Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution. - Jin Jun; Paul Ryvkin; Edward Hemphill; Ion I. Mandoiu; Craig E. Nelson (RECOMB-CG, 2008)

Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates. - Paul Ryvkin; Jin Jun; Edward Hemphill; Craig E. Nelson (RECOMB-CG, 2008)

The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution. - Jin Jun; Paul Ryvkin; Edward Hemphill; Ion I. Mandoiu; Craig E. Nelson (J. Comput. Biol., 2009)

Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates. - Jin Jun; Paul Ryvkin; Edward Hemphill; Craig E. Nelson (J. Comput. Biol., 2009)

Invited: Multiclass RNA function classification using next-generation sequencing. - Paul Ryvkin; Yuk Yee Leung; Li-San Wang; Brian D. Gregory (ICCABS, 2011)

SAVoR: a server for sequencing annotation and visualization of RNA structures. - Fan Li 002; Paul Ryvkin; Daniel M. Childress; Otto Valladares; Brian D. Gregory; Li-San Wang (Nucleic Acids Res., 2012)