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Items: 1 to 20 of 113


Free circular introns with an unusual branchpoint in neuronal projections.

Saini H, Bicknell AA, Eddy SR, Moore MJ.

Elife. 2019 Nov 7;8. pii: e47809. doi: 10.7554/eLife.47809. [Epub ahead of print]


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.

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