2014

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes. S. R. Eddy. Annu. Rev. Biophys., 43:433-456, 2014. [abstract] [preprint]

NSF Workshop Report: Discovering General Principles of Nervous System Organization by Comparing Brain Maps Across Species. G.F. Striedter, T. G. Belgard, C. C. Chen, F. P. Davis, B. L. Finlay, O. Gunturkun, M. E. Hale, J. A. Harris, E. E. Hecht, P. R. Hof, H. A. Hofmann, L. Z. Holland, A. N. Iwaniuk, E. D. Jarvis, H. J. Karten, P. S. Katz, W. B. Kristan, E. R. Macagno, P. P. Mitra, L. L. Moroz, T. M. Preuss, C. W. Ragsdale, C. C. Sherwood, C. F. Stevens, M. C. Stuttgen, T. Tsumoto, W. Wilczynski. Brain Behav. Evol., 83:1-8, 2014. [abstract] [reprint]

Skylign: A Tool for Creating Informative, Interactive Logos Representing Sequence Alignments and Profile Hidden Markov Models. T. J. Wheeler, J. Clements, R. D. Finn. BMC Bioinformatics, 15:7, 2014. [abstract] [reprint]
Analysis server: [Skylign]

Pfam: The Protein Families Database. R. D. Finn, A. Bateman, J. Clements, P. Coggill, R. Y. Eberhardt, S. R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, E. L. L. Sonnhammer, J. Tate, M. Punta. Nucleic Acids Research, 42:D222-D230, 2014. [abstract] [reprint]
Database access: [Pfam Cambridge, UK] [US mirror at Janelia]

 2013

Probabilistic Evolutionary Models Compatible With Standard Affine Gap Cost Sequence Alignment. E. Rivas, S. R. Eddy. Manuscript submitted, 2013. [preprint]
Supplementary material: [Full derivations, math (.pdf)]
Supplementary material: [Code and results files (.tar.zip)]

Annotating Functional RNAs in Genomes Using Infernal. E. P. Nawrocki. Manuscript submitted, 2013. [preprint]

Infernal 1.1: 100-fold Faster RNA Homology Searches. E. P. Nawrocki, S. R. Eddy. Bioinformatics, 29:2933-2935, 2013. [abstract] [reprint]
Supplementary material: [rmark3 benchmark datasets]

nhmmer: DNA Homology Search With Profile HMMs. T. J. Wheeler, S. R. Eddy. Bioinformatics, 29:2487-2489, 2013. [abstract] [reprint]
Supplementary material: [19MB, .tar.gz]

Special Focus: Bioinformatics. E. P. Nawrocki, S. W. Burge. RNA Biol., 10:1160, 2013. [abstract] [reprint]

Challenges in Homology Search: HMMER3 and Convergent Evolution of Coiled-Coil Regions. J. Mistry, R. D. Finn, S. R. Eddy, A. Bateman, M. Punta. Nucleic Acids Research, 41:e121, 2013. [abstract] [reprint]

Computational Identification of Functional RNA Homologs in Metagenomic Data. E. P. Nawrocki, S. R. Eddy. RNA Biol., 10:1170-1179, 2013. [abstract] [reprint]

The Four Ingredients of Single-Sequence RNA Secondary Structure Prediction: A Unifying Perspective. E. Rivas. RNA Biol., 10:1185-1196, 2013. [abstract] [reprint]

The ENCODE Project: Mistakes Overshadowing a Success. S. R. Eddy. Curr. Biol., 23:R259-261, 2013. [abstract] [preprint]

Transcription Factors that Convert Adult Cell Identity are Differentially Polycomb Repressed. F. P. Davis, S. R. Eddy. PLOS ONE, 8:e63407, 2013. [reprint]

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome With 16,000 Tiny Chromosomes. E. C. Swart, J. R. Bracht, V. Magrini, P. Minx, X. Chen, Y. Zhou, J. S. Khurana, A. D. Goldman, M. Nowacki, K. Schotanus, S. Jung, R. S. Fulton, A. Ly, S. McGrath, K. Haub, J. L. Wiggins, D. Storton, J. C. Matese, L. Parsons, W. J. Chang, M. S. Bowen, N. A. Stover, T. A. Jones, S. R. Eddy, G. A. Herrick, T. G. Doak, R. K. Wilson, E. R. Mardis, L. F. Landweber. PLoS Biol., 11:10, 2013. [abstract] [reprint]

Rfam 11.0: 10 Years of RNA Families. S. W. Burge, J. Daub, R. Eberhardt, L. Barquist, E. P. Nawrocki, S. R. Eddy, P. P. Gardner, A. Bateman. Nucleic Acids Research, 41:D226-D232, 2013. [abstract] [reprint]

Dfam: A Database of Repetitive DNA Based on Profile Hidden Markov Models. T. J. Wheeler, J. Clements, S. R. Eddy, R. Hubley, T. A. Jones, J. Jurka, A. F. A. Smit, R. D. Finn. Nucleic Acids Research, 41:D70-D82, 2013. [abstract] [reprint]
Supplementary material: [1MB, .tar.gz]
Supplementary web site: [Data and software downloads]
Database access: [Dfam web site]

 2012

The C-value Paradox, junk DNA and ENCODE. S. R. Eddy. Curr. Biol., 22:R898-899, 2012. [abstract] [preprint]

Cell Type-Specific Genomics of Drosophila Neurons. G. L. Henry, F. P. Davis, S. Picard, S. R. Eddy. Nucleic Acids Research, 40:9691-9704, 2012. [abstract] [reprint]

The Pfam Protein Families Database. M. Punta, P. C. Coggill, R. Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm, E. L. Sonnhammer, S. R. Eddy, A. Bateman, R. D. Finn. Nucleic Acids Research, 40:D290-D301, 2012. [abstract] [reprint]

Discovery of Pyrobaculum Small RNA Families With Atypical Pseudouridine Guide RNA Features. D. L. Bernick, P. P. Dennis, M. Hochsmann, T. M. Lowe. RNA, 18:402-411, 2012. [abstract] [reprint]

A Range of Complex Probabilistic Models for RNA Secondary Structure Prediction That Include the Nearest Neighbor Model and More. E. Rivas, R. Lang, S. R. Eddy. RNA, 18:193-212, 2012. [abstract] [reprint]
Supplementary material: [Source code, grammars, datasets: 42MB gzipped tarball]
Download software: [Current Tornado software distribution (.tar.gz)]

 2011

An Improved Greengenes Taxonomy with Explicit Ranks for Ecological and Evolutionary Analyses of Bacteria and Archaea. D. McDonald, M. N. Price, J. Goodrich, E. P. Nawrocki, T. Z. DeSantis, A. Probst, G. L. Andersen, R. Knight, P. Hugenholtz. ISME J., 6:610-618, 2011. [abstract] [reprint]

Complete Nucleomorph Genome Sequence of the Nonphotosynthetic Alga Cryptomonas paramecium Reveals a Core Nucleomorph Gene Set. G. Tanifuji, N. T. Onodera, T. J. Wheeler, M. Dlutek, N. Donaher, J. M. Archibald. Genome Biol. Evol., 3:44-54, 2011. [abstract] [reprint]

Phosphorylation at the Interface. F. P. Davis. Structure, 19:1726-1727, 2011. [abstract] [reprint]

Meeting Report of the RNA Ontology Consortium, January 8-9, 2011. A. Birmingham, J. C. Clemente, N. Desai, J. Gilbert, A. Gonzalez, N. Kyrpides, F. Meyer, E. Nawrocki, P. Sterk, J. Stombaugh, Z. Weinberg, D. Wendel, N. B. Leontis, C. Zirbel, R. Knight, A. Laederach. Stand. Genomic Sci., 4:252-256, 2011. [abstract] [reprint]

Gene Expression Analysis in the Parvalbumin-Immunoreactive PV1 Nucleus of the Mouse Lateral Hypothalamus. F. Girard, Z. Meszar, C. Marti, F. P. Davis, M. Celio. Eur. J. Neurosci., 34:1934-1943, 2011. [abstract] [reprint]

Fast Filtering for RNA Homology Search. D. L. Kolbe, S. R. Eddy. Bioinformatics, 27:3102-3109, 2011. [abstract] [reprint]
Supplementary material: [Software - code branch of Infernal]

RNIE: Genome-Wide Prediction of Bacterial Intrinsic Terminators. P. P. Gardner, L. Barquist, A. Bateman, E. P. Nawrocki, Z. Weinberg. Nucleic Acids Research, 39:5845-5852, 2011. [abstract] [reprint]

Accelerated profile HMM searches. S. R. Eddy. PLoS Comp. Biol., 7:e1002195, 2011. [abstract] [reprint]

HMMER Web Server: Interactive Sequence Similarity Searching. R. D. Finn, J. Clements, S. R. Eddy. Nucleic Acids Research, 39:W29-37, 2011. [abstract] [reprint]

Exploiting Oxytricha trifallax nanochromosomes to screen for noncoding RNA genes. S. Jung, E. C. Swart, P. J. Minx, V. Magrini, E. R. Mardis, L. F. Landweber, S. R. Eddy. Nucleic Acids Research, 39:7529-7547, 2011. [abstract] [reprint]
Supplementary material: [ncRNA gene annotation of Oxytricha: whitespace-delimited table]
Supplementary material: [Multiple alignment of the Arisong RNA family: Stockholm format]
Supplementary material: [Data, sequences, programs, scripts: 85M gzipped tarball]

Rfam: Wikipedia, Clans and the "Decimal" Release. P. P. Gardner, J. Daub, J. Tate, B. L. Moore, I. H. Osuch, S. Griffiths-Jones, R. D. Finn, E. P. Nawrocki, D. L. Kolbe, S. R. Eddy, A. Bateman. Nucleic Acids Research, 39:D141-D145, 2011. [abstract] [reprint]

Proteome-Wide Prediction of Overlapping Small Molecule and Protein Binding Sites Using Structure. F. P. Davis. Mol Biosyst., 7:545-557, 2011. [abstract] [reprint]
Download software: [HOMOLOBIND]

 2010

Novel Algorithms for Structural Alignment of Non-Coding RNAs. D. L. Kolbe. PhD Thesis: Washington University School of Medicine, 2010.
Supplementary material: [Software tarball: infernal-snap20100607.tar.gz]

Hidden Markov Model Speed Heuristic and Iterative HMM Search Procedure. L. S. Johnson, S. R. Eddy, E. Portugaly. BMC Bioinformatics, 11:431, 2010. [abstract] [reprint]
Supplementary material: [Software tarball: hmmer2.5.1.tar.gz]
Supplementary material: [Scripts/data tarball: scripts_alns_dbs.tar.gz]

The Overlap of Small Molecule and Protein Binding Sites Within Families of Protein Structures. F. P. Davis, A. Sali. PLoS Comp. Biol., 6:e1000668, 2010. [abstract] [reprint]
Database access: [PIBASE]

The Pfam Protein Families Database. R. D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J. E. Pollington, O. L. Gavin, G. Ceric, K. Forslund, L. Holm, E. L. L. Sonnhammer, S. R. Eddy, A. Bateman. Nucleic Acids Research, 38:D211-D222, 2010. [abstract] [reprint]
Database access: [Pfam]

Sequence-Based Classification of Select Agents: A Brighter Line. Committee on Scientific Milestones for the Development of a Gene-Sequence-Based Classification System for the Oversight of Select Agents. National Academies Press, 2010. [reprint]

 2009

A New Generation of Homology Search Tools Based on Probabilistic Inference. S. R. Eddy. Genome Inform., 23:205-211, 2009. [abstract] [reprint]

MODBASE, a Database of Annotated Comparative Protein Structure Models and Associated Resources. U. Pieper, N. Eswar, B. M. Webb, D. Eramian, L. Kelly, D. T. Barkan, H. Carter, P. Mankoo, R. Karchin, M. A. Marti-Renom, F. P. Davis, A. Sali. Nucleic Acids Research, 37:D347-D354, 2009. [abstract] [reprint]

Low Exchangeability of Selenocysteine, the 21st Amino Acid, in Vertebrate Proteins. S. Castellano, A. M. Andres, E. Bosch, M. Bayes, R. Guigo, A. G. Clark. MBE, 26:2031-2040, 2009. [abstract] [reprint]

On the Unique Function of Selenocysteine -- Insights From the Evolution of Selenoproteins. S. Castellano. Biochim. Biophys. Acta., 1790:1463-1470, 2009. [abstract] [reprint]

Structural RNA Homology Search and Alignment Using Covariance Models. E. P. Nawrocki. PhD Thesis: Washington University School of Medicine, 2009.
Download software: [Infernal 1.0.1, version for reproduction of results in the thesis (15 Mb gzipped tarball)] [SSU-ALIGN 0.1, the initial version, released several months after the thesis defense (19 Mb gzipped tarball)]

A Tool for Identification of Genes Expressed in Patterns of Interest Using the Allen Brain Atlas. F. P. Davis, S. R. Eddy. Bioinformatics, 25:1647-1654, 2009. [abstract] [reprint]
Download software: [AllenMiner]

Infernal 1.0: Inference of RNA Alignments. E. P. Nawrocki, D. L. Kolbe, S. R. Eddy. Bioinformatics, 25:1335-1337, 2009. [abstract] [reprint]
Supplementary material: [Benchmark (Figure 1)]
Supplementary material: [Timings (Table 1)]

Local RNA Structure Alignment With Incomplete Sequence. D. L. Kolbe, S. R. Eddy. Bioinformatics, 25:1236-1243, 2009. [abstract] [reprint]
Supplementary material: [Data and scripts (tarball, gzipped)]

Prepublication Data Sharing. Toronto International Data Release Workshop Authors. Nature, 461:168-170, 2009. [abstract] [reprint]

Open Revolution. S. R. Eddy. PLoS Biology, 7:e1000078, 2009. [reprint]

Rfam: Updates to the RNA Families Database. P. P. Gardner, J. Daub, J. G. Tate, E. P. Nawrocki, D. L. Kolbe, S. Lindgreen, A. C. Wilkinson, R. D. Finn, S. Griffiths-Jones, S. R. Eddy, A. Bateman. Nucleic Acids Research, 37:D136-D140, 2009. [abstract] [reprint]

A Survey of Nematode SmY RNAs. T. A. Jones, W. Otto, M. Marz, S. R. Eddy, P. F. Stadler. RNA Biol., 6:5-8, 2009. [abstract] [reprint]
Supplementary material: [Seed alignment]
Supplementary material: [SmY RNAs, table]
Supplementary material: [SmY RNAs, FASTA]
Supplementary web site: [Wikipedia page]

 2008

SelenoDB 1.0 : a Database of Selenoprotein Genes, Proteins and SECIS Elements. S. Castellano, V. N. Gladyshev, R. Guigo, M. J. Berry. Nucleic Acids Research, 36:D332-D338, 2008. [abstract] [reprint]

A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation. S. R. Eddy. PLoS Comput. Biol., 4:e1000069, 2008. [abstract] [reprint]
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]
Database access: [Pfam]

Probabilistic Phylogenetic Inference with Insertions and Deletions. E. Rivas, S. R. Eddy. PLoS Comput. Biol., 4:e1000172, 2008. [abstract] [reprint]
Supplementary material: [C and Perl source code; alignment data (.tar.gz)]

 2007

Host Pathogen Protein Interactions Predicted by Comparative Modeling. F. P. Davis, D. T. Barkan, N. Eswar, J. H. McKerrow, A. Sali. Protein Sci., 16:2585-2596, 2007. [abstract] [reprint]

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. Jimenez-Zurdo. Mol. Microbiol., 66:1080-1091, 2007. [abstract] [reprint]

Query-Dependent Banding (QDB) for Faster RNA Similarity Searches. E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007. [abstract] [reprint]

 2006

Efficient Pairwise RNA Structure Prediction and Alignment Using Sequence Alignment Constraints. R. D. Dowell, S. R. Eddy. BMC Bioinformatics, 7:400, 2006. [abstract] [reprint]
Download software: [CONSAN]

Total Information Awareness for Worm Genetics. S. R. Eddy. Science, 311:381-382, 2006. [abstract] [reprint]

Computational Analysis of RNAs. S. R. Eddy. Cold Spring Harbor Symp. Quant. Biol., 71:117-128, 2006. [reprint]

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

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]
Supplementary material: [C source code (.tgz)]
There is a [correction] for this publication

Antedisciplinary Science. S. R. Eddy. PLoS Comput. Biol., 1:e6, 2005. [abstract] [reprint]

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]

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]
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]
Supplementary web site: [Table 1: ncRNA annotations]

 2004

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]
Supplementary web site: [Supporting material]
Download software: [CONUS]

What is Dynamic Programming?. S. R. Eddy. Nature Biotechnology, 22:909-910, 2004. [abstract] [reprint]
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]
Supplementary material: [Example C program: lambda.c]

What is Bayesian Statistics?. S. R. Eddy. Nature Biotechnology, 22:1177-1178, 2004. [abstract] [reprint]
Supplementary material: [Example C program: pascal-game-portable.c]

What is a Hidden Markov Model?. S. R. Eddy. Nature Biotechnology, 22:1315-1316, 2004. [abstract] [reprint]

How Do RNA Folding Algorithms Work?. S.R. Eddy. Nature Biotechnology, 22:1457-1458, 2004. [abstract] [reprint]

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

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]
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]
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]
Supplementary material: [Table S1: Candidate list.]
Supplementary material: [Table S2: Oligo seqs.]
There is a [corrigendum] for this publication

Sharing 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. [reprint]
Supplementary material: [Executive summary, 9 pp]

 2002

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]
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]

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]
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]
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]
Download software: [RIO]

 2001

The Distributed Annotation System. R. D. Dowell, R. M. Jokerst, A. Day, S. R. Eddy, L. Stein. BMC Bioinformatics, 2:7, 2001. [abstract] [reprint]
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]

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]
Supplementary material: [Table S1]
Supplementary material: [Table S2]
Parsable e-data: [Table 1] [Table 2] [275 candidates, in simple tabular data format] [275 candidates, remapped to NC_000913.2 coli coordinates]

Noncoding RNA Gene Detection Using Comparative Sequence Analysis. E. Rivas, S. R. Eddy. BMC Bioinformatics, 2:8, 2001. [abstract] [reprint]
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]
Download software: [Archaeopteryx (formerly 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]
Download software: [FORESTER]

 2000

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]
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]

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]
Download software: [NCRNASCAN]

 1999

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]
Database access: [Pfam]

Noncoding RNA genes. S. R. Eddy. Current Opinion in Genetics & Development, 9:695-699, 1999. [abstract] [reprint]

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]
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]
Supplementary material: ["technical report" on irreducible surfaces]
Supplementary material: [complete set of recursions in the algorithm]
Download software: [PKNOTS]

 1998

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]
Download software: [HMMER]

Multiple-alignment and -sequence searches. S. R. Eddy. Trends Guide to Bioinformatics, 15-18, 1998. [preprint]

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]
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

A Member of the Immunoglobulin Superfamily in Bacteriophage T4. A. Bateman, S. R. Eddy, V. V. Mesyanzhinov. Virus Genes, 14:163-165, 1997. [abstract] [reprint]

Hidden Markov Models and Large-Scale Genome Analysis. S. R. Eddy. Transactions of the American Crystallographic Association, 1997. [preprint]

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]
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]
Database access: [Pfam]

 1996

Members of the Immunoglobulin Superfamily in Bacteria. A. Bateman, S. R. Eddy, C. Chothia. Protein Science, 5:1939-1941, 1996. [abstract] [reprint]

Hidden Markov Models. S. R. Eddy. Current Opinion in Structural Biology, 6:361-365, 1996. [abstract] [reprint]

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

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. [abstract] [reprint]

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]

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] [reprint]

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

RNA Sequence Analysis Using Covariance Models. S. R. Eddy, R. Durbin. Nucleic Acids Research, 22:2079-2088, 1994. [abstract] [reprint]

The Caenorhabditis elegans Genome Project. In: Advances in Plant Nematology, 3-18. S. R. Eddy. Plenum Press, 1994. [preprint]

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

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

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

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] [reprint]

Introns in the T-Even Bacteriophages. Sean R. Eddy. PhD Thesis: University of Colorado at Boulder, 1991.

 1990

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

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] [reprint]