Zobrazeno 1 - 10
of 34
pro vyhledávání: '"Benjamin J. Ainscough"'
Autor:
Kilannin Krysiak, Arpad M Danos, Jason Saliba, Joshua F McMichael, Adam C Coffman, Susanna Kiwala, Erica K Barnell, Lana Sheta, Cameron J Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Sarah Ridd, Nicholas C Spies, Veronica Andric, Andreea Chiorean, Damian T Rieke, Kaitlin A Clark, Caralyn Reisle, Ajay C Venigalla, Mark Evans, Payal Jani, Hideaki Takahashi, Avila Suda, Peter Horak, Deborah I Ritter, Xin Zhou, Benjamin J Ainscough, Sean Delong, Chimene Kesserwan, Mario Lamping, Haolin Shen, Alex R Marr, My H Hoang, Kartik Singhal, Mariam Khanfar, Brian V Li, Wan-Hsin Lin, Panieh Terraf, Laura B Corson, Yasser Salama, Katie M Campbell, Kirsten M Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Ian King, Kelsy C Cotto, Zachary L Skidmore, Jason R Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y Patel, Rachel H Giles, Raymond H Kim, Lynn M Schriml, Elaine R Mardis, Steven J M Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H Wagner, Malachi Griffith, Obi L Griffith
Publikováno v:
Nucleic Acids Research. 51:D1230-D1241
CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more pre
Autor:
Obi L. Griffith, Nicholas C. Spies, Meenakshi Anurag, Malachi Griffith, Jingqin Luo, Dongsheng Tu, Belinda Yeo, Jason Kunisaki, Christopher A Miller, Kilannin Krysiak, Jasreet Hundal, Benjamin J Ainscough, Zachary L. Skidmore, Katie Campbell, Runjun Kumar, Catrina Fronick, Lisa Cook, Jacqueline E. Snider, Sherri Davies, Shyam M. Kavuri, Eric C. Chang, Vincent Magrini, David E. Larson, Robert S Fulton, Shuzhen Liu, Samuel Leung, David Voduc, Ron Bose, Mitch Dowsett, Richard K. Wilson, Torsten O. Nielsen, Elaine R Mardis, Matthew J. Ellis
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-16 (2018)
Unravelling the link between somatic mutation and prognosis in estrogen positive (ER+) breast cancer requires the use of long-term follow-up data. Here, combining archival formalin-fixed paraffin embedded tissue and targeted sequencing in three cohor
Externí odkaz:
https://doaj.org/article/fe27abc720eb4d50bc7f128d4b6ad490
Autor:
Obi L. Griffith, Nicholas C. Spies, Meenakshi Anurag, Malachi Griffith, Jingqin Luo, Dongsheng Tu, Belinda Yeo, Jason Kunisaki, Christopher A Miller, Kilannin Krysiak, Jasreet Hundal, Benjamin J Ainscough, Zachary L. Skidmore, Katie Campbell, Runjun Kumar, Catrina Fronick, Lisa Cook, Jacqueline E. Snider, Sherri Davies, Shyam M. Kavuri, Eric C. Chang, Vincent Magrini, David E. Larson, Robert S Fulton, Shuzhen Liu, Samuel Leung, David Voduc, Ron Bose, Mitch Dowsett, Richard K. Wilson, Torsten O. Nielsen, Elaine R Mardis, Matthew J. Ellis
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-2 (2018)
The original version of this Article contained errors in the depiction of confidence intervals in the NF1 BCSS data illustrated in Figure 3b. These have now been corrected in both the PDF and HTML versions of the Article. The incorrect version of Fig
Externí odkaz:
https://doaj.org/article/e0785765fab94e23801e3e65819e240a
Autor:
Kilannin Krysiak, Arpad M. Danos, Susanna Kiwala, Joshua F. McMichael, Adam C. Coffman, Erica K. Barnell, Lana Sheta, Jason Saliba, Cameron J. Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Nicholas C. Spies, Andreea Chiorean, Damian T. Rieke, Kaitlin A. Clark, Payal Jani, Hideaki Takahashi, Peter Horak, Deborah I. Ritter, Xin Zhou, Benjamin J. Ainscough, Sean Delong, Mario Lamping, Alex R. Marr, Brian V. Li, Wan-Hsin Lin, Panieh Terraf, Yasser Salama, Katie M. Campbell, Kirsten M. Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Kelsy C. Cotto, Zachary L. Skidmore, Jason R. Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y. Patel, Rachel H. Giles, Raymond H. Kim, Lynn M. Schriml, Elaine R. Mardis, Steven J. M. Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H. Wagner, Obi L. Griffith, Malachi Griffith
Publikováno v:
Nat Cancer
As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ed50e6a9356f3f2f4e3e63d326c2871
https://eprints.gla.ac.uk/279775/1/279775.pdf
https://eprints.gla.ac.uk/279775/1/279775.pdf
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 8, p e1004393 (2015)
Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concep
Externí odkaz:
https://doaj.org/article/2f6932ac1d9444ce9cef80016a415be4
Autor:
Malachi Griffith, Obi L Griffith, Scott M Smith, Avinash Ramu, Matthew B Callaway, Anthony M Brummett, Michael J Kiwala, Adam C Coffman, Allison A Regier, Ben J Oberkfell, Gabriel E Sanderson, Thomas P Mooney, Nathaniel G Nutter, Edward A Belter, Feiyu Du, Robert L Long, Travis E Abbott, Ian T Ferguson, David L Morton, Mark M Burnett, James V Weible, Joshua B Peck, Adam Dukes, Joshua F McMichael, Justin T Lolofie, Brian R Derickson, Jasreet Hundal, Zachary L Skidmore, Benjamin J Ainscough, Nathan D Dees, William S Schierding, Cyriac Kandoth, Kyung H Kim, Charles Lu, Christopher C Harris, Nicole Maher, Christopher A Maher, Vincent J Magrini, Benjamin S Abbott, Ken Chen, Eric Clark, Indraniel Das, Xian Fan, Amy E Hawkins, Todd G Hepler, Todd N Wylie, Shawn M Leonard, William E Schroeder, Xiaoqi Shi, Lynn K Carmichael, Matthew R Weil, Richard W Wohlstadter, Gary Stiehr, Michael D McLellan, Craig S Pohl, Christopher A Miller, Daniel C Koboldt, Jason R Walker, James M Eldred, David E Larson, David J Dooling, Li Ding, Elaine R Mardis, Richard K Wilson
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 7, p e1004274 (2015)
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled
Externí odkaz:
https://doaj.org/article/8bd43ecac4d44f7cbb8d1a284c28cdab
Autor:
John S K Kauwe, Matthew H Bailey, Perry G Ridge, Rachel Perry, Mark E Wadsworth, Kaitlyn L Hoyt, Lyndsay A Staley, Celeste M Karch, Oscar Harari, Carlos Cruchaga, Benjamin J Ainscough, Kelly Bales, Eve H Pickering, Sarah Bertelsen, Alzheimer's Disease Neuroimaging Initiative, Anne M Fagan, David M Holtzman, John C Morris, Alison M Goate
Publikováno v:
PLoS Genetics, Vol 10, Iss 10, p e1004758 (2014)
Cerebrospinal fluid (CSF) 42 amino acid species of amyloid beta (Aβ42) and tau levels are strongly correlated with the presence of Alzheimer's disease (AD) neuropathology including amyloid plaques and neurodegeneration and have been successfully use
Externí odkaz:
https://doaj.org/article/80123cca0e78463c93754376f1acd06d
Autor:
Gavin P. Dunn, Peter Ronning, Benjamin J. Ainscough, Malachi Griffith, Todd A. Fehniger, Ravindra Uppaluri, Alex H. Wagner, S. Joshua Swamidass, Thomas E. Rohan, Elaine R. Mardis, Erica K. Barnell, Katie M. Campbell, Obi L. Griffith, Ramaswamy Govindan
Publikováno v:
Nature Genetics. 50:1735-1743
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somatic variant calls is required as a final step after automated processing. However, manual variant refinement is time-consumin
Autor:
Mitch Dowsett, Benjamin J. Ainscough, Dongsheng Tu, Catrina Fronick, Richard K. Wilson, Vincent Magrini, Kilannin Krysiak, Belinda Yeo, Meenakshi Anurag, David Voduc, Malachi Griffith, Ron Bose, Runjun D. Kumar, Jason Kunisaki, David E. Larson, Shyam M. Kavuri, Lisa Cook, Christopher A. Miller, Katie M. Campbell, Eric C. Chang, Jasreet Hundal, Sherri R. Davies, Jacqueline E. Snider, Nicholas C. Spies, Shuzhen Liu, Matthew J. Ellis, Torsten O. Nielsen, Elaine R. Mardis, Jingqin Luo, Zachary L. Skidmore, Samuel Leung, Robert S. Fulton, Obi L. Griffith
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-2 (2018)
The original version of this Article contained errors in the depiction of confidence intervals in the NF1 BCSS data illustrated in Figure 3b. These have now been corrected in both the PDF and HTML versions of the Article. The incorrect version of Fig
Autor:
Jeffery M. Klco, Benjamin J. Ainscough, Katie M. Campbell, Vincent Magrini, Malachi Griffith, Jason Walker, Nicholas C. Spies, John F. DiPersio, Peter Westervelt, David E. Larson, Sharon Heath, Jin Zhang, Catrina Fronick, Jasreet Hundal, Elaine R. Mardis, Shelly O'Laughlin, Timothy J. Ley, Sean McGrath, Christopher G. Maher, Christopher A. Miller, Kilannin Krysiak, Robert Lesurf, Timothy A. Graubert, Matthew J. Christopher, Robert S. Fulton, Daniel C. Link, Jacqueline E. Payton, James M. Eldred, Alex H. Wagner, Zachary L. Skidmore, Tamara Lamprecht, Avinash Ramu, Rick K. Wilson, Scott M. Smith, Matthew J. Walter, Obi L. Griffith, Shashikant Kulkarni
Publikováno v:
Experimental Hematology. 44:603-613
The genomic events responsible for the pathogenesis of relapsed adult B-lymphoblastic leukemia (B-ALL) are not yet clear. We performed integrative analysis of whole-genome, whole-exome, custom capture, whole-transcriptome (RNA-seq), and locus-specifi