitulates target transcriptomic phenotypes in
Externí odkaz:
https://doaj.org/article/f45a11742fbc460ea578b074849655cc
Publikováno v:
Scientific Reports, Vol 12, Iss 1, Pp 1-11 (2022)
Abstract The SARS-CoV-2 pandemic has challenged humankind’s ability to quickly determine the cascade of health effects caused by a novel infection. Even with the unprecedented speed at which vaccines were developed and introduced into society, iden
Externí odkaz:
https://doaj.org/article/afcaaefd02f545dc951ad72ff9606986
Autor:
Nyasha Chambwe, Rosalyn W. Sayaman, Donglei Hu, Scott Huntsman, Anab Kemal, Samantha Caesar-Johnson, Jean C. Zenklusen, Elad Ziv, Rameen Beroukhim, Andrew D. Cherniack, Jian Carrot-Zhang, Ashton C. Berger, Seunghun Han, Matthew Meyerson, Jeffrey S. Damrauer, Katherine A. Hoadley, Ina Felau, John A. Demchok, Michael K.A. Mensah, Roy Tarnuzzer, Zhining Wang, Liming Yang, Theo A. Knijnenburg, A. Gordon Robertson, Christina Yau, Christopher Benz, Kuan-lin Huang, Justin Y. Newberg, Garrett M. Frampton, R. Jay Mashl, Li Ding, Alessandro Romanel, Francesca Demichelis, Wanding Zhou, Peter W. Laird, Hui Shen, Christopher K. Wong, Joshua M. Stuart, Alexander J. Lazar, Xiuning Le, Ninad Oak
Publikováno v:
STAR Protocols, Vol 3, Iss 3, Pp 101586- (2022)
Summary: Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecul
Externí odkaz:
https://doaj.org/article/58eb09142b5d45b991b34126ef4e9377
Autor:
Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-17 (2020)
Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analys
Externí odkaz:
https://doaj.org/article/d9995364c8fb4afc89d4bb8a8bc2379d
Autor:
Jian Carrot-Zhang, Seunghun Han, Wanding Zhou, Jeffrey S. Damrauer, Anab Kemal, Andrew D. Cherniack, Rameen Beroukhim, Ashton C. Berger, Matthew Meyerson, Katherine A. Hoadley, Ina Felau, Samantha Caesar-Johnson, John A. Demchok, Michael K.A. Mensah, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Nyasha Chambwe, Theo A. Knijnenburg, A. Gordon Robertson, Christina Yau, Christopher Benz, Kuan-lin Huang, Justin Newberg, Garret Frampton, R. Jay Mashl, Li Ding, Alessandro Romanel, Francesca Demichelis, Rosalyn W. Sayaman, Elad Ziv, Peter W. Laird, Hui Shen, Christopher K. Wong, Joshua M. Stuart, Alexander J. Lazar, Xiuning Le, Ninad Oak
Publikováno v:
STAR Protocols, Vol 2, Iss 4, Pp 100766- (2021)
Summary: People of different ancestries vary in cancer risk and outcome, and their molecular differences may indicate sources of these variations. Determining the “local” ancestry composition at each genetic locus across ancestry-admixed populati
Externí odkaz:
https://doaj.org/article/57ccfed30daa47de8636a9bc5c03e2a0
Autor:
Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-1 (2022)
Externí odkaz:
https://doaj.org/article/2e68c62b177945e9b33b29c835967c66
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-6 (2019)
Single cell RNA-Seq data can report on cellular types and states, but low signal-to noise and sparse data can make interpretation of cellular state difficult. Here the authors propose a transformation strategy to map RNA-Seq data to biological proces
Externí odkaz:
https://doaj.org/article/e32e60d474f14311b3573e25cb1cad5f
Autor:
Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros, Justin Guinney
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-9 (2019)
Abstract Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the diversity of software architectures,
Externí odkaz:
https://doaj.org/article/9e24a7fa79d84b2e95c3731262a36bc1
Autor:
Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
Publikováno v:
Genome Biology, Vol 19, Iss 1, Pp 1-15 (2018)
Abstract Background The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-genome sequencing of tumo
Externí odkaz:
https://doaj.org/article/fca34c67ffed4790a306c9523e251762