Zobrazeno 1 - 10
of 115
pro vyhledávání: '"Brent S. Pedersen"'
Autor:
Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, Gianina Ravenscroft, Amy J. LaCroix, Phillipa Lamont, Richard H. Roxburgh, Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing, Aaron R. Quinlan
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-20 (2022)
Abstract Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for “novel
Externí odkaz:
https://doaj.org/article/b354d34ff2e44f32a24f0158d94420d9
Publikováno v:
BMC Bioinformatics, Vol 23, Iss 1, Pp 1-32 (2022)
Abstract Background Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that
Externí odkaz:
https://doaj.org/article/16695b18f8474f139af9cbf5a7074e01
Autor:
Brent S. Pedersen, Joe M. Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, Martin Tristani-Firouzi, Joshua D. Schiffman, Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan
Publikováno v:
npj Genomic Medicine, Vol 6, Iss 1, Pp 1-8 (2021)
Abstract In studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence v
Externí odkaz:
https://doaj.org/article/709f6f141917434d9d3529666fde6ab7
Autor:
Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan, Ryan M. Layer
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-13 (2021)
Abstract Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence alignments necessary to adjudicate
Externí odkaz:
https://doaj.org/article/3469a82678f7486a86d417d184bb1a2f
Autor:
Michael J. Cormier, Jonathan R. Belyeu, Brent S. Pedersen, Joseph Brown, Johannes Köster, Aaron R. Quinlan
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-6 (2021)
Modern biological research is complicated by the difficulty of collecting, transforming, annotating, and integrating datasets. Here, the authors present Go Get Data, a fast, reproducible approach to installing standardized data recipes, with an appli
Externí odkaz:
https://doaj.org/article/229a1630d4cf43f5bf84c23578b10f64
Autor:
Brent S. Pedersen, Preetida J. Bhetariya, Joe Brown, Stephanie N. Kravitz, Gabor Marth, Randy L. Jensen, Mary P. Bronner, Hunter R. Underhill, Aaron R. Quinlan
Publikováno v:
Genome Medicine, Vol 12, Iss 1, Pp 1-9 (2020)
Abstract Background When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential, yet more difficult than in studies of germline variation. In most genomic studies of tumors, genetic variatio
Externí odkaz:
https://doaj.org/article/7318c11f0de746678b1a13cc3f314054
Autor:
Samuel W. Brady, Jasmine A. McQuerry, Yi Qiao, Stephen R. Piccolo, Gajendra Shrestha, David F. Jenkins, Ryan M. Layer, Brent S. Pedersen, Ryan H. Miller, Amanda Esch, Sara R. Selitsky, Joel S. Parker, Layla A. Anderson, Brian K. Dalley, Rachel E. Factor, Chakravarthy B. Reddy, Jonathan P. Boltax, Dean Y. Li, Philip J. Moos, Joe W. Gray, Laura M. Heiser, Saundra S. Buys, Adam L. Cohen, W. Evan Johnson, Aaron R. Quinlan, Gabor Marth, Theresa L. Werner, Andrea H. Bild
Publikováno v:
Nature Communications, Vol 8, Iss 1, Pp 1-15 (2017)
In metastatic breast cancer, subclonal evolution can drive drug resistance. Here, the authors genetically and transcriptionally follow the evolution of four breast cancers over time and treatment, and suggest a phenotype-targeted treatment strategy t
Externí odkaz:
https://doaj.org/article/f22c7e1eec644bd49c349e24a268484e
Autor:
Samuel W. Brady, Jasmine A. McQuerry, Yi Qiao, Stephen R. Piccolo, Gajendra Shrestha, David F. Jenkins, Ryan M. Layer, Brent S. Pedersen, Ryan H. Miller, Amanda Esch, Sara R. Selitsky, Joel S. Parker, Layla A. Anderson, Brian K. Dalley, Rachel E. Factor, Chakravarthy B. Reddy, Jonathan P. Boltax, Dean Y. Li, Philip J. Moos, Joe W. Gray, Laura M. Heiser, Saundra S. Buys, Adam L. Cohen, W. Evan Johnson, Aaron R. Quinlan, Gabor Marth, Theresa L. Werner, Andrea H. Bild
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-1 (2018)
The originally published version of this Article contained an error in Figure 4. In panel a, grey boxes surrounding the subclones associated with patients #2 and #4 obscured adjacent portions of the heatmap. This error has now been corrected in both
Externí odkaz:
https://doaj.org/article/ea7789e347e4466db080d56cf43f191a
Publikováno v:
Nature Methods. 19:445-448
Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heurist
Publikováno v:
bioRxiv
article-version (status) pre
article-version (number) 1
article-version (status) pre
article-version (number) 1
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Previously, four other known coronaviruses moved from animal reservoirs into humans and now cause primarily mild-to-moderate respiratory disease. T