Browsing by Author "Shi, Xinghua"

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    • Extensive Genetic Diversity and Substructuring Among Zebrafish Strains Revealed through Copy Number Variant Analysis 

      Brown, Kim; Dobrinski, Kimberly P.; Lee, Arthur S.; Gokcumen, Omer; Mills, Ryan; Shi, Xinghua; Chong, Wilson W. S.; Chen, Jin Yun Helen; Yoo, Paulo; David, Sthuthi; Peterson, Samuel M.; Raj, Towfique; Choy, Kwong Wai; Stranger, Barbara; Williamson, Robin E.; Zon, Leonard Ira; Freeman, Jennifer L.; Lee, Charles (Proceedings of the National Academy of Sciences, 2012)
      Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model ...

    • A Map of Human Genome Variation from Population Scale Sequencing 

      Altshuler, David Matthew; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Lee, Charles; Mills, Ryan Edward; Shi, Xinghua; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; Nemesh, James C.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya (Nature Publishing Group, 2010)
      The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot ...

    • Mapping Copy Number Variation by Population Scale Genome Sequencing 

      Mills, Ryan Edward; Handsaker, Robert E; Korn, Joshua; Nemesh, James; Shi, Xinghua; Lee, Charles; McCarroll, Steven A.; Altshuler, David Matthew; Gabriel, Stacey B.; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Li, Heng; Maguire, Jared R.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya; DePristo, Mark A.; Wilkinson, Jane (Nature Publishing Group, 2011)
      Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of ...

    • Refinement of Primate Copy Number Variation Hotspots Identifies Candidate Genomic Regions Evolving Under Positive Selection 

      Babb, Paul L; Iskow, Rebecca C; Mills, Ryan E; Ionita-Laza, Iuliana; Gokcumen, Omer; Zhu, Qihui; Shi, Xinghua; Vallender, Eric; Clark, Andrew G.; Johnson, Welkin Eric; Lee, Charles (BioMed Central, 2011)
      Background: Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation. Results: In this study, we identified over 2,000 human CNVs that overlap with ...