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Biblio

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Author Title Type [ Year(Desc)]
Filters: Author is Eddy, Sean R.  [Clear All Filters]
2007
Nawrocki EP, Eddy SR.  2007.  Query-dependent banding (QDB) for faster RNA similarity searches.. PLoS Computational Biology. 3(3):e56.
2009
Nawrocki EP, Kolbe DL, Eddy SR.  2009.  Infernal 1.0: inference of RNA alignments.. Bioinformatics. 25:1335-7.
Kolbe DL, Eddy SR.  2009.  Local RNA structure alignment with incomplete sequence.. Bioinformatics. 25(10):1236-43.
Eddy SR.  2009.  A new generation of homology search tools based on probabilistic inference.. Genome Informatics. International Conference on Genome Informatics. 23(1):205-11.
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.
Jones TA, Otto W, Marz M, Eddy SR, Stadler PF.  2009.  A survey of nematode SmY RNAs.. RNA Biology. 6(1):5-8.
Davis FP, Eddy SR.  2009.  A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.. Bioinformatics. 25(13):1647-54.
2010
L Johnson S, Eddy SR, Portugaly E.  2010.  Hidden Markov model speed heuristic and iterative HMM search procedure.. BMC Bioinformatics. 11:431.
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.
2011
Eddy SR.  2011.  Accelerated profile HMM searches.. PLoS Computational Biology. 7(10):e1002195.
Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, Landweber LF, Eddy SR.  2011.  Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.. Nucleic Acids Research. 39:7529-47.
Kolbe DL, Eddy SR.  2011.  Fast filtering for RNA homology search.. Bioinformatics. 27(22):3102-9.
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.
2012
Henry GL, Davis FP, Picard S, Eddy SR.  2012.  Cell type-specific genomics of Drosophila neurons.. Nucleic Acids Research. 40(19):9691-704.
Eddy SR.  2012.  The C-value paradox, junk DNA and ENCODE.. Current Biology. 22(21):R898-9.
Rivas E, Lang R, Eddy SR.  2012.  A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.. RNA. 18:193-212.
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.
Nawrocki EP, Eddy SR.  2013.  Computational identification of functional RNA homologs in metagenomic data.. RNA Biology. 10:1170-9.
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.
Eddy SR.  2013.  The ENCODE project: missteps overshadowing a success.. Current Biology. 23(7):R259-61.
Nawrocki EP, Eddy SR.  2013.  Infernal 1.1: 100-fold faster RNA homology searches.. Bioinformatics. 29(22):2933-5.
Wheeler TJ, Eddy SR.  2013.  nhmmer: DNA homology search with profile HMMs.. Bioinformatics. 29:2487-9.
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.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.  2013.  Rfam 11.0: 10 years of RNA families.. Nucleic Acids Research. 41:D226-32.