Selected Recent Publications
Aviran S and Pachter L (2014) Rational experiment design for sequencing-based RNA structure mapping. submitted.
Mortimer SA, Trapnell C*, Aviran S*, Pachter L, and Lucks JB (2012) SHAPE-Seq: high throughput RNA structure analysis. Current Protocols in Chemical Biology, 4, 275-299. (* Equal contribution)
Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, and Pachter L (2011) Modeling and automation of sequencing-based characterization of RNA structure. Proc. of the National Academy of Sciences (PNAS), 108, 11069-11074.
Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, and Arkin AP (2011) Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc. of the National Academy of Sciences (PNAS), 108, 11063-11068.
Aviran S, Shah PS, Schaffer DV, and Arkin AP (2010) Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Computational Biology, 6, e1000883.