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The Pfam protein families database in 2019.

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432. doi: 10.1093/nar/gky995.


HMMER web server: 2018 update.

Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD.

Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204. doi: 10.1093/nar/gky448.


Group I introns are widespread in archaea.

Nawrocki EP, Jones TA, Eddy SR.

Nucleic Acids Res. 2018 Sep 6;46(15):7970-7976. doi: 10.1093/nar/gky414.


Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.

Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI.

Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038.


Gene Evolution: Getting Something from Nothing.

Weisman CM, Eddy SR.

Curr Biol. 2017 Jul 10;27(13):R661-R663. doi: 10.1016/j.cub.2017.05.056.


Identification and Characterization of a Class of MALAT1-like Genomic Loci.

Zhang B, Mao YS, Diermeier SD, Novikova IV, Nawrocki EP, Jones TA, Lazar Z, Tung CS, Luo W, Eddy SR, Sanbonmatsu KY, Spector DL.

Cell Rep. 2017 May 23;19(8):1723-1738. doi: 10.1016/j.celrep.2017.05.006.


A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.

Rivas E, Clements J, Eddy SR.

Nat Methods. 2017 Jan;14(1):45-48. doi: 10.1038/nmeth.4066. Epub 2016 Nov 7.


Epigenomic landscapes of retinal rods and cones.

Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J.

Elife. 2016 Mar 7;5:e11613. doi: 10.7554/eLife.11613.


The Pfam protein families database: towards a more sustainable future.

Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. doi: 10.1093/nar/gkv1344. Epub 2015 Dec 15.


Parameterizing sequence alignment with an explicit evolutionary model.

Rivas E, Eddy SR.

BMC Bioinformatics. 2015 Dec 10;16:406. doi: 10.1186/s12859-015-0832-5.


The Dfam database of repetitive DNA families.

Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. doi: 10.1093/nar/gkv1272. Epub 2015 Nov 26.


Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.

Chen X, Jung S, Beh LY, Eddy SR, Landweber LF.

Genome Biol Evol. 2015 Sep 2;7(10):2859-70. doi: 10.1093/gbe/evv172.


Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J.

Neuron. 2015 Jun 17;86(6):1369-84. doi: 10.1016/j.neuron.2015.05.018.


HMMER web server: 2015 update.

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.

Nucleic Acids Res. 2015 Jul 1;43(W1):W30-8. doi: 10.1093/nar/gkv397. Epub 2015 May 5.


Homology searches for structural RNAs: from proof of principle to practical use.

Eddy SR.

RNA. 2015 Apr;21(4):605-7. doi: 10.1261/rna.050484.115. No abstract available.


Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.


Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

Eddy SR.

Annu Rev Biophys. 2014;43:433-56. doi: 10.1146/annurev-biophys-051013-022950. Review.


Pfam: the protein families database.

Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M.

Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30. doi: 10.1093/nar/gkt1223. Epub 2013 Nov 27.


Infernal 1.1: 100-fold faster RNA homology searches.

Nawrocki EP, Eddy SR.

Bioinformatics. 2013 Nov 15;29(22):2933-5. doi: 10.1093/bioinformatics/btt509. Epub 2013 Sep 4.


nhmmer: DNA homology search with profile HMMs.

Wheeler TJ, Eddy SR.

Bioinformatics. 2013 Oct 1;29(19):2487-9. doi: 10.1093/bioinformatics/btt403. Epub 2013 Jul 9.


Computational identification of functional RNA homologs in metagenomic data.

Nawrocki EP, Eddy SR.

RNA Biol. 2013 Jul;10(7):1170-9. doi: 10.4161/rna.25038. Epub 2013 May 20. Review.


Transcription factors that convert adult cell identity are differentially polycomb repressed.

Davis FP, Eddy SR.

PLoS One. 2013 May 1;8(5):e63407. doi: 10.1371/journal.pone.0063407. Print 2013.


Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.

Mistry J, Finn RD, Eddy SR, Bateman A, Punta M.

Nucleic Acids Res. 2013 Jul;41(12):e121. doi: 10.1093/nar/gkt263. Epub 2013 Apr 17.


The ENCODE project: missteps overshadowing a success.

Eddy SR.

Curr Biol. 2013 Apr 8;23(7):R259-61. doi: 10.1016/j.cub.2013.03.023.


The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.

Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF.

PLoS Biol. 2013;11(1):e1001473. doi: 10.1371/journal.pbio.1001473. Epub 2013 Jan 29.


Dfam: a database of repetitive DNA based on profile hidden Markov models.

Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D70-82. doi: 10.1093/nar/gks1265. Epub 2012 Nov 30.


The C-value paradox, junk DNA and ENCODE.

Eddy SR.

Curr Biol. 2012 Nov 6;22(21):R898-9. doi: 10.1016/j.cub.2012.10.002. No abstract available.


Rfam 11.0: 10 years of RNA families.

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3.


Cell type-specific genomics of Drosophila neurons.

Henry GL, Davis FP, Picard S, Eddy SR.

Nucleic Acids Res. 2012 Oct;40(19):9691-704. doi: 10.1093/nar/gks671. Epub 2012 Aug 1.


A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

Rivas E, Lang R, Eddy SR.

RNA. 2012 Feb;18(2):193-212. doi: 10.1261/rna.030049.111. Epub 2011 Dec 22.


The Pfam protein families database.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065. Epub 2011 Nov 29.


Accelerated Profile HMM Searches.

Eddy SR.

PLoS Comput Biol. 2011 Oct;7(10):e1002195. doi: 10.1371/journal.pcbi.1002195. Epub 2011 Oct 20.


Fast filtering for RNA homology search.

Kolbe DL, Eddy SR.

Bioinformatics. 2011 Nov 15;27(22):3102-9. doi: 10.1093/bioinformatics/btr545. Epub 2011 Sep 28.


Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.

Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, Landweber LF, Eddy SR.

Nucleic Acids Res. 2011 Sep 1;39(17):7529-47. doi: 10.1093/nar/gkr501. Epub 2011 Jun 28.


HMMER web server: interactive sequence similarity searching.

Finn RD, Clements J, Eddy SR.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37. doi: 10.1093/nar/gkr367. Epub 2011 May 18.


Rfam: Wikipedia, clans and the "decimal" release.

Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5. doi: 10.1093/nar/gkq1129. Epub 2010 Nov 9.


Hidden Markov model speed heuristic and iterative HMM search procedure.

Johnson LS, Eddy SR, Portugaly E.

BMC Bioinformatics. 2010 Aug 18;11:431. doi: 10.1186/1471-2105-11-431.


A new generation of homology search tools based on probabilistic inference.

Eddy SR.

Genome Inform. 2009 Oct;23(1):205-11.


The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.


A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.

Davis FP, Eddy SR.

Bioinformatics. 2009 Jul 1;25(13):1647-54. doi: 10.1093/bioinformatics/btp288. Epub 2009 May 4.


Infernal 1.0: inference of RNA alignments.

Nawrocki EP, Kolbe DL, Eddy SR.

Bioinformatics. 2009 May 15;25(10):1335-7. doi: 10.1093/bioinformatics/btp157. Epub 2009 Mar 23. Erratum in: Bioinformatics. 2009 Jul 1;25(13):1713.


Local RNA structure alignment with incomplete sequence.

Kolbe DL, Eddy SR.

Bioinformatics. 2009 May 15;25(10):1236-43. doi: 10.1093/bioinformatics/btp154. Epub 2009 Mar 20.


A survey of nematode SmY RNAs.

Jones TA, Otto W, Marz M, Eddy SR, Stadler PF.

RNA Biol. 2009 Jan-Mar;6(1):5-8. Epub 2009 Jan 26. Review.


Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766. Epub 2008 Oct 25.


Probabilistic phylogenetic inference with insertions and deletions.

Rivas E, Eddy SR.

PLoS Comput Biol. 2008 Sep 19;4(9):e1000172. doi: 10.1371/journal.pcbi.1000172.


A probabilistic model of local sequence alignment that simplifies statistical significance estimation.

Eddy SR.

PLoS Comput Biol. 2008 May 30;4(5):e1000069. doi: 10.1371/journal.pcbi.1000069.


The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8. Epub 2007 Nov 26.


C. elegans noncoding RNA genes.

Stricklin SL, Griffiths-Jones S, Eddy SR.

WormBook. 2005 Jun 25:1-7. Review.


Query-dependent banding (QDB) for faster RNA similarity searches.

Nawrocki EP, Eddy SR.

PLoS Comput Biol. 2007 Mar 30;3(3):e56. Epub 2007 Feb 7.


Computational analysis of RNAs.

Eddy SR.

Cold Spring Harb Symp Quant Biol. 2006;71:117-28.


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