Biblio

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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
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.  2015.  HMMER web server: 2015 update.. Nucleic Acids Research.
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.
2014
Finn RD, Miller BL, Clements J, Bateman A.  2014.  iPfam: a database of protein family and domain interactions found in the Protein Data Bank.. Nucleic acids research. 42:D364-73.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J et al..  2014.  Pfam: the protein families database.. Nucleic acids research. 42:D222-30.
Wheeler TJ, Clements J, Finn RD.  2014.  Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.. BMC Bioinformatics. 15:7.
Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L.  2014.  Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.. BMC Bioinformatics. 15:75.
2013
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M.  2013.  Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.. Nucleic Acids Research. 41(12):e121.
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.
Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L et al..  2013.  Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.. BMC Bioinformatics. 14:265.
2012
Finn RD, Gardner PP, Bateman A.  2012.  Making your database available through Wikipedia: the pros and cons.. Nucleic Acids Research. 40(Database issue):D9-12.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al..  2012.  The Pfam protein families database.. Nucleic acids research. 40:D290-301.
2011
Finn RD, Clements J, Eddy SR.  2011.  HMMER web server: interactive sequence similarity searching.. Nucleic Acids Research. 39:W29-37.
Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR et al..  2011.  Rfam: Wikipedia, clans and the "decimal" release.. Nucleic Acids Research. 39(Database issue):D141-5.
2010
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, O Gavin L, Gunasekaran P, Ceric G, Forslund K et al..  2010.  The Pfam protein families database.. Nucleic Acids Research. 38:D211-22.
2009
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR et al..  2009.  Rfam: updates to the RNA families database.. Nucleic Acids Research. 37(Database issue):D136-40.
2008
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJohn, Hotz H-R, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL et al..  2008.  The Pfam protein families database.. Nucleic Acids Research. 36(Database Issue):D281-8.