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2016
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AFA, Wheeler TJ.  2016.  The Dfam database of repetitive DNA families.. Nucleic Acids Research. 44(D1):D81-9.
2015
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J et al..  2015.  Rfam 12.0: updates to the RNA families database.. Nucleic Acids Research. 43(Database issue):D130-7.
2013
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AFA, Finn RD.  2013.  Dfam: a database of repetitive DNA based on profile hidden Markov models.. Nucleic Acids Research. 41:D70-82.
Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K et al..  2013.  The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.. PLoS Biology. 11(1):e1001473.
2009
Jones TA, Otto W, Marz M, Eddy SR, Stadler PF.  2009.  A survey of nematode SmY RNAs.. RNA Biology. 6(1):5-8.