Monthly Archives: May 2016


Spats v1.0 is released!

Spats v1.0.0 is an update to the Spats pipeline for processing Next-Generation Sequencing Reads as part of SHAPE-Seq experiments. The major difference between v0.8.0 and v1.0.0 is the migration to the cutadapt utility for removing adapter sequences from the fastxtoolkit. This release still relies on fastx_revcomp, but the code is structured […]


Our methods paper on SHAPE-Seq v2.1 is out!

Kyle, Angela, Eric and Alex’s paper “Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)” is out in Methods! This is a very comprehensive manuscript, outlining the necessary background for understanding chemical probing of RNA structure – from the experiments that can […]


Our review on RNA Systems Biology is out!

Eric, Kyle and David’s review “RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs” is out in Current Opinion in Biotechnology! In this review, we outline the case that the time is right for a systems-level study of RNA structure and function – partly […]


Cameron’s review on engineered protein machines is out!

Cameron’s review “Engineered Protein Machines: Emergent Tools for Synthetic Biology” is out in the inaugural edition of Cell Chemical Biology! This is a great summary of recent work in synthetic biology to make ‘orthogonal’ versions of core cellular protein machines – from polymerases all the way to ribosomes. By acting […]