Paul’s paper using replica-exchange simulations to interpret in-vivo SHAPE data for synthetic transcriptional attenuators is out in RNA! This is in collaboration with the lab of synthetic biologist and SHAPE-seq inventor Julius Lucks of Northwestern Univ.
Takahashi, Melissa K.; Watters, Kyle E.; Gasper, Paul; Abbott, Timothy R.; Chen, Alan A.; Lucks, Julius B. (2016) “Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators” RNA 22, pp. 920-933 DOI: 10.1261/rna.054916.115