Sean R Eddy

Summary

Affiliation: Howard Hughes Medical Institute
Country: USA

Publications

  1. ncbi Computational analysis of conserved RNA secondary structure in transcriptomes and genomes
    Sean R Eddy
    Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia 20147 email
    Annu Rev Biophys 43:433-56. 2014
  2. pmc Fast filtering for RNA homology search
    Diana L Kolbe
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 27:3102-9. 2011
  3. pmc Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes
    Seolkyoung Jung
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn VA 20147, USA
    Nucleic Acids Res 39:7529-47. 2011
  4. doi The ENCODE project: missteps overshadowing a success
    Sean R Eddy
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Curr Biol 23:R259-61. 2013
  5. pmc Hidden Markov model speed heuristic and iterative HMM search procedure
    L Steven Johnson
    Department of Immunology and Pathology, Washington University School of Medicine, St Louis, Missouri, USA
    BMC Bioinformatics 11:431. 2010
  6. ncbi A new generation of homology search tools based on probabilistic inference
    Sean R Eddy
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Genome Inform 23:205-11. 2009
  7. pmc A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    Sean R Eddy
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
    PLoS Comput Biol 4:e1000069. 2008
  8. pmc Accelerated Profile HMM Searches
    Sean R Eddy
    HHMI Janelia Farm Research Campus, Ashburn, Virginia, United States of America
    PLoS Comput Biol 7:e1002195. 2011
  9. pmc nhmmer: DNA homology search with profile HMMs
    Travis J Wheeler
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 29:2487-9. 2013
  10. pmc Probabilistic phylogenetic inference with insertions and deletions
    Elena Rivas
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
    PLoS Comput Biol 4:e1000172. 2008

Detail Information

Publications52

  1. ncbi Computational analysis of conserved RNA secondary structure in transcriptomes and genomes
    Sean R Eddy
    Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia 20147 email
    Annu Rev Biophys 43:433-56. 2014
    ..Such analyses include homology search and genome-wide detection of new structural RNAs. ..
  2. pmc Fast filtering for RNA homology search
    Diana L Kolbe
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 27:3102-9. 2011
    ..Typical acceleration strategies rely on at least one filtering stage using sequence-only search...
  3. pmc Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes
    Seolkyoung Jung
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn VA 20147, USA
    Nucleic Acids Res 39:7529-47. 2011
    ..Other than new members of known ncRNA classes including C/D and H/ACA snoRNAs, our screen identified one new family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs...
  4. doi The ENCODE project: missteps overshadowing a success
    Sean R Eddy
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Curr Biol 23:R259-61. 2013
    ..Neither story line does justice to our actual understanding of genomes, to ENCODE's results, or to the role of big science in biology...
  5. pmc Hidden Markov model speed heuristic and iterative HMM search procedure
    L Steven Johnson
    Department of Immunology and Pathology, Washington University School of Medicine, St Louis, Missouri, USA
    BMC Bioinformatics 11:431. 2010
    ..Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases...
  6. ncbi A new generation of homology search tools based on probabilistic inference
    Sean R Eddy
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Genome Inform 23:205-11. 2009
    ..The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods...
  7. pmc A probabilistic model of local sequence alignment that simplifies statistical significance estimation
    Sean R Eddy
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
    PLoS Comput Biol 4:e1000069. 2008
    ..This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments...
  8. pmc Accelerated Profile HMM Searches
    Sean R Eddy
    HHMI Janelia Farm Research Campus, Ashburn, Virginia, United States of America
    PLoS Comput Biol 7:e1002195. 2011
    ..HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches...
  9. pmc nhmmer: DNA homology search with profile HMMs
    Travis J Wheeler
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 29:2487-9. 2013
    ..This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome...
  10. pmc Probabilistic phylogenetic inference with insertions and deletions
    Elena Rivas
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
    PLoS Comput Biol 4:e1000172. 2008
    ....
  11. pmc Infernal 1.0: inference of RNA alignments
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1335-7. 2009
    ....
  12. pmc Local RNA structure alignment with incomplete sequence
    Diana L Kolbe
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1236-43. 2009
    ....
  13. pmc Infernal 1.1: 100-fold faster RNA homology searches
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 29:2933-5. 2013
    ..This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches...
  14. pmc A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more
    Elena Rivas
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
    RNA 18:193-212. 2012
    ..The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases...
  15. pmc Dfam: a database of repetitive DNA based on profile hidden Markov models
    Travis J Wheeler
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Nucleic Acids Res 41:D70-82. 2013
    ..5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps...
  16. pmc Pfam: the protein families database
    Robert D Finn
    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
    Nucleic Acids Res 42:D222-30. 2014
    ..Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. ..
  17. pmc A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas
    Fred P Davis
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Bioinformatics 25:1647-54. 2009
    ..Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest...
  18. pmc Query-dependent banding (QDB) for faster RNA similarity searches
    Eric P Nawrocki
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
    PLoS Comput Biol 3:e56. 2007
    ..Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization...
  19. pmc Transcription factors that convert adult cell identity are differentially polycomb repressed
    Fred P Davis
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia United States of America
    PLoS ONE 8:e63407. 2013
    ..This genomic model of cell identity helps rationalize a growing number of transdifferentiation protocols and may help facilitate the engineering of cell identity for regenerative medicine...
  20. ncbi A survey of nematode SmY RNAs
    Thomas A Jones
    HHMI Janelia Farm Research Campus, Ashburn, Virginia, USA
    RNA Biol 6:5-8. 2009
    ..A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database...
  21. pmc HMMER web server: interactive sequence similarity searching
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Nucleic Acids Res 39:W29-37. 2011
    ....
  22. ncbi Computational genomics of noncoding RNA genes
    Sean R Eddy
    Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Cell 109:137-40. 2002
    ..However, noncoding RNAs present computational genomics with a new set of challenges...
  23. pmc Cell type-specific genomics of Drosophila neurons
    Gilbert L Henry
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Nucleic Acids Res 40:9691-704. 2012
    ..Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity...
  24. pmc Sharing publication-related data and materials: responsibilities of authorship in the life sciences
    Thomas R Cech
    Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
    Plant Physiol 132:19-24. 2003
  25. pmc Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
    Jaina Mistry
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 41:e121. 2013
    ..They also highlight the need for developing new methods that can correct for this particular type of compositional bias...
  26. pmc Rfam 11.0: 10 years of RNA families
    Sarah W Burge
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 41:D226-32. 2013
    ..0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license...
  27. pmc RSEARCH: finding homologs of single structured RNA sequences
    Robert J Klein
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    BMC Bioinformatics 4:44. 2003
    ..No programs have yet been published that allow searching a sequence database for homologs of a single RNA molecule on the basis of secondary structure...
  28. pmc Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    Robin D Dowell
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, St Louis, MO 63108, USA
    BMC Bioinformatics 7:400. 2006
    ..There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm...
  29. pmc RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    Christian M Zmasek
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    BMC Bioinformatics 3:14. 2002
    ..The utility of phylogenetic information in high-throughput genome annotation ("phylogenomics") is widely recognized, but existing approaches are either manual or not explicitly based on phylogenetic trees...
  30. pmc A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110 USA
    BMC Bioinformatics 3:18. 2002
    ..The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs...
  31. pmc Automated de novo identification of repeat sequence families in sequenced genomes
    Zhirong Bao
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Genome Res 12:1269-76. 2002
    ..When tested on the human genome, our approach was able to properly identify and group known transposable elements. The program, should be useful for first-pass automatic classification of repeats in newly sequenced genomes...
  32. pmc Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
    John P McCutcheon
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Nucleic Acids Res 31:4119-28. 2003
    ..Thirteen showed discrete transcripts when assayed by northern blot. Of these, eight appear to be novel ncRNAs ranging in size from 268 to 775 nt, including three new H/ACA box small nucleolar RNAs...
  33. ncbi What is dynamic programming?
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, Saint Louis, Missouri 63108, USA
    Nat Biotechnol 22:909-10. 2004
  34. ncbi What is Bayesian statistics?
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, Saint Louis, Missouri 63108, USA
    Nat Biotechnol 22:1177-8. 2004
  35. ncbi What is a hidden Markov model?
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, Saint Louis, Missouri 63108, USA
    Nat Biotechnol 22:1315-6. 2004
  36. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
    ..New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource...
  37. pmc A model of the statistical power of comparative genome sequence analysis
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine Saint Louis, Missouri United States of America
    PLoS Biol 3:e10. 2005
    ....
  38. pmc Pfam: clans, web tools and services
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nucleic Acids Res 34:D247-51. 2006
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/)...
  39. ncbi Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus
    Wayne A Speckmann
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Curr Biol 12:199-203. 2002
    ..Our studies have revealed the remarkable ability of archaeal Box C/D RNAs to assemble into functional RNA-protein complexes in the eukaryotic nucleus...
  40. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nucleic Acids Res 36:D281-8. 2008
    ..sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/)...
  41. ncbi Generation and annotation of the DNA sequences of human chromosomes 2 and 4
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 434:724-31. 2005
    ..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions...
  42. pmc Rfam: an RNA family database
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:439-41. 2003
    ..wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database...
  43. ncbi An active DNA transposon family in rice
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Nature 421:163-7. 2003
    ..Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation...
  44. pmc Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes
    Jennifer C Darnell
    Howard Hughes Medical Institute and Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York, USA
    Genes Dev 19:903-18. 2005
    ....
  45. ncbi The DNA sequence of human chromosome 7
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 424:157-64. 2003
    ..Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame...
  46. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  47. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/)...
  48. pmc Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
    Robin D Dowell
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St, Louis, MO 63108 USA
    BMC Bioinformatics 5:71. 2004
    ..Thus a key question is, what small, simple SCFG designs perform best for RNA secondary structure prediction?..
  49. ncbi How do RNA folding algorithms work?
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, Saint Louis, Missouri 63108, USA
    Nat Biotechnol 22:1457-8. 2004
    ..Programs such as MFOLD and ViennaRNA are widely used to predict RNA secondary structures. How do these algorithms work? Why can't they predict RNA pseudoknots? How accurate are they, and will they get better?..
  50. ncbi Where did the BLOSUM62 alignment score matrix come from?
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, Saint Louis, Missouri 63108, USA
    Nat Biotechnol 22:1035-6. 2004
    ..Many sequence alignment programs use the BLOSUM62 score matrix to score pairs of aligned residues. Where did BLOSUM62 come from?..
  51. ncbi Pack-MULE transposable elements mediate gene evolution in plants
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Nature 431:569-73. 2004
    ....
  52. pmc Rfam: annotating non-coding RNAs in complete genomes
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 33:D121-4. 2005
    ..Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/...