Paul Shannon

TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

TL;DR: An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.

TL;DR: Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits.

TL;DR: Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four and demonstrate the value of complete genome sequencing in families.

TL;DR: The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data, and successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data.