Zobrazeno 1 - 10
of 87
pro vyhledávání: '"Kyle, Ellrott"'
Autor:
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-27 (2020)
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Gen
Externí odkaz:
https://doaj.org/article/d9cb28829f31451aa7d92697e8efd186
Autor:
Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O’Donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O’Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet, Alexander Baumann, Andrew Rula, Anton Kovalsy, Clare Bernard, Derek Caetano-Anollés, Geraldine A. Van der Auwera, Justin Canas, Kaan Yuksel, Kate Herman, M. Morgan Taylor, Marianie Simeon, Michael Baumann, Qi Wang, Robert Title, Ruchi Munshi, Sushma Chaluvadi, Valerie Reeves, William Disman, Salin Thomas, Allie Hajian, Elizabeth Kiernan, Namrata Gupta, Trish Vosburg, Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Dave Rogers, Frances McDade, Mim Hastie, Nitesh Turaga, Alexander Ostrovsky, Alexandru Mahmoud, Dannon Baker, Dave Clements, Katherine E.L. Cox, Keith Suderman, Nataliya Kucher, Sergey Golitsynskiy, Samantha Zarate, Sarah J. Wheelan, Kai Kammers, Ana Stevens, Carolyn Hutter, Christopher Wellington, Elena M. Ghanaim, Ken L. Wiley, Jr., Shurjo K. Sen, Valentina Di Francesco, Deni s Yuen, Brian Walsh, Luke Sargent, Vahid Jalili, John Chilton, Lori Shepherd, B.J. Stubbs, Ash O’Farrell, Benton A. Vizzier, Jr., Charles Overbeck, Charles Reid, David Charles Steinberg, Elizabeth A. Sheets, Julian Lucas, Lon Blauvelt, Louise Cabansay, Noah Warren, Brian Hannafious, Tim Harris, Radhika Reddy, Eric Torstenson, M. Katie Banasiewicz, Haley J. Abel, Jason Walker
Publikováno v:
Cell Genomics, Vol 2, Iss 1, Pp 100085- (2022)
Summary: The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, managemen
Externí odkaz:
https://doaj.org/article/95ac1623e901491c821d128f529da364
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
Autor:
Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P’ng, Kathleen E Houlahan, Cristian Caloian, Michael Fraser, SMC-DNA Challenge Participants, Kyle Ellrott, Adam A Margolin, Robert G Bristow, Joshua M Stuart, Paul C Boutros
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-11 (2018)
Abstract Background Platform-specific error profiles necessitate confirmatory studies where predictions made on data generated using one technology are additionally verified by processing the same samples on an orthogonal technology. However, verifyi
Externí odkaz:
https://doaj.org/article/523eeedb54fb4c0eaf90704f90a6d119
Autor:
Mary A. Wood, Mayur Paralkar, Mihir P. Paralkar, Austin Nguyen, Adam J. Struck, Kyle Ellrott, Adam Margolin, Abhinav Nellore, Reid F. Thompson
Publikováno v:
BMC Cancer, Vol 18, Iss 1, Pp 1-15 (2018)
Abstract Background Tumor neoantigens are drivers of cancer immunotherapy response; however, current prediction tools produce many candidates requiring further prioritization. Additional filtration criteria and population-level understanding may assi
Externí odkaz:
https://doaj.org/article/f1cc876bd8654bfd9c5b53d659bf98bc
Autor:
Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)
Abstract Background The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlle
Externí odkaz:
https://doaj.org/article/ab0b15f9663d47eca47e4595ae0cd171
Autor:
Joshua M. Stuart, Olena Morozova, David Haussler, Theodore C. Goldstein, Manu Chopra, Kyle Ellrott, Sofie R. Salama, Robert Baertsch, Alana S. Weinstein, Kiley Graim, Sahil Chopra, Duncan C. McColl, Teresa Swatloski, Adam M. Novak, Yulia Newton
Enrichment of Immune signaling in the integrated pan-cancer cluster. Different level of evidence support the association of the integrated pan-cancer cluster with an immune phenotype. (A) Enrichment of T- and B-cell signaling shown on the integrated
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::033f5c5991b186b598f5290a611e375a
https://doi.org/10.1158/0008-5472.22419030
https://doi.org/10.1158/0008-5472.22419030
Autor:
Joshua M. Stuart, Olena Morozova, David Haussler, Theodore C. Goldstein, Manu Chopra, Kyle Ellrott, Sofie R. Salama, Robert Baertsch, Alana S. Weinstein, Kiley Graim, Sahil Chopra, Duncan C. McColl, Teresa Swatloski, Adam M. Novak, Yulia Newton
Supplemental Figure 1: RSS transformed correlations correct for platform-specific inflation biases. Maps produced from different molecular data types. Samples in the maps are colored by tissue of origin. (A) Similarity score distributions for every p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::085d2f6da7a832b71d3d16cee91ed83a
https://doi.org/10.1158/0008-5472.22419039
https://doi.org/10.1158/0008-5472.22419039
Autor:
Joshua M. Stuart, Olena Morozova, David Haussler, Theodore C. Goldstein, Manu Chopra, Kyle Ellrott, Sofie R. Salama, Robert Baertsch, Alana S. Weinstein, Kiley Graim, Sahil Chopra, Duncan C. McColl, Teresa Swatloski, Adam M. Novak, Yulia Newton
Molecular subtype visualization. Known biology recapitulated by the mRNA expression map. (A) BRCA molecular subtypes and their layout in the map. The map shows that tumors of the same molecular subtype tend to cluster together, with very little mixin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::652ef3c77b81608a07222cd4d32daf0e
https://doi.org/10.1158/0008-5472.22419036.v1
https://doi.org/10.1158/0008-5472.22419036.v1