R
Royden A. Clark
Researcher at University of Virginia
Publications - 13
Citations - 3823
Royden A. Clark is an academic researcher from University of Virginia. The author has contributed to research in topics: Genome & Human genome. The author has an hindex of 13, co-authored 13 publications receiving 3560 citations. Previous affiliations of Royden A. Clark include Brigham and Women's Hospital & Case Western Reserve University.
Papers
More filters
Journal ArticleDOI
Recent Segmental Duplications in the Human Genome
Jeffrey A. Bailey,Zhiping Gu,Royden A. Clark,Knut Reinert,Rhea Vallente Samonte,Stuart Schwartz,Mark Raymond Adams,Eugene W. Myers,Peter W. Li,Evan E. Eichler +9 more
TL;DR: A method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity.
Journal ArticleDOI
Segmental Duplications and Copy-Number Variation in the Human Genome
Andrew J. Sharp,Devin P. Locke,Sean McGrath,Ze Cheng,Jeffrey A. Bailey,Rhea U. Vallente,Lisa M. Pertz,Royden A. Clark,Stuart Schwartz,Rick Segraves,Vanessa V. Oseroff,Donna G. Albertson,Daniel Pinkel,Evan E. Eichler +13 more
TL;DR: This study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements.
Journal ArticleDOI
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
Aaron R. Quinlan,Royden A. Clark,Svetlana Sokolova,Mitchell L. Leibowitz,Yujun Zhang,Matthew E. Hurles,Joshua Chang Mell,Ira M. Hall +7 more
TL;DR: An algorithm to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences are developed, which demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications.
Journal ArticleDOI
Integrative detection and analysis of structural variation in cancer genomes
Jesse R. Dixon,Jie Xu,Vishnu Dileep,Ye Zhan,Fan Song,Victoria T. Le,Galip Gürkan Yardımcı,Abhijit Chakraborty,Darrin V. Bann,Yanli Wang,Royden A. Clark,Lijun Zhang,Hongbo Yang,Tingting Liu,Sriranga Iyyanki,Lin An,Christopher Pool,Takayo Sasaki,Juan Carlos Rivera-Mulia,Hakan Ozadam,Bryan R. Lajoie,Rajinder Kaul,Michael Buckley,Kristen Lee,Morgan Diegel,Dubravka Pezic,Christina Ernst,Suzana Hadjur,Duncan T. Odom,Duncan T. Odom,John A. Stamatoyannopoulos,James R. Broach,Ross C. Hardison,Ferhat Ay,Ferhat Ay,William Stafford Noble,Job Dekker,Job Dekker,David M. Gilbert,Feng Yue +39 more
TL;DR: An integrative framework for identifying structural variants (SVs) in cancer that applies optical mapping, Hi-C, and whole-genome sequencing is presented and finds SVs affecting distal regulatory sequences, DNA replication, and three-dimensional chromatin structure.
Journal ArticleDOI
Shotgun sequence assembly and recent segmental duplications within the human genome
Xinwei She,Zhaoshi Jiang,Royden A. Clark,Ge Liu,Ze Cheng,Eray Tüzün,Deanna M. Church,Granger G. Sutton,Aaron L. Halpern,Evan E. Eichler +9 more
TL;DR: Comparable analyses of mouse genome assemblies confirm that strict WGS sequence assembly will oversimplify the understanding of mammalian genome structure and evolution; a hybrid strategy using a targeted clone-by-clone approach to resolve duplications is proposed.