Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to (...) genomic features and that support numerous user-defined statistical tests. To summarize integration site data from human gene therapy samples, we developed a reproducible report format that catalogs sample population structure, longitudinal dynamics, and integration frequency near cancer-associated genes. We also introduce a novel summary statistic, the UC50, which provides a single number summarizing possible clonal expansion. Using these tools, we characterize ongoing longitudinal characterization of a patient from the first trial to treat severe combined immunodeficiency-X1, showing successful reconstitution for 15 years accompanied by persistence of a cell clone with an integration site near the cancer-associated gene CCND2. Software is available at https://github.com/BushmanLab/INSPIIRED. (shrink)

It is widely recognized that the Web contributes to user polarization, and such polarization affects not just politics but also peoples’ stances about public health, such as vaccination. Understanding polarization in social networks is challenging because it depends not only on user attitudes but also their interactions and exposure to information. We adopt Social Judgment Theory to operationalize attitude shift and model user behavior based on empirical evidence from past studies. We design a social simulation to analyze how content sharing (...) affects user satisfaction and polarization in a social network. We investigate the influence of varying tolerance in users and selectively exposing users to congenial views. We find that (1) higher user tolerance slows down polarization and leads to lower user satisfaction; (2) higher selective exposure leads to higher polarization and lower user reach; and (3) both higher tolerance and higher selective exposure lead to a more homophilic social network. (shrink)