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for term "sites"

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  • Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
    Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew J. Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
    G3: Genes|Genomes|Genetics August 2014 4: 1429-1444; https://doi.org/10.1534/g3.114.011759
    ...been linked to lung brosis development (Deng et al. 2013). Alternative transcription is also important in the host response to virus infection. Transcriptional start site (TSS) selections and posttranscriptional modication to host transcripts have been linked to dengue virus virulence (Sessions et al ~~~
  • Quantitative Trait Loci Association Mapping by Imputation of Strain Origins in Multifounder Crosses
    Jin J. Zhou, Anatole Ghazalpour, Eric M. Sobel, Janet S. Sinsheimer, Kenneth Lange
    Genetics February 2012 190: 459-473; https://doi.org/10.1534/genetics.111.135095
    ...as the percentage of sites where the estimated founder ancestry matches the truth. Our matching criterion takes into account that many inbred strains are related (Flint 2010) and have common chromosome blocks identical by descent (IBD). If two or more founder strains genotypes are identical across an entire window ~~~
  • The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
    Collaborative Cross Consortium
    Genetics February 2012 190: 389-401; https://doi.org/10.1534/genetics.111.132639
    .... Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Currently, this innovative project is breeding independent CC lines at the University of North Carolina (UNC), at Tel Aviv University (TAU), and at Geniad in Western Australia (GND ~~~
  • Imputation of Single-Nucleotide Polymorphisms in Inbred Mice Using Local Phylogeny
    Jeremy R. Wang, Fernando Pardo-Manuel de Villena, Heather A. Lawson, James M. Cheverud, Gary A. Churchill, Leonard McMillan
    Genetics February 2012 190: 449-458; https://doi.org/10.1534/genetics.111.132381
    ...rate in highcondence regions is 0.083% compared to 0.27% and 4.4% reported in previous studies. Our error rate in high-condence regions is in line with sequencing error and the rate of recurrent mutations at highly mutable sites (homoplasy). These improvements are due, in part, to the use of a more ~~~
  • Varying Coefficient Models for Mapping Quantitative Trait Loci Using Recombinant Inbred Intercrosses
    Yi Gong, Fei Zou
    Genetics February 2012 190: 475-486; https://doi.org/10.1534/genetics.111.132522
    ...the genotypes of the parental RI lines. RIX mice with identical genotypes can be regenerated whenever needed. Compared to RI, the RIX design has several advantages that include twice the number of recombination sites in a single individual since each is derived from two parental RI, dominance effects can ~~~
  • HTreeQA: Using Semi-Perfect Phylogeny Trees in Quantitative Trait Loci Study on Genotype Data
    Zhaojun Zhang, Xiang Zhang, Wei Wang
    G3: Genes|Genomes|Genetics February 2012 2: 175-189; https://doi.org/10.1534/g3.111.001768
    ...the evolutionary history of these two markers without recombination events, given the assumption of an innite site model (i.e., no homoplasy). For a given interval, a perfect phylogeny exists if and only if the interval is a compatible interval. If a compatible interval is not a subinterval of another compatible ~~~
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