S R Eddy

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. 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
  8. 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
  9. 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
  10. 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

Research Grants

  1. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2003
  2. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2006

Detail Information

Publications47

  1. 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
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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?..
  5. ncbi 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...
  6. ncbi 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...
  7. 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...
  8. 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
  9. 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?..
  10. 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
  11. ncbi Non-coding RNA genes and the modern RNA world
    S R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    Nat Rev Genet 2:919-29. 2001
    ....
  12. 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?..
  13. ncbi 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
    ....
  14. ncbi Genetics. Total information awareness for worm genetics
    Sean R Eddy
    Howard Hughes Medical Institute and the Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
    Science 311:1381-2. 2006
  15. ncbi Noncoding RNA genes
    S R Eddy
    Department of Genetics, Washington University School of Medicine, St Louis 63110, USA
    Curr Opin Genet Dev 9:695-9. 1999
    ..Genome sequences and new algorithms have begun to make systematic computational screens for noncoding RNA genes possible...
  16. ncbi Profile hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA
    Bioinformatics 14:755-63. 1998
    ..Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise...
  17. ncbi Hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Curr Opin Struct Biol 6:361-5. 1996
    ..During the past year, applications of these powerful new HMM-based profiles have begun to appear in the fields of protein-structure prediction and large-scale genome-sequence analysis...
  18. ncbi Noncoding RNA gene detection using comparative sequence analysis
    E Rivas
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, USA
    BMC Bioinformatics 2:8. 2001
    ..Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. A reliable general purpose computational genefinder for noncoding RNA genes has been elusive...
  19. 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
    ....
  20. ncbi 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...
  21. ncbi Computational analysis of RNAs
    S R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63108, USA
    Cold Spring Harb Symp Quant Biol 71:117-28. 2006
    ..The INFERNAL and RSEARCH programs are capable of identifying distant RNA homologs in a database search by looking for both sequence and secondary structure conservation...
  22. ncbi A computational screen for methylation guide snoRNAs in yeast
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA
    Science 283:1168-71. 1999
    ..Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs...
  23. ncbi Computational identification of noncoding RNAs in E. coli by comparative genomics
    E Rivas
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
    Curr Biol 11:1369-73. 2001
    ..Our computational approach may be used to discover structural ncRNA genes in any genome for which appropriate comparative genome sequence data are available...
  24. ncbi The distributed annotation system
    R D Dowell
    Howard Hughes Medical Institute and Department of Genetics, Washington University, St Louis, MO 63110 USA
    BMC Bioinformatics 2:7. 2001
    ..Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory...
  25. ncbi ATV: display and manipulation of annotated phylogenetic trees
    C M Zmasek
    Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Bioinformatics 17:383-4. 2001
    ..A Tree Viewer (ATV) is a Java tool for the display and manipulation of annotated phylogenetic trees. It can be utilized both as a standalone application and as an applet in a web browser...
  26. ncbi A simple algorithm to infer gene duplication and speciation events on a gene tree
    C M Zmasek
    Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Bioinformatics 17:821-8. 2001
    ..AVAILABILITY: http://www.genetics.wustl.edu/eddy/forester...
  27. 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...
  28. ncbi 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...
  29. ncbi 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...
  30. 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...
  31. 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...
  32. ncbi 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
  33. ncbi Noncoding RNA genes identified in AT-rich hyperthermophiles
    Robert J Klein
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 99:7542-7. 2002
    ..furiosus. Nine of the 30 new candidate genes predicted by these screens have been verified to produce discrete, apparently noncoding transcripts with sizes ranging from 97 to 277 nucleotides...
  34. ncbi 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/)...
  35. ncbi 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...
  36. ncbi 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
    ....
  37. ncbi 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/)...
  38. ncbi 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 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
    ....
  40. ncbi 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/...
  41. ncbi 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...
  42. 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
    ....
  43. ncbi Circular box C/D RNAs in Pyrococcus furiosus
    Natalia G Starostina
    Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Science Building, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:14097-101. 2004
    ..Moreover, the unexpected discovery of circular box C/D RNAs points to the existence of a previously unrecognized biogenesis pathway for box C/D RNAs in archaea...
  44. ncbi 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...
  45. ncbi 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...
  46. 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...
  47. 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...

Research Grants9

  1. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2003
    ..Additionally, a "simulated evolution" algorithm is proposed for increasing HMMER's sensitivity. ..
  2. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2006
    ..A final aim proposes a method for identifying the mRNA targets of regulatory RNAs (such as the newly discovered micro RNAs) by comparative genome analysis. ..