Publications by authors named "Sean R Eddy"

85Publications

Estimating the power of sequence covariation for detecting conserved RNA structure.

Bioinformatics 2020 05;36(10):3072-3076

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214042PMC
May 2020

A genetic, genomic, and computational resource for exploring neural circuit function.

Elife 2020 Jan 15;9. Epub 2020 Jan 15.

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.

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http://dx.doi.org/10.7554/eLife.50901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7034979PMC
January 2020

Representation learning of genomic sequence motifs with convolutional neural networks.

PLoS Comput Biol 2019 12 19;15(12):e1007560. Epub 2019 Dec 19.

Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941814PMC
December 2019

Free circular introns with an unusual branchpoint in neuronal projections.

Elife 2019 11 7;8. Epub 2019 Nov 7.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.

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http://dx.doi.org/10.7554/eLife.47809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879206PMC
November 2019

HMMER web server: 2018 update.

Nucleic Acids Res 2018 07;46(W1):W200-W204

EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gky448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030962PMC
July 2018

Group I introns are widespread in archaea.

Nucleic Acids Res 2018 09;46(15):7970-7976

Howard Hughes Medical Institute, Harvard University, Cambridge, USA.

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http://dx.doi.org/10.1093/nar/gky414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125680PMC
September 2018

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

Nucleic Acids Res 2018 01;46(D1):D335-D342

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkx1038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753348PMC
January 2018

Gene Evolution: Getting Something from Nothing.

Curr Biol 2017 07;27(13):R661-R663

HHMI & Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2017.05.056DOI Listing
July 2017

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

Nat Methods 2017 01 7;14(1):45-48. Epub 2016 Nov 7.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.4066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554622PMC
January 2017

Epigenomic landscapes of retinal rods and cones.

Elife 2016 Mar 7;5:e11613. Epub 2016 Mar 7.

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.

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http://dx.doi.org/10.7554/eLife.11613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798964PMC
March 2016

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

Nucleic Acids Res 2016 Jan 15;44(D1):D279-85. Epub 2015 Dec 15.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkv1344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702930PMC
January 2016

Parameterizing sequence alignment with an explicit evolutionary model.

BMC Bioinformatics 2015 Dec 10;16:406. Epub 2015 Dec 10.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, 02138, MA, USA.

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http://dx.doi.org/10.1186/s12859-015-0832-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676179PMC
December 2015

The Dfam database of repetitive DNA families.

Nucleic Acids Res 2016 Jan 26;44(D1):D81-9. Epub 2015 Nov 26.

University of Montana, Missoula, MT 59812, USA

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http://dx.doi.org/10.1093/nar/gkv1272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702899PMC
January 2016

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

Genome Biol Evol 2015 Sep 2;7(10):2859-70. Epub 2015 Sep 2.

Department of Ecology and Evolutionary Biology, Princeton University

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http://dx.doi.org/10.1093/gbe/evv172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684698PMC
September 2015

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Neuron 2015 Jun;86(6):1369-84

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2015.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499463PMC
June 2015

HMMER web server: 2015 update.

Nucleic Acids Res 2015 Jul 5;43(W1):W30-8. Epub 2015 May 5.

HHMI Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gkv397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489315PMC
July 2015

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

Authors:
Sean R Eddy

RNA 2015 Apr;21(4):605-7

Janelia Research Campus, Ashburn, Virginia 20147, USA

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http://dx.doi.org/10.1261/rna.050484.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371300PMC
April 2015

Rfam 12.0: updates to the RNA families database.

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

HHMI Janelia Farm Research Campus, Ashburn, VA, USA European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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http://dx.doi.org/10.1093/nar/gku1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383904PMC
January 2015

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

Authors:
Sean R Eddy

Annu Rev Biophys 2014 ;43:433-56

Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia 20147; email:

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http://www.annualreviews.org/doi/10.1146/annurev-biophys-051
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http://dx.doi.org/10.1146/annurev-biophys-051013-022950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541781PMC
August 2014

Pfam: the protein families database.

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

HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 (Viikinkaari 5), 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1093/nar/gkt1223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965110PMC
January 2014

Infernal 1.1: 100-fold faster RNA homology searches.

Bioinformatics 2013 Nov 4;29(22):2933-5. Epub 2013 Sep 4.

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810854PMC
November 2013

nhmmer: DNA homology search with profile HMMs.

Bioinformatics 2013 Oct 9;29(19):2487-9. Epub 2013 Jul 9.

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777106PMC
October 2013

Computational identification of functional RNA homologs in metagenomic data.

RNA Biol 2013 Jul 20;10(7):1170-9. Epub 2013 May 20.

Janelia Farm Research Campus; Ashburn, VA USA.

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http://dx.doi.org/10.4161/rna.25038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849165PMC
July 2013

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

PLoS One 2013 1;8(5):e63407. Epub 2013 May 1.

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063407PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641127PMC
November 2013

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

Nucleic Acids Res 2013 Jul 17;41(12):e121. Epub 2013 Apr 17.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkt263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695513PMC
July 2013

The ENCODE project: missteps overshadowing a success.

Authors:
Sean R Eddy

Curr Biol 2013 Apr;23(7):R259-61

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1016/j.cub.2013.03.023DOI Listing
April 2013

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

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

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gks1265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531169PMC
January 2013

The C-value paradox, junk DNA and ENCODE.

Authors:
Sean R Eddy

Curr Biol 2012 Nov;22(21):R898-9

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1016/j.cub.2012.10.002DOI Listing
November 2012

Rfam 11.0: 10 years of RNA families.

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

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gks1005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531072PMC
January 2013

Cell type-specific genomics of Drosophila neurons.

Nucleic Acids Res 2012 Oct 1;40(19):9691-704. Epub 2012 Aug 1.

Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gks671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479168PMC
October 2012

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

RNA 2012 Feb 22;18(2):193-212. Epub 2011 Dec 22.

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.

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http://dx.doi.org/10.1261/rna.030049.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264907PMC
February 2012

The Pfam protein families database.

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

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkr1065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245129PMC
January 2012

Accelerated Profile HMM Searches.

Authors:
Sean R Eddy

PLoS Comput Biol 2011 Oct 20;7(10):e1002195. Epub 2011 Oct 20.

HHMI Janelia Farm Research Campus, Ashburn, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197634PMC
October 2011

Fast filtering for RNA homology search.

Bioinformatics 2011 Nov 28;27(22):3102-9. Epub 2011 Sep 28.

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208395PMC
November 2011

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

Nucleic Acids Res 2011 Sep 28;39(17):7529-47. Epub 2011 Jun 28.

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gkr501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177221PMC
September 2011

HMMER web server: interactive sequence similarity searching.

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

HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gkr367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125773PMC
July 2011

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

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

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA.

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http://dx.doi.org/10.1093/nar/gkq1129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013711PMC
January 2011

Hidden Markov model speed heuristic and iterative HMM search procedure.

BMC Bioinformatics 2010 Aug 18;11:431. Epub 2010 Aug 18.

Department of Immunology and Pathology, Washington University School of Medicine, St Louis, Missouri, USA.

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http://dx.doi.org/10.1186/1471-2105-11-431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931519PMC
August 2010

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

Authors:
Sean R Eddy

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

Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.

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October 2009

The Pfam protein families database.

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

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkp985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889PMC
January 2010

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

Bioinformatics 2009 Jul 4;25(13):1647-54. Epub 2009 May 4.

HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940243PMC
July 2009

Infernal 1.0: inference of RNA alignments.

Bioinformatics 2009 May 23;25(10):1335-7. Epub 2009 Mar 23.

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732312PMC
May 2009

Local RNA structure alignment with incomplete sequence.

Bioinformatics 2009 May 20;25(10):1236-43. Epub 2009 Mar 20.

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677745PMC
May 2009

A survey of nematode SmY RNAs.

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

HHMI Janelia Farm Research Campus, Ashburn, Virginia, USA.

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http://dx.doi.org/10.4161/rna.6.1.7634DOI Listing
April 2009

Rfam: updates to the RNA families database.

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

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkn766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686503PMC
January 2009

Probabilistic phylogenetic inference with insertions and deletions.

PLoS Comput Biol 2008 Sep 19;4(9):e1000172. Epub 2008 Sep 19.

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527138PMC
September 2008

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

Authors:
Sean R Eddy

PLoS Comput Biol 2008 May 30;4(5):e1000069. Epub 2008 May 30.

Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396288PMC
May 2008

The Pfam protein families database.

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

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkm960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238907PMC
January 2008

C. elegans noncoding RNA genes.

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

Howard Hughes Medical Institute and Department of Genetics, Washington University, St. Louis, MO 63108, USA.

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http://www.wormbook.org/chapters/www_noncodingRNA/noncodingR
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http://dx.doi.org/10.1895/wormbook.1.1.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781554PMC
June 2005

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

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

Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.0030056
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http://dx.doi.org/10.1371/journal.pcbi.0030056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847999PMC
March 2007

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.

BMC Bioinformatics 2006 Sep 4;7:400. Epub 2006 Sep 4.

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, St. Louis, MO 63108, USA.

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http://www.springerlink.com/index/261731L482864770.pdf
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http://www.springerlink.com/index/u25h361836361070.pdf
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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1579236PMC
September 2006

Genetics. Total information awareness for worm genetics.

Authors:
Sean R Eddy

Science 2006 Mar;311(5766):1381-2

Howard Hughes Medical Institute and the Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1126/science.1125655DOI Listing
March 2006

Pfam: clans, web tools and services.

Nucleic Acids Res 2006 Jan;34(Database issue):D247-51

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkj149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347511PMC
January 2006

"Antedisciplinary" science.

Authors:
Sean R Eddy

PLoS Comput Biol 2005 Jun;1(1):e6

Howard Hughes Medical Institute, Department of Genetics at Washington University School of Medicine, Saint Louis, Missouri, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0010006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183512PMC
June 2005

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

Authors:
Ladeana W Hillier Tina A Graves Robert S Fulton Lucinda A Fulton Kymberlie H Pepin Patrick Minx Caryn Wagner-McPherson Dan Layman Kristine Wylie Mandeep Sekhon Michael C Becker Ginger A Fewell Kimberly D Delehaunty Tracie L Miner William E Nash Colin Kremitzki Lachlan Oddy Hui Du Hui Sun Holland Bradshaw-Cordum Johar Ali Jason Carter Matt Cordes Anthony Harris Amber Isak Andrew van Brunt Christine Nguyen Feiyu Du Laura Courtney Joelle Kalicki Philip Ozersky Scott Abbott Jon Armstrong Edward A Belter Lauren Caruso Maria Cedroni Marc Cotton Teresa Davidson Anu Desai Glendoria Elliott Thomas Erb Catrina Fronick Tony Gaige William Haakenson Krista Haglund Andrea Holmes Richard Harkins Kyung Kim Scott S Kruchowski Cynthia Madsen Strong Neenu Grewal Ernest Goyea Shunfang Hou Andrew Levy Scott Martinka Kelly Mead Michael D McLellan Rick Meyer Jennifer Randall-Maher Chad Tomlinson Sara Dauphin-Kohlberg Amy Kozlowicz-Reilly Neha Shah Sharhonda Swearengen-Shahid Jacqueline Snider Joseph T Strong Johanna Thompson Martin Yoakum Shawn Leonard Charlene Pearman Lee Trani Maxim Radionenko Jason E Waligorski Chunyan Wang Susan M Rock Aye-Mon Tin-Wollam Rachel Maupin Phil Latreille Michael C Wendl Shiaw-Pyng Yang Craig Pohl John W Wallis John Spieth Tamberlyn A Bieri Nicolas Berkowicz Joanne O Nelson John Osborne Li Ding Rekha Meyer Aniko Sabo Yoram Shotland Prashant Sinha Patricia E Wohldmann Lisa L Cook Matthew T Hickenbotham James Eldred Donald Williams Thomas A Jones Xinwei She Francesca D Ciccarelli Elisa Izaurralde James Taylor Jeremy Schmutz Richard M Myers David R Cox Xiaoqiu Huang John D McPherson Elaine R Mardis Sandra W Clifton Wesley C Warren Asif T Chinwalla Sean R Eddy Marco A Marra Ivan Ovcharenko Terrence S Furey Webb Miller Evan E Eichler Peer Bork Mikita Suyama David Torrents Robert H Waterston Richard K Wilson

Nature 2005 Apr;434(7034):724-31

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature03466DOI Listing
April 2005

Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes.

Genes Dev 2005 Apr 1;19(8):903-18. Epub 2005 Apr 1.

Howard Hughes Medical Institute and Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York, USA.

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http://dx.doi.org/10.1101/gad.1276805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1080130PMC
April 2005

A model of the statistical power of comparative genome sequence analysis.

Authors:
Sean R Eddy

PLoS Biol 2005 Jan 4;3(1):e10. Epub 2005 Jan 4.

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine Saint Louis, Missouri United States of America.

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http://dx.doi.org/10.1371/journal.pbio.0030010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539325PMC
January 2005

Rfam: annotating non-coding RNAs in complete genomes.

Nucleic Acids Res 2005 Jan;33(Database issue):D121-4

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gki081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540035PMC
January 2005

How do RNA folding algorithms work?

Authors:
Sean R Eddy

Nat Biotechnol 2004 Nov;22(11):1457-8

Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., Box 8510, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nbt1104-1457DOI Listing
November 2004

What is a hidden Markov model?

Authors:
Sean R Eddy

Nat Biotechnol 2004 Oct;22(10):1315-6

Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., Box 8510, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nbt1004-1315DOI Listing
October 2004

Pack-MULE transposable elements mediate gene evolution in plants.

Nature 2004 Sep;431(7008):569-73

Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1038/nature02953DOI Listing
September 2004

Circular box C/D RNAs in Pyrococcus furiosus.

Proc Natl Acad Sci U S A 2004 Sep 16;101(39):14097-101. Epub 2004 Sep 16.

Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Science Building, Athens, GA 30602, USA.

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http://dx.doi.org/10.1073/pnas.0403520101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521125PMC
September 2004

What is Bayesian statistics?

Authors:
Sean R Eddy

Nat Biotechnol 2004 Sep;22(9):1177-8

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., Box 8510, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nbt0904-1177DOI Listing
September 2004

Where did the BLOSUM62 alignment score matrix come from?

Authors:
Sean R Eddy

Nat Biotechnol 2004 Aug;22(8):1035-6

Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., Box 8510, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nbt0804-1035DOI Listing
August 2004

What is dynamic programming?

Authors:
Sean R Eddy

Nat Biotechnol 2004 Jul;22(7):909-10

Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., Box 8510, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nbt0704-909DOI Listing
July 2004

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

BMC Bioinformatics 2004 Jun 4;5:71. Epub 2004 Jun 4.

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St, Louis, MO 63108 USA.

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http://dx.doi.org/10.1186/1471-2105-5-71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC442121PMC
June 2004

The Pfam protein families database.

Nucleic Acids Res 2004 Jan;32(Database issue):D138-41

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkh121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308855PMC
January 2004

RSEARCH: finding homologs of single structured RNA sequences.

BMC Bioinformatics 2003 Sep 22;4:44. Epub 2003 Sep 22.

Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1186/1471-2105-4-44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC239859PMC
September 2003

The DNA sequence of human chromosome 7.

Authors:
Ladeana W Hillier Robert S Fulton Lucinda A Fulton Tina A Graves Kymberlie H Pepin Caryn Wagner-McPherson Dan Layman Jason Maas Sara Jaeger Rebecca Walker Kristine Wylie Mandeep Sekhon Michael C Becker Michelle D O'Laughlin Mark E Schaller Ginger A Fewell Kimberly D Delehaunty Tracie L Miner William E Nash Matt Cordes Hui Du Hui Sun Jennifer Edwards Holland Bradshaw-Cordum Johar Ali Stephanie Andrews Amber Isak Andrew Vanbrunt Christine Nguyen Feiyu Du Betty Lamar Laura Courtney Joelle Kalicki Philip Ozersky Lauren Bielicki Kelsi Scott Andrea Holmes Richard Harkins Anthony Harris Cynthia Madsen Strong Shunfang Hou Chad Tomlinson Sara Dauphin-Kohlberg Amy Kozlowicz-Reilly Shawn Leonard Theresa Rohlfing Susan M Rock Aye-Mon Tin-Wollam Amanda Abbott Patrick Minx Rachel Maupin Catrina Strowmatt Phil Latreille Nancy Miller Doug Johnson Jennifer Murray Jeffrey P Woessner Michael C Wendl Shiaw-Pyng Yang Brian R Schultz John W Wallis John Spieth Tamberlyn A Bieri Joanne O Nelson Nicolas Berkowicz Patricia E Wohldmann Lisa L Cook Matthew T Hickenbotham James Eldred Donald Williams Joseph A Bedell Elaine R Mardis Sandra W Clifton Stephanie L Chissoe Marco A Marra Christopher Raymond Eric Haugen Will Gillett Yang Zhou Rose James Karen Phelps Shawn Iadanoto Kerry Bubb Elizabeth Simms Ruth Levy James Clendenning Rajinder Kaul W James Kent Terrence S Furey Robert A Baertsch Michael R Brent Evan Keibler Paul Flicek Peer Bork Mikita Suyama Jeffrey A Bailey Matthew E Portnoy David Torrents Asif T Chinwalla Warren R Gish Sean R Eddy John D McPherson Maynard V Olson Evan E Eichler Eric D Green Robert H Waterston Richard K Wilson

Nature 2003 Jul;424(6945):157-64

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01782DOI Listing
July 2003

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics.

Nucleic Acids Res 2003 Jul;31(14):4119-28

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165953PMC
http://dx.doi.org/10.1093/nar/gkg438DOI Listing
July 2003

An active DNA transposon family in rice.

Nature 2003 Jan;421(6919):163-7

Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1038/nature01214DOI Listing
January 2003

Rfam: an RNA family database.

Nucleic Acids Res 2003 Jan;31(1):439-41

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165453PMC
http://dx.doi.org/10.1093/nar/gkg006DOI Listing
January 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002

Automated de novo identification of repeat sequence families in sequenced genomes.

Genome Res 2002 Aug;12(8):1269-76

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1101/gr.88502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186642PMC
August 2002

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.

Authors:
Sean R Eddy

BMC Bioinformatics 2002 Jul 2;3:18. Epub 2002 Jul 2.

Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110 USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC119854PMC
http://dx.doi.org/10.1186/1471-2105-3-18DOI Listing
July 2002

Noncoding RNA genes identified in AT-rich hyperthermophiles.

Proc Natl Acad Sci U S A 2002 May;99(11):7542-7

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.

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http://dx.doi.org/10.1073/pnas.112063799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124278PMC
May 2002

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.

BMC Bioinformatics 2002 May 16;3:14. Epub 2002 May 16.

Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC116988PMC
http://dx.doi.org/10.1186/1471-2105-3-14DOI Listing
May 2002

Computational genomics of noncoding RNA genes.

Authors:
Sean R Eddy

Cell 2002 Apr;109(2):137-40

Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1016/s0092-8674(02)00727-4DOI Listing
April 2002

Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus.

Curr Biol 2002 Feb;12(3):199-203

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1016/s0960-9822(02)00655-3DOI Listing
February 2002

The Pfam protein families database.

Nucleic Acids Res 2002 Jan;30(1):276-80

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99071PMC
http://dx.doi.org/10.1093/nar/30.1.276DOI Listing
January 2002