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作者：Hunter, David R.; Bao, Le; Poss, Mary
作者单位：Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park
摘要：Structural variation occurs in the genomes of individuals because of the different positions occupied by repetitive genome elements like endogenous retroviruses, or ERVs. The presence or absence of ERVs can be determined by identifying the junction with the host genome using high-throughput sequence technology and a clustering algorithm. The resulting data give the number of sequence reads assigned to each ERV-host junction sequence for each sampled individual. Variability in the number of rea...
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作者：Kelly, Luke J.; Nicholls, Geoff K.
作者单位：University of Oxford
摘要：Lateral transfer, a process whereby species exchange evolutionary traits through nonancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable, as the parameters are the solution of a seq...
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作者：Chen, Hao; Jiang, Yuchao; Maxwell, Kara N.; Nathanson, Katherine L.; Zhang, Nancy
作者单位：University of California System; University of California Davis; University of Pennsylvania; University of Pennsylvania
摘要：Whole exome sequencing is currently a technology of choice in large-scale cancer genomics studies, where the priority is to identify cancer-associated variants in coding regions. We describe a method for estimating allele-specific copy number using whole exome sequencing data from tumor and matched normal.
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作者：Ogburn, Elizabeth L.; VanderWeele, Tyler J.
作者单位：Johns Hopkins University; Johns Hopkins Bloomberg School of Public Health; Harvard University; Harvard T.H. Chan School of Public Health
摘要：Consider the causal effect that one individual's treatment may have on another individual's outcome when the outcome is contagious, with specific application to the effect of vaccination on an infectious disease outcome. The effect of one individual's vaccination on another's outcome can be decomposed into two different causal effects, called the infectiousness and contagion effects. We present identifying assumptions and estimation or testing procedures for infectiousness and contagion effect...
