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2008 TOP A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation .
S. R. Eddy.
PLoS Comput. Biol., 4:e1000069, 2008.
[reprint] [preprint]
Supplementary material: [Notes and C source code (.tgz)]
The Pfam Protein Families Database .
R. D. Finn, J. Tate, J. Mistry, P. C. Coggill, S. J. Sammut, H.-R. Hotz, G. Ceric, K. Forslund, S. R. Eddy, E. L. L. Sonnhammer, A. Bateman.
Nucleic Acids Research, 36:D281-D288, 2008.
[abstract] [reprint] [preprint]
Database access: [Pfam]
Probabilistic Phylogenetic Inference with Insertions and Deletions .
E. Rivas, S. R. Eddy.
Manuscript submitted, 2008.
[preprint]
Supplementary material: [C and Perl source code; alignment data (.tar.gz)]
2007 TOP Identification of Differentially Expressed Small Non-Coding RNAs in the Legume Endosymbiont Sinorhizobium meliloti by Comparative Genomics .
C. del Val, E. Rivas, O. Torres-Quesada, N. Toro, J. I. Jim\'enez-Zurdo.
Mol. Microbiol., 66:1080-1091, 2007.
[abstract] [reprint] [preprint]
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches .
E. P. Nawrocki, S. R. Eddy.
PLoS Comput. Biol., 3:e56, 2007.
[abstract] [reprint] [preprint]
2006 TOP Efficient Pairwise RNA Structure Prediction and Alignment Using Sequence Alignment Constraints .
R. D. Dowell, S. R. Eddy.
BMC Bioinformatics, 7:400, 2006.
[abstract] [reprint] [preprint]
Download software: [CONSAN]
Total Information Awareness for Worm Genetics .
S. R. Eddy.
Science, 311:381-382, 2006.
[abstract] [reprint] [preprint]
Computational Analysis of RNAs .
S. R. Eddy.
Cold Spring Harbor Symp. Quant. Biol., 71:117-128, 2006.
[preprint]
Pfam: Clans, Web Tools and Services .
R. D. Finn, J. Mistry, B. Schuster-Bockler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. Sonnhammer, A. Bateman.
Nucleic Acids Research, 34:D247-D251, 2006.
[abstract] [reprint]
Database access: [Pfam]
Remote Protein Homology Detection Using Hidden Markov Models .
S. Johnson.
PhD Thesis: Washington University School of Medicine, 2006.
Screens for noncoding RNAs and strange lifeforms .
J. P. McCutcheon.
PhD Thesis: Washington University School of Medicine, 2006.
Noncoding RNA Genes in Caenorhabditis elegans .
S. L. Stricklin.
PhD Thesis: Washington University School of Medicine, 2006.
2005 TOP Kissing Complex RNAs Mediate Interaction Between the Fragile-X Mental Retardation Protein KH2 Domain and Brain Polyribosomes .
J. C. Darnell, C. E. Fraser, O. Mostovetsky, G. Stefani, T. A. Jones, S. R. Eddy, R. B. Darnell.
Genes & Development, 19:903-918, 2005.
[abstract] [reprint]
A Model of the Statistical Power of Comparative Genome Sequence Analysis .
S. R. Eddy.
PLoS Biol., 3:e10, 2005.
[abstract] [reprint] [preprint]
Supplementary material: [C source code (.tgz)]
There is a [correction] for this publicationAntedisciplinary Science .
S. R. Eddy.
PLoS Comput. Biol., 1:e6, 2005.
[abstract] [reprint] [preprint]
Rfam: Annotating Non-Coding RNAs in Complete Genomes .
S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S. R. Eddy, A. Bateman.
Nucleic Acids Research, 33:D121-D141, 2005.
[abstract] [reprint] [preprint]
Generation and Annotation of the DNA Sequences of Human Chromosomes 2 and 4 .
L. W. Hillier, T. A. Graves, R. S. Fulton, L. A. Fulton, K. H. Pepin, P. Minx, C. Wagner-McPherson, D. Layman, K. Wylie, M. Sekhon, M. C. Becker, G. A. Fewell, K. D. Delehaunty, T. L. Miner, W. E. Nash, C. Kremitzki, L. Oddy, H. Du, H. Sun, H. Bradshaw-Cordum, J. Ali, J. Carter, M. Cordes, A. Harris, A. Isak, A. van Brunt, C. Nguyen, F. Du, L. Courtney, J. Kalicki, P. Ozersky, S. Abbott, J. Armstrong, E. A. Belter, L. Caruso, M. Cedroni, M. Cotton, T. Davidson, A. Desai, G. Elliott, T. Erb, C. Fronick, T. Gaige, W. Haakenson, K. Haglund, A. Holmes, R. Harkins, K. Kim, S. S. Kruchowski, C. M. Strong, N. Grewal, E. Goyea, S. Hou, A. Levy, S. Martinka, K. Mead, M. D. McLellan, R. Meyer, J. Randall-Maher, C. Tomlinson, S. Dauphin-Kohlberg, A. Kozlowicz-Reilly, N. Shah, S. Swearengen-Shahid, J. Snider, J. T. Strong, J. Thompson, M. Yoakum, S. Leonard, C. Pearman, L. Trani, M. Radionenko, J. E. Waligorski, C. Wang, S. M. Rock, A. M. Tin-Wollam, R. Maupin, P. Latreille, M. C. Wendl, S. P. Yang, C. Pohl, J. W. Wallis, J. Spieth, T. A. Bieri, N. Berkowicz, J. O. Nelson, J. Osborne, L. Ding, R. Meyer, A. Sabo, Y. Shotland, P. Sinha, P. E. Wohldmann, L. L. Cook, M. T. Hickenbotham, J. Eldred, D. Williams, T. A. Jones, X. She, F. D. Ciccarelli, E. Izaurralde, J. Taylor, J. Schmutz, R. M. Myers, D. R. Cox, X. Huang, J. D. McPherson, E. R. Mardis, S. W. Clifton, W. C. Warren, A. T. Chinwalla, S. R. Eddy, M. A. Marra, I. Ovcharenko, T. S. Furey, W. Miller, E. E. Eichler, P. Bork, M. Suyama, D. Torrents, R. H. Waterston, R. K. Wilson.
Nature, 434:724-731, 2005.
[abstract] [reprint]
Evolutionary Models for Insertions and Deletions in a Probabilistic Modeling Framework .
E. Rivas.
BMC Bioinformatics., 6:63, 2005.
[abstract] [reprint] [preprint]
Supplementary material: [C source code]
Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome .
J. Shendure, G. J. Porreca, N. B. Reppas, X. Lin, J. P. McCutcheon, A. M. Rosenbaum, M. D. Wang, K. Zhang, R. D. Mitra, G. M. Church.
Science, 309:1728-1732, 2005.
[abstract] [reprint]
C. elegans Noncoding RNA Genes .
In: WormBook, .
S. L. Stricklin, S. Griffiths-Jones, S. R. Eddy.
doi/10.1895/wormbook.1.7.1, http://www.wormbook.org, 2005.
[reprint] [preprint]
Supplementary web site: [Table 1: ncRNA annotations]
2004 TOP The Pfam Protein Families Database .
A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. L. L. Sonnhammer, D. J. Studholme, C. Yeats, S. R. Eddy.
Nucleic Acids Research, 32:D138-141, 2004.
[abstract] [reprint]
Database access: [Pfam database]
RNA Structural Alignment Using Stochastic Context-Free Grammars .
Robin D. Dowell.
PhD Thesis: Washington University School of Medicine, 2004.
Evaluation of Several Lightweight Stochastic Context-Free Grammars for RNA Secondary Structure Prediction .
R. D. Dowell, S. R. Eddy.
BMC Bioinformatics, 5:71, 2004.
[abstract] [reprint] [preprint]
Supplementary web site: [Supporting material]
Download software: [CONUS]
What is Dynamic Programming? .
S. R. Eddy.
Nature Biotechnology, 22:909-910, 2004.
[abstract] [reprint] [preprint]
Supplementary material: [Example C program:global.c]
Where Did the BLOSUM62 Alignment Score Matrix Come From? .
S. R. Eddy.
Nature Biotechnology, 22:1035-1036, 2004.
[abstract] [reprint] [preprint]
Supplementary material: [Example C program: lambda.c]
What is Bayesian Statistics? .
S. R. Eddy.
Nature Biotechnology, 22:1177-1178, 2004.
[abstract] [reprint] [preprint]
What is a Hidden Markov Model? .
S. R. Eddy.
Nature Biotechnology, 22:1315-1316, 2004.
[abstract] [reprint] [preprint]
How Do RNA Folding Algorithms Work? .
S.R. Eddy.
Nature Biotechnology, 22:1457-1458, 2004.
[abstract] [reprint] [preprint]
Pack-MULEs: Transposon-Mediated Gene Evolution in Plants .
N. Jiang, Z. Bao, X. Zhang, S. R. Eddy, S. R. Wessler.
Nature, 431:569-573, 2004.
[abstract] [reprint]
Circular Box C/D RNAs in Pyrococcus furiosus .
N. G. Starostina, S. Marshburn, L. S. Johnson, S. R. Eddy, R. M. Terns, M. P. Terns.
Proc. of the National Academy of Sciences USA, 101:14097-14101, 2004.
[abstract] [reprint]
2003 TOP A Uniform System for microRNA Annotation .
V. Ambros, B. Bartel, D. P. Bartel, C. B. Burge, J. C. Carrington, X. Chen, G. Dreyfuss, S. R. Eddy, S. Griffiths-Jones, M. Marshall, M. Matzke, G. Ruvkun, T. Tuschl.
RNA, 9:277-279, 2003.
[abstract] [reprint]
Database access: [The miRNA registry]
Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences .
T. R. Cech, S. R. Eddy, D. Eisenberg, K. Hersey, S. H. Holtzman, G. H. Poste, N. V. Raikhel, R. H. Scheller, D. B. Singer, M. C. Waltham.
Plant Physiol., 132:19-24, 2003.
[abstract] [reprint]
Rfam: an RNA Family Database .
S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, S. R. Eddy.
Nucleic Acids Research, 31:439-441, 2003.
[abstract] [reprint] [preprint]
Database access: [Rfam]
The DNA Sequence of Human Chromosome 7 .
L. W. Hillier, R. S. Fulton, L. A. Fulton, T. A. Graves, K. H. Pepin, C. Wagner-McPherson, D. Layman, J. Maas, S. Jaeger, R. Walker, K. Wylie, M. Sekhon, M. C. Becker, M. D. O'Laughlin, M. E. Schaller, G. A. Fewell, K. D. Delehaunty, T. L. Miner, W. E. Nash, M. Cordes, H. Du, H. Sun, J. Edwards, H. Bradshaw-Cordum, J. Ali, S. Andrews, A. Isak, A. Vanbrunt, C. Nguyen, F. Du, B. Lamar, L. Courtney, J. Kalicki, P. Ozersky, L. Bielicki, K. Scott, A. Holmes, R. Harkins, A. Harris, C. M. Strong, S. Hou, C. Tomlinson, S. Dauphin-Kohlberg, A. Kozlowicz-Reilly, S. Leonard, T. Rohlfing, S. M. Rock, A. M. Tin-Wollam, A. Abbott, P. Minx, R. Maupin, C. Strowmatt, P. Latreille, N. Miller, D. Johnson, J. Murray, J. P. Woessner, M. C. Wendl, S. P. Yang, B. R. Schultz, J. W. Wallis, J. Spieth, T. A. Bieri, J. O. Nelson, N. Berkowicz, P. E. Wohldmann, L. L. Cook, M. T. Hickenbotham, J. Eldred, D. Williams, J. A. Bedell, E. R. Mardis, S. W. Clifton, S. L. Chissoe, M. A. Marra, C. Raymond, E. Haugen, W. Gillett, Y. Zhou, R. James, K. Phelps, S. Iadanoto, K. Bubb, E. Simms, R. Levy, J. Clendenning, R. Kaul, W. J. Kent, T. S. Furey, R. A. Baertsch, M. R. Brent, E. Keibler, P. Flicek, P. Bork, M. Suyama, J. A. Bailey, M. E. Portnoy, D. Torrents, A. T. Chinwalla, W. R. Gish, S. R. Eddy, J. D. McPherson, M. V. Olson, E. E. Eichler, E. D. Green, R. H. Waterston, R. K. Wilson.
Nature, 424:157-164, 2003.
[abstract] [reprint]
An Active DNA Transposon Family in Rice .
N. Jiang, Z. Bao, X. Zhang, H. Hirochika, S. R. Eddy, S. R. Eddy, S. R. McCouch.
Nature, 421:163-167, 2003.
[abstract] [reprint]
Finding Noncoding RNA Genes in Genomic Sequences .
Robert J. Klein.
PhD Thesis: Washington University School of Medicine, 2003.
RSEARCH: Finding Homologs of Single Structured RNA Sequences .
R. J. Klein, S. R. Eddy.
BMC Bioinformatics, 4:44, 2003.
[abstract] [reprint] [preprint]
Download software: [RSEARCH]
Computational Identification of Non-Coding RNAs in Saccharomyces cerevisiae by Comparative Genomics .
J. P. McCutcheon, S. R. Eddy.
Nucleic Acids Research, 31:4119-4128, 2003.
[abstract] [reprint] [preprint]
Supplementary material: [Table S1: Candidate list.] [Table S2: Oligo seqs.]
There is a [corrigendum] for this publicationSharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences .
Committee on Responsibilities of Authorship in the Biological Sciences.
National Academies Press, 2003.
[preprint]
Supplementary material: [Executive summary, 9 pp]
2002 TOP Computational Identification and Characterization of Repeats in Sequenced Eukaryotic Genomes .
Zhirong Bao.
PhD Thesis: Washington University School of Medicine, 2002.
Automated de Novo Identification of Repeat Sequence Families in Sequenced Genomes .
Z. Bao, S. R. Eddy.
Genome Research, 12:1269-1276, 2002.
[abstract] [reprint] [preprint]
Supplementary material: [Notes on assessment method]
Download software: [RECON]
The Pfam Protein Families Database .
A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, E. L. Sonnhammer.
Nucleic Acids Research, 30:276-280, 2002.
[abstract] [reprint]
Database access: [Pfam]
Computational Genomics of Noncoding RNA Genes .
S. R. Eddy.
Cell, 109:137-140, 2002.
[abstract] [reprint] [preprint]
A Memory-Efficient Dynamic Programming Algorithm for Optimal Alignment of a Sequence to an RNA Secondary Structure .
S. R. Eddy.
BMC Bioinformatics, 3:18, 2002.
[abstract] [reprint] [preprint]
Download software: [Infernal]
Dasheng: a Recently Amplified Nonautonomous Long Terminal Repeat Element That is a Major Component of Pericentromeric Regions in Rice .
N. Jiang, Z. Bao, S. Temnykh, Z. Cheng, J. Jiang, R. A. Wing, S. R. McCouch, S. R. Wessler.
Genetics, 161:1293-1305, 2002.
[abstract] [reprint]
Noncoding RNA Genes Identified in AT-Rich Hyperthermophiles .
R. J. Klein, Z. Misulovin, S. R. Eddy.
Proc. of the National Academy of Sciences USA, 99:7542-7547, 2002.
[abstract] [reprint] [preprint]
Supplementary material: [Source code tarball]
Archaeal Guide RNAs Function in rRNA Modification in the Eukaryotic Nucleus .
W. A. Speckmann, Z. H. Li, T. M. Lowe, S. R. Eddy, R. M. Terns, M. P. Terns.
Current Biology, 12:199-203, 2002.
[abstract] [reprint]
Initial Sequencing and Comparative Analysis of the Mouse Genome .
Mouse Genome Sequencing Consortium.
Nature, 420:520-562, 2002.
[abstract] [reprint]
Functional Analyses of Proteomes by Phylogenetic Methods .
Christian M. Zmasek.
PhD Thesis: Washington University School of Medicine, 2002.
RIO: Analyzing Proteomes by Automated Phylogenomics Using Resampled Inference of Orthologs .
C. M. Zmasek, S. R. Eddy.
BMC Bioinformatics, 3:14, 2002.
[abstract] [reprint] [preprint]
Download software: [RIO]
2001 TOP The Distributed Annotation System .
R. D. Dowell, R. M. Jokerst, A. Day, S. R. Eddy, L. Stein.
BMC Bioinformatics, 2:7, 2001.
[abstract] [reprint] [preprint]
Supplementary web site: [biodas.org: DAS home page]
A Distributed Annotation System .
Robin Dowell.
Masters Thesis: Washington University, 2001.
Non-Coding RNA Genes and the Modern RNA World .
S. R. Eddy.
Nature Reviews Genetics, 2:919-929, 2001.
[abstract] [reprint] [preprint]
Hints on Using LaTeX to Produce PDF .
S. R. Eddy.
2001.
Supplementary material: [Tarball of LaTeX source]
Changes in Gene Expression Associated With Developmental Arrest and Longevity in Caenorhabditis elegans .
S. J. Jones, D. L. Riddle, A. T. Pouzyrev, V. E. Velculescu, L. Hillier, S. R. Eddy, S. L. Stricklin, D. L. Baillie, R. Waterston, M. A. Marra.
Genome Research, 11:1346-1352, 2001.
[abstract] [reprint]
Initial Sequencing and Analysis of the Human Genome .
International Human Genome Sequencing Consortium.
Nature, 409:860-921, 2001.
[abstract] [reprint]
Computational Identification of Noncoding RNAs in E. coli by Comparative Genomics .
E. Rivas, R. J. Klein, T. A. Jones, S. R. Eddy.
Current Biology, 11:1369-1373, 2001.
[abstract] [reprint] [preprint]
Supplementary material: [Table S1] [Table S2]
Parsable e-data: [Table 1] [Table 2]
Noncoding RNA Gene Detection Using Comparative Sequence Analysis .
E. Rivas, S. R. Eddy.
BMC Bioinformatics, 2:8, 2001.
[abstract] [reprint] [preprint]
Parsable e-data: [Fig 1] [Fig 2] [Fig 3] [Fig 4] [Fig 5] [Fig 6] [Fig 7] [Fig 8]
Download software: [QRNA]
ATV: Display and Manipulation of Annotated Phylogenetic Trees .
C. M. Zmasek, S. R. Eddy.
Bioinformatics, 17:383-384, 2001.
[abstract] [reprint] [preprint]
Download software: [ATV]
A Simple Algorithm to Infer Gene Duplication and Speciation Events on a Gene Tree .
C. M. Zmasek, S. R. Eddy.
Bioinformatics, 17:821-826, 2001.
[abstract] [reprint] [preprint]
Download software: [FORESTER]
2000 TOP The Pfam Protein Families Database .
A. Bateman, E. Birney, R. Durbin, S. R. Eddy, K. L. Howe, E. L. Sonnhammer.
Nucleic Acids Research, 28:263-266, 2000.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Database access: [Pfam]
Homologs of Small Nucleolar RNAs in Archaea .
A. D. Omer, T. M. Lowe, A. G. Russell, H. Ebhardt, S. R. Eddy, P. P. Dennis.
Science, 288:517-522, 2000.
[abstract] [reprint]
Database access: [snoRNA database]
The Language of RNA: A Formal Grammar That Includes Pseudoknots .
E. Rivas, S. R. Eddy.
Bioinformatics, 16:326-333, 2000.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Secondary Structure Alone is Generally Not Statistically Significant for the Detection of Noncoding RNAs .
E. Rivas, S. R. Eddy.
Bioinformatics, 6:583-605, 2000.
[abstract] [reprint] [preprint]
Download software: [NCRNASCAN]
1999 TOP Pfam 3.1: 1313 Multiple Alignments and Profile HMMs Match the Majority of Proteins .
A. Bateman, E. Birney, R. Durbin, S. R. Eddy, R. D. Finn, E. L. Sonnhammer.
Nucleic Acids Research, 27:260-262, 1999.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Database access: [Pfam]
Noncoding RNA genes .
S. R. Eddy.
Current Opinion in Genetics & Development, 9:695-699, 1999.
[abstract] [preprint (PDF)] [preprint (PS)]
Shotgun Coverage of Human Genome Computing .
S. R. Eddy.
Trends in Biochemical Sciences, 24:124, 1999.
[reprint]
Combining New Computational and Traditional Experimental Methods to Identify tRNA and snoRNA Gene Families .
Todd M. J. Lowe.
PhD Thesis: Washington University School of Medicine, 1999.
A Computational Screen for Methylation Guide snoRNAs in Yeast .
T. M. Lowe, S. R. Eddy.
Science, 283:1168-1171, 1999.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Database access: [snoRNA database]
A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots .
E. Rivas, S. R. Eddy.
Journal of Molecular Biology, 285:2053-2068, 1999.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Supplementary material: ["technical report" on irreducible surfaces] [complete set of recursions in the algorithm]
Download software: [PKNOTS]
1998 TOP Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids .
R. Durbin, S. R. Eddy, A. Krogh, G. J. Mitchison.
Cambridge University Press, 1998.
Profile Hidden Markov Models .
S. R. Eddy.
Bioinformatics, 14:755-763, 1998.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Download software: [HMMER]
Multiple-alignment and -sequence searches .
S. R. Eddy.
Trends Guide to Bioinformatics, 15-18, 1998.
[preprint (PDF)] [preprint (PS)]
Pfam: Multiple Sequence Alignments and HMM-Profiles of Protein Domains .
E. L. L. Sonnhammer, S. R. Eddy, E. Birney, A. Bateman, R. Durbin.
Nucleic Acids Research, 26:320-322, 1998.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Database access: [Pfam]
Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology .
The C. elegans Genome Sequencing Consortium.
Science, 282:2012-2018, 1998.
[abstract] [reprint]
1997 TOP A Member of the Immunoglobulin Superfamily in Bacteriophage T4 .
A. Bateman, S. R. Eddy, V. V. Mesyanzhinov.
Virus Genes, 14:163-165, 1997.
[abstract]
Hidden Markov Models and Large-Scale Genome Analysis .
S. R. Eddy.
Transactions of the American Crystallographic Association, 1997.
[preprint (PDF)] [preprint (PS)]
Maximum Likelihood Fitting of Extreme Value Distributions .
S. R. Eddy.
1997.
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence .
T. M. Lowe, S. R. Eddy.
Nucleic Acids Research, 25:955-964, 1997.
[abstract] [reprint] [preprint]
Download software: [tRNAscan-SE]
Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments .
E. L. L. Sonnhammer, S. R. Eddy, R. Durbin.
Proteins, 28:405-420, 1997.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
Database access: [Pfam]
1996 TOP Members of the Immunoglobulin Superfamily in Bacteria.
A. Bateman, S. R. Eddy, C. Chothia.
Protein Science, 5:1939-1941, 1996.
[abstract]
Hidden Markov Models .
S. R. Eddy.
Current Opinion in Structural Biology, 6:361-365, 1996.
[abstract] [preprint (PDF)] [preprint (PS)]
Molecular Genetics in silico: Fourth International Conference on Intelligent Systems in Molecular Biology.
S. R. Eddy.
Trends in Genetics, 12:372, 1996.
Is the Pope the Pope? .
S. R. Eddy, D. J. C. MacKay.
Nature, 382:490, 1996.
[reprint]
1995 TOP Genome Maps VI: Caenorhabditis elegans.
M. Chalfie, S. Eddy, M. O. Hengartner, J. Hodgkin, Y. Kohara, R. H. A. Plasterk, R. H. Waterston, J. G. White.
Science, 270:415, 1995.
Maximum Discrimination Hidden Markov Models of Sequence Consensus .
S. R. Eddy, G. Mitchison, R. Durbin.
Journal of Computational Biology, 2:9-23, 1995.
[abstract] [preprint (PDF)] [preprint (PS)]
Multiple Alignment Using Hidden Markov Models .
In: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology, 114-120.
S. R. Eddy.
AAAI Press, 1995.
[abstract] [preprint (PDF)] [preprint (PS)]
RNA Structure Alignment on a Massively Parallel Computer.
In: Lecture Notes in Computer Science 919: High Performance Computing and Networking, 502-507.
H. Ellingworth, S. R. Eddy.
Springer, 1995.
1994 TOP RNA Sequence Analysis Using Covariance Models .
S. R. Eddy, R. Durbin.
Nucleic Acids Research, 22:2079-2088, 1994.
[abstract] [reprint] [preprint (PDF)] [preprint (PS)]
The Caenorhabditis elegans Genome Project .
In: Advances in Plant Nematology, 3-18.
S. R. Eddy.
Plenum Press, 1994.
[preprint (PDF)] [preprint (PS)]
The Human Genome Project According to Los Alamos.
S. R. Eddy.
Trends in Biochemical Sciences, 20:91-92, 1994.
Effects of Bacterial Growth Conditions and Physiology on T4 Infection.
In: Molecular Biology of Bacteriophage T4, 406-418.
E. Kutter, E. Kellenberger, K. C., S. Eddy, J. Neitzel, L. Messinger, J. North, B. Guttman.
American Society for Microbiology, 1994.
Amino Acid Sequence Motif of Group I Intron Endonucleases is Conserved in Open Reading Frames of Group II Introns.
D. A. Shub, H. Goodrich-Blair, S. R. Eddy.
Trends in Biochemical Sciences, 19:402-404, 1994.
[abstract]
1993 TOP RNA: The Shape of Things to Come.
In: The RNA World, 497-509.
L. Gold, C. Tuerk, P. Allen, J. Binkley, D. Brown, L. Green, S. MacDougal, D. Schneider, D. Tasset, S. R. Eddy.
Cold Spring Harbor Laboratory Press, 1993.
1992 TOP Artificial Mobile DNA Element Constructed from the EcoRI Endonuclease Gene .
S. R. Eddy, L. Gold.
Proc. of the National Academy of Sciences USA, 89:1544-1547, 1992.
[abstract] [reprint]
1991 TOP The Phage T4 nrdB Intron: A Deletion Mutant of a Version Found in the Wild.
S. R. Eddy, L. Gold.
Genes & Development, 5:1032-1041, 1991.
[abstract]
Introns in the T-Even Bacteriophages .
Sean R. Eddy.
PhD Thesis: University of Colorado at Boulder, 1991.
1990 TOP Autogenous Translational Operator Recognized by Bacteriophage T4 DNA Polymerase.
C. Tuerk, S. Eddy, D. Parma, L. Gold.
Journal of Molecular Biology, 213:749-761, 1990.
[abstract]
1985 TOP Nucleotide Sequence of Yellow Fever Virus: Implications for Flavivirus Gene Expression and Evolution.
C. M. Rice, E. M. Lenches, S. R. Eddy, S. J. Shin, R. L. Sheets, J. H. Strauss.
Science, 229:726-733, 1985.
[abstract]
