lab.bib

% Lab publication database.
%
% note the "reprinturl" record. This is the link to the
% online publication. Can't use "url" as the keyword -
% some .bst styles will pick that up and try to use it
% in their reference (bmc_article.bst, for example).
%
% Emacs shortcuts:
%   C-C C-e C-a  for Article                  
%   C-c C-e C-u  for Unpublished, including preprints                 
%   C-c C-e P    for PhD thesis
                  

                  

@Unpublished{CevrimMcKinley25,
  author =       {\c{C}. \c{C}evrim and N. J. Hilgert and A. M. Kaage
                  and A. J. C. Russell and A. E. Goldstein and
                  C. J. Ang and J. L. R. Gable and L. E. Bagamery and
                  A. Breznik and D. J. {Di Bella} and M. Talay and
                  J. Peng and K. E. O'Neill and F.  Chen and
                  S. R. Eddy and K. L. McKinley},
  title =        {Induction of Menstruation in Mice Reveals the Regulation of Menstrual Shedding},
  note =         {Manuscript submitted},
  year =      2025,
  reprinturl = {https://www.biorxiv.org/content/10.1101/2025.10.08.681007v1}
}

@Article{Merk25,
  author =    {L. N. Merk and T. A. Jones and S. R. Eddy},
  title =     {Presence of Group {II} Introns in Phage Genomes},
  journal =   NAR,
  year =      2025,
  volume =    53,
  pages =     {gkaf761},
  pmid =      40808305,
  pmcid =     {PMC12350094},
  reprinturl = {https://doi.org/10.1093/nar/gkaf761}
}

@Article{ChenHoekstra25,
  author =       {J. Chen and P. R. Richardson and C. Kirby and S. R. Eddy and H. E. Hoekstra},
  title =        {Cellular Evolution of the Hypothalmic Preoptic Area of Behaviorally Divergent Deer Mice},
  journal =      {eLife},
  year =         2025,
  volume =    13,
  pages =     {RP103019},
  pmid =      40191998,
  pmcid =      {PMC11975375},
  reprinturl = {https://doi.org/10.7554/eLife.103109.3}
}

@Unpublished{Sarkar24,
  author = 	 {A. Sarkar and K. Krishnan and S. R. Eddy},
  title = 	 {Protein Sequence Domain Annotation using Language Models},
  note = 	 {bioRxiv preprint},
  year = 	 2024,
  reprinturl = {https://doi.org/10.1101/2024.06.04.596712},
}

@Article{Eddy24,
  author     = {S. R. Eddy},
  title      = {Mammalian Cells Repress Random {DNA} That Yeast Transcribes},
  journal    = {Nature},
  year       = 2024,
  volume     = 628,
  pages      = {271--273},
  pmid       = 38448526,
  reprinturl = {https://doi.org/10.1038/d41586-024-00575-x},
}

@PhdThesis{Richardson23,
  author = 	 {M. O. Richardson},
  title = 	 {Computational Prediction of Alternative Translation Events},
  school = 	 {Harvard University},
  year = 	 2023,
}

@Article{RichardsonEddy23,
  author = 	 {M. O. Richardson and S. R. Eddy},
  title = 	 {{ORFeus:} A Computational Method to Detect Programmed
                  Ribosomal Frameshifts and Other Non-Canonical
                  Translation Events},
  journal = 	 {BMC Bioinformatics},
  year = 	 2023,
  volume = 	 24,
  pages = 	 471,
  pmid = 	 38093195,
  pmcid =        {PMC10720069},
  reprinturl = {https://doi.org/10.1186/s12859-023-05602-8},
}

@Article{Petti23,
  author = 	 {S. Petti and N. Bhattacharya and R. Rao and J. Dauparas and N. Thomas and J. Zhou and A. M. Rush and P. K. Koo and S. Ovchinnikov},
  title = 	 {End-to-End Learning of Multiple Sequence Alignments with Differentiable {S}mith-{W}aterman},
  journal = 	 {Bioinformatics},
  year = 	 2023,
  volume = 	 39,
  pages = 	 {btac724},
  pmid = 	 36355460,
  pmcid = 	 {PMC9805565},
}
                  
@Article{PettiDesai23,
  author = 	 {S. Petti and G. Reddy and M. M. Desai},
  title = 	 {Inferring Sparse Structure in Genotype-Phenotype Maps},
  journal = 	 {Genetics},
  year = 	 2023,
  volume = 	 225,
  pages = 	 {iyad127},
  pmid = 	 37437111,
  pmcid = 	 {PMC10471201},
  reprinturl = {https://doi.org/10.1093/genetics/iyad127},
}

@Article{Shulgina23,
  author = 	 {Y. Shulgina and S. R. Eddy},
  title = 	 {Codetta: Predicting the Genetic Code from Nucleotide Sequence},
  journal = 	 {Bioinformatics},
  year = 	 2023,
  volume = 	 39,
  pages = 	 {btac802},
  pmid = 	 36511586,
  pmcid = 	 {PMC9825746},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btac802},
}

@PhdThesis{Shulgina22,
  author = 	 {Y. Shulgina},
  title = 	 {The Evolution of Alternative Genetic Codes},
  school = 	 {Harvard University},
  year = 	 2022,
}

@Article{Weisman22,
  author = 	 {C. M. Weisman and A. W. Murray and S. R. Eddy},
  title = 	 {Mixing Genome Annotation Methods in a Comparative Analysis Inflates the Apparent Number of Lineage-Specific Genes},
  journal = 	 {Curr. Biol.},
  year = 	 2022,
  volume = 	 32,
  pages = 	 {2632-2639},
  pmid =         35588743,                   
  pmcid =        {PMC9346927},                  
  reprinturl =   {https://doi.org/10.1016/j.cub.2022.04.085},
}

@Article{Petti22,
  author = 	 {S. N. Petti and S. R. Eddy},
  title = 	 {Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms},
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2022,
  volume = 	 18,
  pages = 	 {e1009492},
  pmid = 	 35255082,
  pmcid = 	 {PMC8929697},
  reprinturl = {https://doi.org/10.1371/journal.pcbi.1009492},
}

@Article{GaoRivas21,
  author = 	 {W. Gao and T. A. Jones and E. Rivas},
  title = 	 {Discovery of 17 Conserved Structural {RNAs} in Fungi},
  journal = 	 NAR,
  year = 	 2021,
  volume = 	 49,
  pages = 	 {6128--6143},
  pmid = 	 34086938,
  pmcid = 	 {PMC8216456},
  reprinturl = {https://doi.org/10.1093/nar/gkab355},
}

@Article{Shulgina21,
  author = 	 {Y. Shulgina and S. R. Eddy},
  title = 	 {A Computational Screen for Alternative Genetic Codes in Over 250,000 Genomes},
  journal = 	 {eLife},
  year = 	 2021,
  volume = 	 10,
  pages = 	 {e71402},
  pmid = 	 34751130,
  pmcid = 	 {PMC8629427},
  reprinturl =   {https://doi.org/10.7554/eLife.71402},
}

@PhdThesis{Weisman21,
  author = 	 {C. M. Weisman},
  title = 	 {Novelty or Nuisance? Where Lineage-Specific Genes Come From and Why It Matters},
  school = 	 {Harvard University},
  year = 	 2021,
}

@PhdThesis{Wilburn21,
  author = 	 {G. W. Wilburn},
  title = 	 {An Inverse Statistical Physics Method for Biological Sequence Analysis},
  school = 	 {Harvard University},
  year = 	 2021,
}

@Article{KalvariPetrov21,
  author  = {I. Kalvari and E. P. Nawrocki and N. Ontiveros-Palacios
                  and J. Argasinska and K. Lamkiewicz and M. Marz and
                  S. Griffiths-Jones and C. Toffano-Nioche and
                  D. Gautheret and Z. Weinberg and E. Rivas and
                  S. R. Eddy and R. D. Finn and A. Bateman and
                  A. I. Petrov}, 
  title   = {Rfam 14: Expanded Coverage of Metagenomic, Viral and {microRNA} Families},
  journal = NAR,
  year    = 2021,
  volume  = 49,                  
  pages   = {D192-D200},
  pmid    = 33211869,
  reprinturl = {https://doi.org/10.1093/nar/gkaa1047},
}
                  
@Unpublished{Kaxiras21,
  author = 	 {D. A. Kaxiras},
  title = 	 {Modeling Non-Homologous Protein Sequences Using a Variation on Traditional {kth} Order {M}arkov Models},
  note = 	 {Undergraduate senior thesis, Harvard College},
  year = 	 2021,
}

@Unpublished{Walker21,
  author = 	 {J. C. Walker},
  title = 	 {Restricted {B}oltzmann Machines and Sequence Homology Search},
  note = 	 {Undergraduate senior thesis, Harvard College},
  year = 	 2021,
}

@Article{Wilburn20,
  author = 	 {G. W. Wilburn and S. R. Eddy},
  title = 	 {Remote Homology Search with Hidden {P}otts Models},
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2020,
  volume = 	 16,
  pages = 	 {e1008085},
  pmid = 	 33253143,
  pmcid = 	 {PMC7728182},
  reprinturl = {https://doi.org/10.1371/journal.pcbi.1008085},
}

@Article{Weisman20,
  author = 	 {C. M. Weisman and A. W. Murray and S. R. Eddy},
  title = 	 {Many, but Not All, Lineage-Specific Genes Can Be Explained by Homology Detection Failure},
  journal = 	 {PLOS Biol.},
  year = 	 2020,
  volume = 	 18,
  pages = 	 {e3000862},
  pmid = 	 33137085,
  pmcid = 	 {PMC7660931},
  reprinturl = {https://doi.org/10.1371/journal.pbio.3000862}
}

@Article{RivasEddy20,
  author  = {E. Rivas and J. Clements and S. R. Eddy},
  title   = {Estimating the power of sequence covariation for detecting conserved {RNA} structure},
  journal = {Bioinformatics},
  year = 	 2020,
  volume = 	 36,
  pages = 	 {3072--3076},
  pmid = 	 32031582,
  pmcid = 	 {PMC7214042},
  reprinturl = {https://doi.org/10.1093/bioinformatics/btaa080},
}

@Article{DavisHenry20,
  author = 	 {F. P. Davis and A. Nern and S. Picard and
                  M. B. Reiser and G. M. Rubin and S. R. Eddy and
                  G. L. Henry},
  title = 	 {A Genetic, Genomic, and Computational Resource for
                  Exploring Neural Circuit Function},
  journal = 	 {eLife},
  year = 	 2020,
  volume = 	 9,
  pages = 	 {e50901},
  pmid = 	 31939737,
  pmcid =        {PMC7034979},                  
  reprinturl = {https://doi.org/10.7554/eLife.50901},
}

@Unpublished{KooEddy18b,
  author = 	 {P. Koo and P. Anand and S. Paul and S. R. Eddy},
  title = 	 {Inferring Sequence-Structure Preferences of {RNA}-Binding Proteins with Convolutional Neural Networks},
  note = 	 {bioRxiv preprint},
  year = 	 2018,
  reprinturl = {https://doi.org/10.1101/418459},
}

@Article{Saini19,
  author = 	 {H. Saini and A. A. Bicknell and S. R. Eddy and M. J. Moore},
  title = 	 {Free Circular Introns with an Unusual Branchpoint in Neuronal Projections},
  journal = 	 {eLife},
  year = 	 2019,
  volume = 	 8,
  pages = 	 {e47809},
  pmid = 	 31697236,
  pmcid =        {PMC6879206},
  reprinturl = {https://doi.org/10.7554/eLife.47809},
}

@Article{KooEddy19,
  author = 	 {P. Koo and S. R. Eddy},
  title = 	 {Representation Learning of Genomic Sequence Motifs
                  with Convolutional Neural Networks},               
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2019,
  volume = 	 15,
  pages = 	 {e1007560},
  pmid = 	 31856220,
  pmcid =        {PMC6941814},                    
  reprinturl = {https://doi.org/10.1371/journal.pcbi.1007560},
}

@PhdThesis{Saini19b,
  author = 	 {H. Saini},
  title = 	 {Intron and Small {RNA} Localization in Mammalian Neurons},
  school = 	 {University of Massachusetts, Worcester},
  year = 	 2019,
  reprinturl =   {https://doi.org/10.13028/srmk-pk14},                  
}

@Article{ElGebali19,
  author = 	 {S. El-Gebali and J. Mistry and A. Bateman and
                  S. R. Eddy and A. Luciani and S. C. Potter and
                  M. Qureshi and L. J. Richardson and G. A. Salazar
                  and A. Smart and E. L. L. Sonnhammer and L. Hirsh
                  and L. Paladin and D. Piovesan and S. C. E. Tosatto
                  and R. D. Finn},
  title = 	 {The {P}fam Protein Families Database in 2019},
  journal =      NAR,
  year =         2019,
  volume =       47,
  pages =        {D427--D432},
  pmid =         30357350,                  
  pmcid =        {PMC6324024},                   
  reprinturl =   {https://doi.org/10.1093/nar/gky995},                  
}


@Unpublished{RivasEddy18,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {Response to {T}avares et al., "{C}ovariation Analysis with Improved Parameters Reveals Conservation in {lncRNA} Structures"},
  note = 	 {bioRxiv preprint},
  year = 	 2018,
  reprinturl = {https://doi.org/10.1101/2020.02.18.955047},
}

@Article{Nawrocki18,
  author = 	 {E. P. Nawrocki and T. A. Jones and S. R. Eddy},
  title = 	 {Group {I} Introns Are Widespread in Archaea},
  journal = 	 NAR,
  year = 	 2018,
  volume = 	 46,
  pages = 	 {7970--7976},
  pmcid = 	 {PMC6125680},
  pmid =         29788499,                   
  reprinturl =   {https://doi.org/10.1093/nar/gky414}                  
}

@Article{Potter18,
  author = 	 {S. C. Potter and A. Luciani and S. R. Eddy and
                  Y. Park and R. Lopez and R. D. Finn},
  title = 	 {{HMMER} Web Server: 2018 Update},
  journal =      NAR,                  
  year = 	 2018,
  volume =       46,                  
  pages =        {W200--W204},                  
  pmid = 	 29905871,
  pmcid =        {PMC6030962},
  reprinturl =   {https://doi.org/10.1093/nar/gky448},
}

@Article{KalvariPetrov18,
  author =       {I. Kalvari and J. Argasinska and N. Quinones-Olvera
                  and E. P. Nawrocki and E. Rivas and S. R. Eddy and
                  A. Bateman and R. D. Finn and A. I. Petrov},
  title =        {Rfam 13.0: Shifting to a Genome-Centric Resource for
                  Non-Coding {RNA} Families},
  journal = 	 NAR,
  year = 	 2018,
  volume = 	 46,
  pages = 	 {D335--D342},
  pmid = 	 29112718,
  pmcid = 	 {PMC5753348},
  reprinturl =   {https://doi.org/10.1093/nar/gkx1038},
}

@Article{KuoSilver18,
  author =       {J. Kuo and F. Stirling and Y. H. Lau and Y. Shulgina
                  and J. C. Way and P. A. Silver},
  title =        {Synthetic Genome Recoding: New Genetic Codes for New Features},
  journal = 	 {Curr. Genet.},
  year = 	 2018,
  volume = 	 64,
  pages = 	 {327--333},
  pmid = 	 28983660,
  pmcid = 	 {PMC5849531},
  reprinturl =  {https://doi.org/10.1007/s00294-017-0754-z},                  
}

@Article{WeismanEddy17,
  author =       {C. M. Weisman and S. R. Eddy},
  title =        {Gene Evolution: Getting Something for Nothing},
  journal =      {Curr. Biol.},
  volume =       27,
  pages =        {R661-R663},
  pmid =         28697368,
  reprinturl =   {https://doi.org/10.1016/j.cub.2017.05.056},
  year =         2017,
}

@Unpublished{DunnKoo17,
  author =       {T. W. Dunn and P. K. Koo},
  title =        {Inferring Functional Neural Connectivity with Deep Residual Convolutional Networks},
  note =         {bioRxiv},
  year =         2017,
  reprinturl = {https://doi.org/10.1101/141010},
}

@Article{ZhangSpector17,
  author =       {B. Zhang and Y. S. Mao and S. D. Diermeier and
                  I. V. Novikova and E. P. Nawrocki and T. A. Jones
                  and Z. Lazar and C.-S. Tung and W. Luo and
                  S. R. Eddy and K. Y. Sanbonmatsu and D. L. Spector}, 
  title =        {Identification and Characterization of a Class of
                  {MALAT1}-like Genomic Loci},
  journal =      {Cell Reports},
  year =         2017,
  volume =    19,
  pages =     {1723--1738},
  pmid =      28538188,
  reprinturl = {https://doi.org/10.1016/j.celrep.2017.05.006},
}

@Article{RivasEddy17,
  author = 	 {E. Rivas and J. Clements and S. R. Eddy},
  title = 	 {A Statistical Test for Conserved {RNA} Structure Shows Lack of Evidence for Structure
                  in {lncRNAs}},
  journal =      {Nature Methods},
  year =         2017,
  volume =    14,
  pages =     {45--48},
  pmid =      27819659,
  pmcid =     {PMC5554622},                  
  reprinturl = {https://doi.org/10.1038/nmeth.4066},
  URL = {http://eddylab.org/R-scape/},
}

@Article{MoNathans16,
  author = 	 {A. Mo and C. Luo and F. P. Davis and E. A. Mukamel
                   and G. L. Henry and J. R. Nery and M. A. Urich and
                   S. Picard and R. Lister and S. R. Eddy and
                   M. A. Beer and J. R. Ecker and J. Nathans},
  title = 	 {Epigenomic Landscapes of Retinal Rods and Cones},
  journal = 	 {eLife},
  year = 	 2016,
  volume = 	 5,
  pages = 	 {e11613},
  pmid = 	 26949250,
  pmcid =        {PMC4798964},                   
  reprinturl =   {https://doi.org/10.7554/eLife.11613},
}

@Article{HubleyWheeler16,
   author = 	 {R. Hubley and R. D. Finn and
                   J. Clements and S. R. Eddy and T. A. Jones and
                   W. Bao and A. F. A. Smit and T. J. Wheeler},
   title = 	 {The {D}fam Database of Repetitive {DNA} Families},
   journal = 	 NAR,
   year = 	 2016,
   volume = 	 44,
   pages = 	 {D81--D89},
   pmid = 	 26612867,
   pmcid =       {PMC4702899},
   reprinturl =  {https://doi.org/10.1093/nar/gkv1272},
}

@Article{FinnBateman16,
  author = 	 {R. D. Finn and P. Coggill and
                  R. Y. Eberhardt and S. R. Eddy and J. Mistry and
                  A. L. Mitchell and S. C. Potter and M. Punta and
                  M. Qureshi and A. Sangrador-Vegas and G. A. Salazar
                  and J. Tate and A. Bateman},
  title = 	 {The {P}fam Protein Families Database: Toward a More Sustainable Future},
  journal =      NAR,
  year =         2016,
  volume =       44,
  pages =        {D279--D285},
  pmid =         26673716,              
  pmcid =        {PMC4702930},
  reprinturl =   {https://doi.org/10.1093/nar/gkv1344},
}

@Article{RivasEddy15,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {Parameterizing Sequence Alignment with an Explicit Evolutionary Model},
  journal =      {BMC Bioinformatics},                  
  year = 	 2015,
  volume = 	 16,
  pages = 	 406,
  pmid = 	 26652060,
  pmcid = 	 {PMC4676179},
  reprinturl =   {https://doi.org/10.1186/s12859-015-0832-5},
}


@Article{ChenLandweber15,
  author = 	 {X. Chen and S. Jung and L. Y. Beh and S. R. Eddy and L. F. Landweber},
  title = 	 {Combinatorial {DNA} Rearrangement Facilitates the
                  Origin of New Genes in Ciliates},
  journal = 	 {Genome Biol. Evol.},
  year = 	 2015,
  volume = 	 7,
  pages = 	 {2859--2870},
  pmid = 	 26338187,
  pmcid =        {PMC4684698},                  
  reprinturl =   {https://doi.org/10.1093/gbe/evv172},
}


@Article{MoNathans15,
  author = 	 {A. Mo and E. A. Mukamel and F. P. Davis and C. Luo
                  and G. L. Henry and S. Picard and M. A. Urich and
                  J. R. Nery and T. J. Sejnowski and R. Lister and
                  S. R. Eddy and J. R. Ecker and J. Nathans},
  title = 	 {Epigenomic Signatures of Neuronal Diversity in the
                  Mammalian Brain},
  journal = 	 {Neuron},
  year = 	 2015,
  volume = 	 86,
  pages = 	 {1369--1384},
  pmid = 	 26087164,
  pmcid =        {PMC4499463},
  reprinturl =   {https://doi.org/10.1016/j.neuron.2015.05.018},
}

@Article{Finn15,
  author = 	 {R. D. Finn and J. Clements and W. Arndt and
                  B. L. Miller and T. J. Wheeler and F. Schreiber and
                  A. Bateman and S. R. Eddy},
  title = 	 {{HMMER} Web Server: 2015 Update},
  journal = 	 NAR,
  year = 	 2015,
  volume = 	 43,
  pages = 	 {W30--W38},
  pmid = 	 25943547,
  pmcid =        {PMC4489315},
  reprinturl =   {https://doi.org/10.1093/nar/gkv397},
}

@Article{Eddy15,
  author = 	 {S. R. Eddy},
  title = 	 {Homology Searches for Structural {RNAs}: From Proof of Principle to Practical Use},
  journal = 	 {RNA},
  year = 	 2015,
  volume = 	 21,
  pages = 	 {605--607},
  pmid = 	 25780158,
  pmcid =        {PMC4371300},
  reprinturl =   {https://doi.org/10.1261/rna.050484.115},
}

@Article{Nawrocki15,
  author = 	 {E. P. Nawrocki and S. W. Burge and A. Bateman and
                  J. Daub and R. Y. Eberhardt and S. R. Eddy and
                  E. W. Floden and P. P. Gardner and T. A. Jones and
                  J. Tate and R. D. Finn},
  title = 	 {Rfam 12.0: updates to the {RNA} Families Database},
  journal = 	 NAR,
  year = 	 2015,
  volume = 	 43,
  pages = 	 {D130-D137},
  pmid = 	 25392425,
  pmcid =        {PMC4371300},
  reprinturl =   {https://doi.org/10.1093/nar/gku1063},
}

                  
@Article{ViswanathanLooger15,
  author =       {S. Viswanathan and M. E. Williams and E. B. Bloss
                  and T. J. Stasevich and C. M. Speer and A. Nern and
                  B. D. Pfeiffer and B. M. Hooks and W. P. Li and
                  B. P. English and T. Tian and G. L. Henry and
                  J. J. Macklin and R. Patel and C. R. Gerfen and
                  X. Zhuang and Y. Wang and G. M. Rubin and
                  L. L. Looger}, 
  title =        {High-Performance Probes for Light and Electron
                  Microscopy},
  journal =      {Nat. Methods},
  year =         2015,
  volume =       12,
  pages =        {568--576},
  pmid =         25915120,
  reprinturl =   {https://doi.org/10.1038/nmeth.3365},
}

@Article{Dennis15,
  author =       {P. P. Dennis and V. Tripp and L. Lui and T. Lowe and L. Randau},
  title =        {{C/D} box {sRNA}-Guided 2'-{O}-Methylation Patterns of Archaeal {rRNA} Molecules},
  journal =      {BMC Genomics},
  year =         2015,
  volume =       16,
  pages =        632,
  pmid =         26296872,
  reprinturl =   {https://doi.org/10.1186/s12864-015-1839-z},
}

@Article{Eddy14,
  author = 	 {S. R. Eddy},
  title = 	 {Computational Analysis of Conserved {RNA} Secondary Structure in Transcriptomes and Genomes},
  journal = 	 {Annu. Rev. Biophys.},
  year = 	 2014,
  volume = 	 43,
  pages = 	 {433--456},
  pmid = 	 24895857,
  pmcid =        {PMC5541781},                   
  reprinturl =   {https://doi.org/10.1146/annurev-biophys-051013-022950},
}

@Article{Striedter14,
 author =       {G.F. Striedter and T. G. Belgard and C. C. Chen and F. P. Davis and
                  B. L. Finlay and O. G{\"u}nt{\"u}rk{\"u}n and M. E. Hale and
                  J. A. Harris and E. E. Hecht and P. R. Hof and
                  H. A. Hofmann and L. Z. Holland and A. N. Iwaniuk
                  and E. D. Jarvis and H. J. Karten and P. S. Katz and
                  W. B. Kristan and E. R. Macagno and P. P. Mitra and
                  L. L. Moroz and T. M. Preuss and C. W. Ragsdale and
                  C. C. Sherwood and C. F. Stevens and M. C. St{\"u}ttgen
                  and T. Tsumoto and W. Wilczynski}, 
  title =        {{NSF} Workshop Report: Discovering General
                  Principles of Nervous System Organization by
                  Comparing Brain Maps Across Species}, 
  journal =      {Brain Behav. Evol.},
  volume =       83,
  pages =        {1--8},                    
  year =         2014,
  pmid =         24596113,
  reprinturl =   {https://doi.org/10.1159/000360152},
}

                  
@Article{Nawrocki14,
  author = 	 {E. P. Nawrocki},
  title = 	 {Annotating Functional {RNA}s in Genomes Using {I}nfernal},
  journal =      {Methods Mol. Biol.},
  year =         2014,
  volume =       1097,
  pages =        {163--197},
  pmid =         24639160,
  reprinturl =   {https://doi.org/10.1007/978-1-62703-709-9_9},
}

@Article{Wheeler14,
  author = 	 {T. J. Wheeler and J. Clements and R. D. Finn},
  title = 	 {Skylign: A Tool for Creating Informative,
                  Interactive Logos Representing Sequence Alignments
                  and Profile Hidden {M}arkov Models},
  journal = 	 {BMC Bioinformatics},
  year = 	 2014,
  volume = 	 15,
  pages = 	 7,
  pmid = 	 24410852,
  pmcid =        {PMC3893531},
  reprinturl =   {https://doi.org/10.1186/1471-2105-15-7},
}

@Article{Finn14,
  author = 	 {R. D. Finn and A. Bateman and J. Clements and
                  P. Coggill and R. Y. Eberhardt and S. R. Eddy and
                  A. Heger and K. Hetherington and L. Holm and
                  J. Mistry and E. L. L. Sonnhammer and J. Tate and
                  M. Punta},
  title = 	 {Pfam: The Protein Families Database},
  journal = 	 NAR,
  year = 	 2014,
  volume = 	 42,
  pages = 	 {D222-D230},
  pmid = 	 24288371,
  pmcid =        {PMC3965110},
  reprinturl =   {https://doi.org/10.1093/nar/gkt1223},
}

@Article{Nawrocki13c,
  author = 	 {E. P. Nawrocki and S. R. Eddy},
  title = 	 {Infernal 1.1: 100-fold Faster {RNA} Homology Searches},
  journal = 	 {Bioinformatics},
  year = 	 2013,
  volume = 	 29,
  pages = 	 {2933-2935},
  pmid =         24008419,
  pmcid =        {PMC3810854},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btt509},
}

@Article{Wheeler13b,
  author = 	 {T. J. Wheeler and S. R. Eddy},
  title = 	 {{nhmmer}: {DNA} Homology Search With Profile {HMMs}},
  journal = 	 {Bioinformatics},
  year = 	 2013,
  volume =       29,
  pages =        {2487-2489},
  pmid =         23842809,
  pmcid =        {PMC3777106},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btt403},
}

@Article{Nawrocki13d,
  author = 	 {E. P. Nawrocki and S. W. Burge},
  title = 	 {Special Focus: Bioinformatics},
  journal = 	 {RNA Biol.},
  year = 	 2013,
  volume = 	 10,
  pages = 	 1160,
  pmid = 	 23948768,
  reprinturl =   {https://doi.org/10.4161/rna.25606},
}

@Article{Mistry13,
  author = 	 {J. Mistry and R. D. Finn and S. R. Eddy and
                  A. Bateman and M. Punta},
  title = 	 {Challenges in Homology Search: {HMMER3} and
                  Convergent Evolution of Coiled-Coil Regions},
  journal =      NAR,
  year = 	 2013,
  volume =       41,
  pages =        {e121},
  pmid = 	 23598997,
  pmcid =        {PMC3695513},
  reprinturl =   {https://doi.org/10.1093/nar/gkt263},
}

@Article{Nawrocki13b,
  author = 	 {E. P. Nawrocki and S. R. Eddy},
  title = 	 {Computational Identification of Functional {RNA}
                  Homologs in Metagenomic Data},
  journal =      {RNA Biol.},
  year = 	 2013,
  volume =       10,
  pages =        {1170--1179},
  pmid =         23722291,
  pmcid =        {PMC3849165},
  reprinturl =   {https://doi.org/10.4161/rna.25038},
}

@Article{Rivas13,
  author = 	 {E. Rivas},
  title = 	 {The Four Ingredients of Single-Sequence {RNA}
                  Secondary Structure Prediction: A Unifying
                  Perspective},
  journal =      {RNA Biol.},
  year = 	 2013,
  volume =       10,
  pages =        {1185--1196},
  pmid =         23695796,
  pmcid =        {PMC3849167},                   
  reprinturl =   {https://doi.org/10.4161/rna.24971},
}


@Article{Eddy13,
  author = 	 {S. R. Eddy},
  title = 	 {The {ENCODE} Project: Mistakes Overshadowing a Success},
  journal = 	 {Curr. Biol.},
  year = 	 2013,
  volume = 	 23,
  pages = 	 {R259-261},
  pmid = 	 23578867,
  reprinturl =   {https://doi.org/10.1016/j.cub.2013.03.023},
}

@Article{Davis13,
  author = 	 {F. P. Davis and S. R. Eddy},
  title = 	 {Transcription Factors that Convert Adult Cell
                  Identity are Differentially {P}olycomb Repressed},
  journal = 	 {PLOS ONE},
  year = 	 2013,
  volume = 	 8,
  pmid   =       23650565,
  pmcid  =       {PMC3641127},
  pages = 	 {e63407},
  reprinturl =   {https://doi.org/10.1371/journal.pone.0063407},
}

@Article{Swart13,
  author =       {E. C. Swart and J. R. Bracht and V. Magrini and
                  P. Minx and X. Chen and Y. Zhou and J. S. Khurana
                  and A. D. Goldman and M. Nowacki and K. Schotanus
                  and S. Jung and R. S. Fulton and A. Ly and
                  S. McGrath and K. Haub and J. L. Wiggins and
                  D. Storton and J. C. Matese and L. Parsons and
                  W. J. Chang and M. S. Bowen and N. A. Stover and
                  T. A. Jones and S. R. Eddy and G. A. Herrick and
                  T. G. Doak and R. K. Wilson and E. R. Mardis and
                  L. F. Landweber},
  title =        {The \emph{{O}xytricha trifallax} Macronuclear Genome: A
                  Complex Eukaryotic Genome With 16,000 Tiny
                  Chromosomes},
  journal =      {PLOS Biol.},
  year =         2013,
  volume =       11,
  pages =        10,
  pmid =         23382650,
  pmcid =        {PMC3558436},
  reprinturl =   {https://doi.org/10.1371/journal.pbio.1001473},
}

@Article{BurgeBateman13,
  author = 	 {S. W. Burge and J. Daub and R. Eberhardt and
                  L. Barquist and E. P. Nawrocki and S. R. Eddy and
                  P. P. Gardner and A. Bateman},
  title = 	 {Rfam 11.0: 10 Years of {RNA} Families},
  journal = 	 NAR,
  year =         2013,
  volume =       41,
  pages =        {D226-D232},
  pmid = 	 23125362,
  pmcid =        {PMC3531072},
  reprinturl =   {https://doi.org/10.1093/nar/gks1005},
}

@Article{Wheeler13,
  author = 	 {T. J. Wheeler and J. Clements and S. R. Eddy and
              R. Hubley and T. A. Jones and J. Jurka and
              A. F. A. Smit and R. D. Finn},
  title =    {{Dfam:} A Database of Repetitive {DNA} Based on
              Profile Hidden {M}arkov Models},
  journal =  NAR,
  year = 	 2013,
  volume =       41,
  pages =        {D70--D82},
  pmid =         23203985,
  pmcid =        {PMC3531169},
  reprinturl =   {https://doi.org/10.1093/nar/gks1265},
}

@Article{Eddy12,
  author = 	 {S. R. Eddy},
  title = 	 {The {C}-value Paradox, junk {DNA} and {ENCODE}},
  journal = 	 {Curr. Biol.},
  year = 	 2012,
  volume = 	 22,
  pages = 	 {R898-899},
  pmid = 	 23137679,
  reprinturl =   {https://doi.org/10.1016/j.cub.2012.10.002},
}

@Article{HenryEddy12,
  author = 	 {G. L. Henry and F. P. Davis and S. Picard and S. R. Eddy},
  title = 	 {Cell Type-Specific Genomics of \emph{{D}rosophila} Neurons},
  journal = 	 NAR,
  year = 	 2012,
  volume = 	 40,
  pages = 	 {9691-9704},
  pmid = 	 22855560,
  pmcid =        {PMC3479168},                 
  reprinturl =   {https://doi.org/10.1093/nar/gks671},
}

@Article{Punta12,
  author =       {M. Punta and P. C. Coggill and R. Y. Eberhardt and
                  J. Mistry and J. Tate and C. Boursnell and N. Pang
                  and K. Forslund and G. Ceric and J. Clements and
                  A. Heger and L. Holm and E. L. Sonnhammer and
                  S. R. Eddy and A. Bateman and R. D. Finn},
  title =        {The {P}fam Protein Families Database},
  journal =      {NAR},
  year =         2012,
  volume =       40,
  pages =        {D290--D301},
  pmid =         22127870,
  pmcid =        {PMC3245129},
  reprinturl =   {https://doi.org/10.1093/nar/gkr1065},
}

@Article{Bernick12,
  author = 	 {D. L. Bernick and P. P. Dennis and M. H{\"o}chsmann and T. M. Lowe},
  title = 	 {Discovery of \emph{{P}yrobaculum} Small {RNA} Families With Atypical Pseudouridine Guide {RNA} Features},
  journal = 	 {RNA},
  year = 	 2012,
  volume = 	 18,
  pages = 	 {402--411},
  pmid = 	 22282340,
  reprinturl =   {https://doi.org/10.1261/rna.031385.111},
}

@Article{Bernick12b,
  author =       {D. L. Bernick and C. L. Cox and P. P. Dennis and T. M. Lowe},
  title =        {Comparative Genomic and Transcriptional Analyses of
                  {CRISPR} Systems Across the Genus \emph{{P}yrobaculum}},
  journal =      {Front. Microbiol.},
  year =         2012,
  volume =       3,
  pages =        251,
  pmid =      22811677,
  reprinturl =   {https://doi.org/10.3389/fmicb.2012.00251},
}
                  
@Article{Bernick12c,
  author =       {D. L. Bernick and P. P. Dennis and L. M. Lui and
                  T. M. Lowe},
  title =        {Diversity of Antisense and Other Non-Coding {RNAs}
                  in {A}rchaea Revealed by Comparative Small {RNA}
                  Sequencing in Four \emph{{P}yrobaculum} Species},
  journal =      {Front. Microbiol.},
  year =         2012,
  volume =       3,
  pages =        231,
  pmid =         22783241,
  PMCID =        {PMC3396285},
  reprinturl =   {https://doi.org/10.3389/fmicb.2012.00251},
}

@Article{RivasEddy12,
  author = 	 {E. Rivas and R. Lang and S. R. Eddy},
  title = 	 {A Range of Complex Probabilistic Models for {RNA}
                  Secondary Structure Prediction That Include the
                  Nearest Neighbor Model and More},
  journal = 	 {RNA},
  year = 	 2012,
  volume = 	 18,
  pages = 	 {193--212},
  pmid = 	 22194308,
  pmcid =        {PMC3264907},                  
  reprinturl =   {https://doi.org/10.1261/rna.030049.111},
}

@Article{McDonald11,
  author = 	 {D. McDonald and M. N. Price and J. Goodrich and
                  E. P. Nawrocki and T. Z. DeSantis and A. Probst and
                  G. L. Andersen and R. Knight and P. Hugenholtz},
  title = 	 {An Improved {G}reengenes Taxonomy with Explicit
                  Ranks for Ecological and Evolutionary Analyses of
                  Bacteria and Archaea},
  journal = 	 {ISME J.},
  year = 	 2011,
  volume = 	 6,
  pages = 	 {610--618},
  pmid =         22134646,
  reprinturl =   {https://doi.org/10.1038/ismej.2011.139},
}

@Article{Tanifuji11,
  author = 	 {G. Tanifuji and N. T. Onodera and T. J. Wheeler and
                  M. Dlutek and N. Donaher and J. M. Archibald},
  title = 	 {Complete Nucleomorph Genome Sequence of the
                  Nonphotosynthetic Alga \emph{{C}ryptomonas paramecium}
                  Reveals a Core Nucleomorph Gene Set},
  journal = 	 {Genome Biol. Evol.},
  year =         2011,
  volume =       3,
  pages =        {44--54},
  pmid = 	 21147880,
  reprinturl =   {https://doi.org/10.1093/gbe/evq082},
}

@Article{Davis11b,
  author = 	 {F. P. Davis},
  title = 	 {Phosphorylation at the Interface},
  journal = 	 {Structure},
  year = 	 2011,
  volume = 	 19,
  pages = 	 {1726--1727},
  pmid =         22153492,
  reprinturl =   {https://doi.org/10.1016/j.str.2011.11.006},
}

@Article{Birmingham11,
  author = 	 {A. Birmingham and J. C. Clemente and N. Desai and
                  J. Gilbert and A. Gonzalez and N. Kyrpides and
                  F. Meyer and E. Nawrocki and P. Sterk and
                  J. Stombaugh and Z. Weinberg and D. Wendel and
                  N. B. Leontis and C. Zirbel and R. Knight and
                  A. Laederach},
  title = 	 {Meeting Report of the {RNA} {O}ntology {C}onsortium,
                  {J}anuary 8-9, 2011},
  journal = 	 {Stand. Genomic Sci.},
  year = 	 2011,
  volume = 	 4,
  pages = 	 {252--256},
  pmid = 	 21677862,
  pmcid =        {PMC3111981},                   
  reprinturl =   {https://doi.org/10.4056%2Fsigs.1724282},
}

@Article{Girard11,
  author = 	 {F. Girard and Z. Meszar and C. Marti and F. P. Davis
                  and M. Celio},
  title = 	 {Gene Expression Analysis in the
                  Parvalbumin-Immunoreactive {PV1} Nucleus of the
                  Mouse Lateral Hypothalamus},
  journal = 	 {Eur. J. Neurosci.},
  year = 	 2011,
  volume = 	 34,
  pages = 	 {1934--1943},
  pmid = 	 22128821,
  reprinturl =   {https://doi.org/10.1111/j.1460-9568.2011.07918.x},
}

@Article{KolbeEddy11,
  author = 	 {D. L. Kolbe and S. R. Eddy},
  title = 	 {Fast Filtering for {RNA} Homology Search},
  journal = 	 {Bioinformatics},
  year = 	 2011,
  volume = 	 27,
  pages = 	 {3102--3109},
  pmid = 	 21965818,
  pmcid =        {PMC3208395},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btr545},
}

@Article{Gardner11b,
  author = 	 {P. P. Gardner and L. Barquist and A. Bateman and E. P. Nawrocki and Z. Weinberg},
  title = 	 {{RNIE}: Genome-Wide Prediction of Bacterial Intrinsic Terminators},
  journal = 	 NAR,
  year = 	 2011,
  volume = 	 39,
  pages = 	 {5845--5852},
  pmid = 	 21478170,
  reprinturl =   {https://doi.org/10.1093/nar/gkr168},
}

@Article{Eddy11,
  author = 	 {S. R. Eddy},
  title = 	 {Accelerated profile {HMM} searches},
  journal = 	 {PLOS Comp. Biol.},
  year = 	 2011,
  volume = 	 7,
  pages = 	 {e1002195},
  pmid = 	 22039361,
  pmcid =        {PMC3197634},
  reprinturl =   {https://doi.org/10.1371/journal.pcbi.1002195},
}

@Article{Finn11,
  author = 	 {R. D. Finn and J. Clements and S. R. Eddy},
  title = 	 {{HMMER} Web Server: Interactive Sequence Similarity Searching},
  journal = 	 NAR,
  year = 	 2011,
  volume = 	 39,
  pages = 	 {W29--37},
  pmid = 	 21593126,
  pmcid =        {PMC3125773},
  reprinturl =   {https://doi.org/10.1093/nar/gkr367},
}

@Article{JungEddy11,
  author = 	 {S. Jung and E. C. Swart and P. J. Minx and
                  V. Magrini and E. R. Mardis and L. F. Landweber and
                  S. R. Eddy},
  title = 	 {Exploiting \emph{{O}xytricha trifallax}
                  nanochromosomes to screen for noncoding {RNA} genes},
  journal = 	 NAR,
  year = 	 2011,
  volume = 	 39,
  pages = 	 {7529--7547},
  pmid = 	 21715380,
  pmcid =        {PMC3177221},
  reprinturl =   {https://doi.org/10.1093/nar/gkr501},
}

@Article{Gardner11,
  author =       {P. P. Gardner and J. Daub and J. Tate and
                  B. L. Moore and I. H. Osuch and S. Griffiths-Jones
                  and R. D. Finn and E. P. Nawrocki and D. L. Kolbe
                  and S. R. Eddy and A. Bateman},
  title =        {Rfam: Wikipedia, Clans and the "Decimal" Release},
  journal =      NAR,
  year =         2011,
  volume =       39,
  pages =        {D141--D145},
  pmid =         21062808,
  pmcid =        {PMC3013711},
  reprinturl =   {https://doi.org/10.1093/nar/gkq1129},
}

@Article{Davis11,
  author =       {F. P. Davis},
  title =        {Proteome-Wide Prediction of Overlapping Small
                  Molecule and Protein Binding Sites Using Structure},
  journal =      {Mol Biosyst.},
  year =         2011,
  volume =       7,
  pages =        {545--557},
  pmid =         21103609,
  reprinturl =   {https://doi.org/10.1039/c0mb00200c},
}

@PhdThesis{Kolbe10,
  author = 	 {D. L. Kolbe},
  title = 	 {Novel Algorithms for Structural Alignment of Non-Coding RNAs},
  school = 	 {Washington University School of Medicine},
  year = 	 2010,
}

@Article{Johnson10,
  author = 	 {L. S. Johnson and S. R. Eddy and E. Portugaly},
  title = 	 {Hidden {M}arkov Model Speed Heuristic and Iterative
                  {HMM} Search Procedure},
  journal = 	 {BMC Bioinformatics},
  year = 	 2010,
  volume = 	 11,
  pages = 	 431,
  pmid = 	 20718988,
  pmcid =        {PMC2931519},
  reprinturl =   {https://doi.org/10.1186/1471-2105-11-431},
}

@Article{DavisSali10,
  author =       {F. P. Davis and A. Sali},
  title =        {The Overlap of Small Molecule and Protein Binding
                  Sites Within Families of Protein Structures},
  journal =      {PLOS Comp. Biol.},
  year =         2010,
  volume =       6,
  pages =        {e1000668},
  pmid =         20140189,
  reprinturl =   {https://doi.org/10.1371/journal.pcbi.1000668},
}

@Article{Finn10,
  author = 	 {R. D. Finn and J. Mistry and J. Tate and P. Coggill
                  and A. Heger and J. E. Pollington and O. L. Gavin
                  and G. Ceric and K. Forslund and L. Holm and
                  E. L. L. Sonnhammer and S. R. Eddy and A. Bateman},
  title = 	 {The {P}fam Protein Families Database},
  journal =      NAR,
  year =         2010,
  volume =       38,
  pages =        {D211--D222},
  pmid =         19920124,
  pmcid =        {PMC2808889},
  reprinturl =   {https://doi.org/10.1093/nar/gkp985},
}

@Book{NAS10,
  author =	 {{Committee on Scientific Milestones for the
                  Development of a Gene-Sequence-Based Classification
                  System for the Oversight of Select Agents}},
  title = 	 {Sequence-Based Classification of Select Agents: A
                  Brighter Line},
  publisher = 	 {National Academies Press},
  address =	 {Washington DC},
  year = 	 2010,
  isbn =         9780309159043,
  reprinturl =   {https://doi.org/10.17226/12970},
}

@Article{Eddy09b,
  author = 	 {S. R. Eddy},
  title = 	 {A New Generation of Homology Search Tools Based on Probabilistic Inference},
  journal =      {Genome Inform.},
  year =         2009,
  volume =       23,
  pages =        {205--211},
  pmid =         20180275,
}

@Article{Pieper09,
  author =       {U. Pieper and N. Eswar and B. M. Webb and D. Eramian
                  and L. Kelly and D. T. Barkan and H. Carter and
                  P. Mankoo and R. Karchin and M. A. Marti-Renom and
                  F. P. Davis and A. Sali},
  title =        {{MODBASE,} a Database of Annotated Comparative
                  Protein Structure Models and Associated Resources},
  journal =      NAR,
  year =         2009,
  volume =       37,
  pages =        {D347--D354},
  pmid =      18948282,
  reprinturl =   {https://doi.org/10.1093/nar/gkn791},
}

@Article{Castellano09,
  author =       {S. Castellano and A. M. Andr{\'e}s and E. Bosch and M. Bayes and R. Guig{\'o} and A. G. Clark},
  title =        {Low Exchangeability of Selenocysteine, the 21st Amino Acid, in Vertebrate Proteins},
  journal =      MBE,
  year =         2009,
  volume =       26,
  pages =        {2031--2040},
  pmid =      19487332,
  reprinturl =   {https://doi.org/10.1093/molbev/msp109},
}

@Article{Castellano09b,
  author =       {S. Castellano},
  title =        {On the Unique Function of Selenocysteine -- Insights From the Evolution of Selenoproteins},
  journal =      {Biochim. Biophys. Acta.},
  year =         2009,
  volume =       1790,
  pages =        {1463--1470},
  pmid =      19345253,
  reprinturl =   {https://doi.org/10.1016/j.bbagen.2009.03.027},
}

@PhdThesis{Nawrocki09b,
  author = 	 {E. P. Nawrocki},
  title = 	 {Structural {RNA} Homology Search and Alignment Using Covariance Models},
  school = 	 {Washington University School of Medicine},
  year = 	 2009,
}

@Article{DavisEddy09,
  author = 	 {F. P. Davis and S. R. Eddy},
  title = 	 {A Tool for Identification of Genes Expressed in
                  Patterns of Interest Using the {A}llen {B}rain
                  {Atlas}},
  journal = 	 {Bioinformatics},
  year = 	 2009,
  volume = 	 25,
  pages = 	 {1647--1654},
  pmid = 	 19414530,
  pmcid =        {PMC2940243},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btp288},
}

@Article{Nawrocki09,
  author = 	 {E. P. Nawrocki and D. L. Kolbe and S. R. Eddy},
  title = 	 {Infernal 1.0: Inference of {RNA} Alignments},
  journal = 	 {Bioinformatics},
  year = 	 2009,
  volume = 	 25,
  pages = 	 {1335-1337},
  pmid = 	 19307242,
  pmcid =        {PMC2732312},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btp157},
}

@Article{KolbeEddy09,
  author = 	 {D. L. Kolbe and S. R. Eddy},
  title = 	 {Local {RNA} Structure Alignment With Incomplete Sequence},
  journal = 	 {Bioinformatics},
  year =         2009,
  volume = 	 25,
  pages = 	 {1236--1243},
  pmid = 	 19304875,
  pmcid =        {PMC2677745},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btp154},
}

@Article{Jones09,
  author = 	 {T. A. Jones and W. Otto and M. Marz and S. R. Eddy and P. F. Stadler},
  title = 	 {A Survey of Nematode {SmY} {RNAs}},
  journal = 	 {RNA Biol.},
  year = 	 2009,
  volume = 	 6,
  pages = 	 {5--8},
  pmid = 	 19106623,
  reprinturl =   {https://doi.org/10.4161/rna.6.1.7634},
}


@Article{Castellano08,
  author =       {S. Castellano and V. N. Gladyshev and R. Guig{\'o} and M. J. Berry},
  title =        {{SelenoDB} 1.0 : a Database of Selenoprotein Genes, Proteins and {SECIS} Elements},
  journal =      NAR,
  year =         2008,
  volume =       36,
  pages =        {D332--D338},
  pmid =      18174224,
  reprinturl =   {https://doi.org/10.1093/nar/gkm731},
}

@Article{Davis07,
  author =       {F. P. Davis and D. T. Barkan and N. Eswar and
                  J. H. McKerrow and A. Sali},
  title =        {Host Pathogen Protein Interactions Predicted by
                  Comparative Modeling},
  journal =      {Protein Sci.},
  year =         2007,
  volume =       16,
  pages =        {2585--2596},
  pmid =      17965183,
  reprinturl =   {https://doi.org/10.1110/ps.073228407},
}

@Article{Ambros03,
  author =       {V. Ambros and B. Bartel and D. P. Bartel and
                  C. B. Burge and J. C. Carrington and X. Chen and
                  G. Dreyfuss and S. R. Eddy and S. Griffiths-Jones
                  and M. Marshall and M. Matzke and G. Ruvkun and
                  T. Tuschl},
  title =        {A Uniform System for {microRNA} Annotation},
  journal =      {RNA},
  year =         2003,
  volume =       9,
  pages =        {277--279},
  pmid =	 12592000,
  pmcid =        {PMC1370393},
  reprinturl =   {https://doi.org/10.1261/rna.2183803},
}

@PhdThesis{Bao02,
  author = 	 {Zhirong Bao},
  title = 	 {Computational Identification and Characterization of
                  Repeats in Sequenced Eukaryotic Genomes},
  school = 	 {Washington University School of Medicine},
  year = 	 2002,
}

@Article{BaoEddy02,
  author =       {Z. Bao and S. R. Eddy},
  title =        {Automated de Novo Identification of Repeat Sequence
                  Families in Sequenced Genomes},
  journal =      GR,
  year =         2002,
  volume =       12,
  pages =        {1269--1276},
  pmid =	 12176934,
  pmcid =        {PMC186642},
  reprinturl =   {https://doi.org/10.1101/gr.88502},
}

@Article{Bateman00,
  author =       {A. Bateman and E. Birney and R. Durbin and
                  S. R. Eddy and K. L. Howe and E. L. Sonnhammer},
  title =        {The {P}fam Protein Families Database},
  journal =      NAR,
  year =         2000,
  volume =       28,
  pages =        {263--266},
  pmid =	 10592242,
  pmcid =        {PMC102420},                    
  reprinturl =   {https://doi.org/10.1093/nar/28.1.263},
}

@Article{Bateman02,
  author =       {A. Bateman and E. Birney and L. Cerruti and
                  R. Durbin and L. Etwiller and S. R. Eddy and
                  S. Griffiths-Jones and K. L. Howe and M. Marshall
                  and E. L. Sonnhammer},
  title =        {The {Pfam} Protein Families Database},
  journal =      NAR,
  year =         2002,
  volume =       30,
  pages =        {276--280},
  pmid =	 11752314,
  reprinturl =   {https://doi.org/10.1093/nar/30.1.276},
}

@Article{Bateman04,
  author = 	 {A. Bateman and L. Coin and R. Durbin and R. D. Finn
                  and V. Hollich and S. Griffiths-Jones and A. Khanna
                  and M. Marshall and S. Moxon and E. L. L. Sonnhammer
                  and D. J. Studholme and C. Yeats and S. R. Eddy},
  title = 	 {The {P}fam Protein Families Database},
  journal = 	 NAR,
  year = 	 2004,
  volume =	 32,
  pages =	 {D138-141},
  pmid =	 14681378,
  pmcid =        {PMC308855},                  
  reprinturl =   {https://doi.org/10.1093/nar/gkh121},
}

@Article{Bateman96b,
  author = 	 {A. Bateman and S. R. Eddy and C. Chothia},
  title = 	 {Members of the Immunoglobulin Superfamily in Bacteria},
  journal = 	 {Protein Sci.},
  year = 	 1996,
  volume =	 5,
  pages =	 {1939--1941},
  pmid =         8880921,
  reprinturl =   {https://doi.org/10.1002/pro.5560050923},
}

@Article{Bateman97b,
  author = 	 {A. Bateman and S. R. Eddy and V. V. Mesyanzhinov},
  title = 	 {A Member of the Immunoglobulin Superfamily in
                  Bacteriophage {T4}},
  journal = 	 {Virus Genes},
  year = 	 1997,
  volume =	 14,
  pages =	 {163--165},
  pmid =         9237357,
  reprinturl =   {https://doi.org/10.1023/a:1007977503658},
}

@Article{Bateman99,
  author =       {A. Bateman and E. Birney and R. Durbin and
                  S. R. Eddy and R. D. Finn and E. L. Sonnhammer},
  title =        {Pfam 3.1: 1313 Multiple
                  Alignments and Profile {HMMs} Match the Majority of
                  Proteins},
  journal =      NAR,
  year =         1999,
  volume =       27,
  pages =        {260--262},
  pmid =	 9847196,
  pmcid =        {PMC148151},                   
  reprinturl =   {https://doi.org/10.1093/nar/27.1.260},
}

@Article{Toronto09,
  author =       {{Toronto International Data Release Workshop Authors}},
  title =        {Prepublication Data Sharing},
  journal =      {Nature},
  year =         2009,
  volume =       461,
  pages =        {168--170},
  pmid =         19741685,
  reprinturl =   {https://doi.org/10.1038/461168a},
}

@Article{Cech03,
  author =       {T. R. Cech and S. R. Eddy and D. Eisenberg and
                  K. Hersey and S. H. Holtzman and G. H. Poste and
                  N. V. Raikhel and R. H. Scheller and D. B. Singer
                  and M. C. Waltham},
  title =        {Sharing Publication-Related Data and Materials:
                  Responsibilities of Authorship in the Life
                  Sciences},
  journal =      {Plant Physiol.},
  year =         2003,
  volume =       132,
  pages =        {19--24},
  pmid =	 12746507,
  pmcid =        {PMC1540310},
  reprinturl =   {https://doi.org/10.1104/pp.900068},
}

@Article{Chalfie95,
  author = 	 {M. Chalfie and S. Eddy and M. O. Hengartner and
                  J. Hodgkin and Y. Kohara and R. H. A. Plasterk and
                  R. H. Waterston and J. G. White},
  title = 	 {Genome Maps {VI}: \emph{{C}aenorhabditis elegans}},
  journal = 	 {Science},
  year = 	 1995,
  volume =	 270,
  pages =	 415,
  pmid =         7569996,
}

@Article{Darnell05,
  author =       {J. C. Darnell and C. E. Fraser and O. Mostovetsky
                  and G. Stefani and T. A. Jones and S. R. Eddy and
                  R. B. Darnell},
  title =        {Kissing Complex {RNAs} Mediate Interaction Between
                  the Fragile-{X} Mental Retardation Protein {KH2}
                  Domain and Brain Polyribosomes},
  journal =      GDEV,
  year =         2005,
  volume =       19,
  pages =        {903--918},
  pmid =	 15805463,
  pmcid =        {PMC1080130},
  reprinturl =   {https://doi.org/10.1101/gad.1276805},
}

@Article{delVal07,
  author = 	 {C. {del Val} and E. Rivas and O. Torres-Quesada and
                  N. Toro and J. I. Jim{\'e}nez-Zurdo},
  title = 	 {Identification of Differentially Expressed Small
                  Non-Coding {RNAs} in the Legume Endosymbiont
                  \emph{{S}inorhizobium meliloti} by Comparative
                  Genomics},
  journal = 	 {Mol. Microbiol.},
  year = 	 2007,
  volume =	 66,
  pages =	 {1080-1091},
  pmid =	 17971083,
  pmcid =        {PMC2780559},                   
  reprinturl =   {https://doi.org/10.1111/j.1365-2958.2007.05978.x},
}

@Article{Dowell01,
  author = 	 {R. D. Dowell and R. M. Jokerst and A. Day and
                  S. R. Eddy and L. Stein},
  title = 	 {The {D}istributed {A}nnotation {S}ystem},
  journal = 	 {BMC Bioinformatics},
  year = 	 2001,
  volume =	 2,
  pages =	 7,
  pmid =	 11667947,
  reprinturl =   {https://doi.org/10.1186/1471-2105-2-7},
}

@MastersThesis{Dowell01b,
  author = 	 {Robin Dowell},
  title = 	 {A Distributed Annotation System},
  school = 	 {Washington University},
  year = 	 2001,
}

@PhdThesis{Dowell04,
  author = 	 {Robin D. Dowell},
  title = 	 {{RNA} Structural Alignment Using Stochastic Context-Free Grammars},
  school = 	 {Washington University School of Medicine},
  year = 	 2004,
  website =      {http://selab.wustl.edu/people/robin/dissertation/},
}

@Article{DowellEddy04,
  author = 	 {R. D. Dowell and S. R. Eddy},
  title =        {Evaluation of Several Lightweight Stochastic
                  Context-Free Grammars for {RNA} Secondary Structure
                  Prediction},
  journal =      {BMC Bioinformatics},
  year =         2004,
  volume =       5,
  pages =        71,
  pmid =	 15180907,
  pmcid =        {PMC442121},          
  reprinturl =   {https://doi.org/10.1186/1471-2105-5-71},
}

@Article{DowellEddy06,
  author = 	 {R. D. Dowell and S. R. Eddy},
  title = 	 {Efficient Pairwise {RNA} Structure Prediction and
                  Alignment Using Sequence Alignment Constraints},
  journal = 	 {BMC Bioinformatics},
  year = 	 2006,
  volume =	 7,
  pages =	 400,
  pmid =	 16952317,
  reprinturl =   {https://doi.org/10.1186/1471-2105-7-400},
}

@Book{Durbin98,
  author = 	 {R. Durbin and S. R. Eddy and A. Krogh and G. J. Mitchison},
  title = 	 {Biological Sequence Analysis: Probabilistic Models
                  of Proteins and Nucleic Acids},
  publisher = 	 {Cambridge University Press},
  address =      {Cambridge UK},
  year = 	 1998,
  isbn =         0521629713,
  reprinturl =   {http://eddylab.org/cupbook.html},
}

@Article{Eddy-ATG1,
  author = 	 {S. R. Eddy},
  title = 	 {What is Dynamic Programming?},
  journal = 	 NBT,
  year = 	 2004,
  volume =	 22,
  pages =	 {909-910},
  pmid =	 15229554,
  reprinturl =   {https://doi.org/10.1038/nbt0704-909},
}

@Article{Eddy-ATG2,
  author = 	 {S. R. Eddy},
  title = 	 {Where Did the {BLOSUM62} Alignment Score Matrix Come From?},
  journal = 	 NBT,
  year = 	 2004,
  volume =	 22,
  pages =	 {1035-1036},
  pmid =         15286655,
  reprinturl =   {https://doi.org/10.1038/nbt0804-1035},
}

@Article{Eddy-ATG3,
  author = 	 {S. R. Eddy},
  title = 	 {What is {B}ayesian Statistics?},
  journal = 	 NBT,
  year = 	 2004,
  volume =	 22,
  pages =	 {1177-1178},
  pmid =	 15340486,
  reprinturl =   {https://doi.org/10.1038/nbt0904-1177},
}

@Article{Eddy-ATG4,
  author = 	 {S. R. Eddy},
  title = 	 {What is a Hidden {M}arkov Model?},
  journal = 	 NBT,
  year =	 2004,
  volume =	 22,
  pages =	 {1315-1316},
  pmid =	 15470472,
  reprinturl =   {https://doi.org/10.1038/nbt1004-1315},
}

@Article{Eddy-ATG5,
  author = 	 {S.R. Eddy},
  title = 	 {How Do {RNA} Folding Algorithms Work?},
  journal =      NBT,
  year =	 2004,
  volume =       22,
  pages =        {1457-1458},
  pmid =         15529172,
  reprinturl =   {https://doi.org/10.1038/nbt1104-1457},
}

@Article{Eddy01,
  author =       {S. R. Eddy},
  title =        {Non-Coding {RNA} Genes and the Modern {RNA} World},
  journal =      NRG,
  year =         2001,
  volume =       2,
  pages =        {919--929},
  pmid =	 11733745,
  reprinturl =   {https://doi.org/10.1038/35103511},
}

@TechReport{Eddy01b,
  author = 	 {S. R. Eddy},
  title = 	 {Hints on Using {LaTeX} to Produce {PDF}},
  institution =  {Washington University School of Medicine},
  year = 	 2001
}

@Article{Eddy02,
  author = 	 {S. R. Eddy},
  title = 	 {Computational Genomics of Noncoding {RNA} Genes},
  journal = 	 {Cell},
  year = 	 2002,
  volume =	 109,
  pages =	 {137-140},
  pmid =	 12007398,
  reprinturl =   {https://doi.org/10.1016/s0092-8674(02)00727-4},
}

@Article{Eddy02b,
  author = 	 {S. R. Eddy},
  title = 	 {A Memory-Efficient Dynamic Programming Algorithm for
                  Optimal Alignment of a Sequence to an {RNA}
                  Secondary Structure},
  journal = 	 {BMC Bioinformatics},
  year = 	 2002,
  volume =	 3,
  pages =	 18,
  pmid =	 12095421,
  pmcid =        {PMC119854},
  reprinturl =   {https://doi.org/10.1186/1471-2105-3-18},
}

@Article{Eddy05,
  author = 	 {S. R. Eddy},
  title = 	 {A Model of the Statistical Power of Comparative Genome Sequence Analysis},
  journal = 	 {PLOS Biol.},
  year = 	 2005,
  volume =	 3,
  pages =	 {e10},
  pmid =	 15660152,
  pmcid =        {PMC539325},
  reprinturl =   {https://doi.org/10.1371/journal.pbio.0030010},
}

@Article{Eddy05b,
  author = 	 {S. R. Eddy},
  title = 	 {Antedisciplinary Science},
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2005,
  volume =	 1,
  pages =	 {e6},
  pmid =	 16103907,
  pmcid =        {PMC1183512},
  reprinturl =   {https://doi.org/10.1371/journal.pcbi.0010006},
}

@Article{Eddy06,
  author = 	 {S. R. Eddy},
  title = 	 {Total Information Awareness for Worm Genetics},
  journal = 	 {Science},
  year = 	 2006,
  volume =	 311,
  pages =	 {381--382},
  pmid =	 16527956,
  reprinturl =   {https://doi.org/10.1126/science.1125655},
}

@Article{Eddy06b,
  author = 	 {S. R. Eddy},
  title = 	 {Computational Analysis of {RNAs}},
  journal = 	 CSHSQB,
  year = 	 2006,
  volume =	 71,
  pages =	 {117--128},
  reprinturl =   {https://doi.org/10.1101/sqb.2006.71.003},
}

@Article{Eddy08,
  author =       {S. R. Eddy},
  title = 	 {A Probabilistic Model of Local Sequence Alignment
                  that Simplifies Statistical Significance
                  Estimation},
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2008,
  volume =	 4,
  pages =	 {e1000069},
  pmid =         18516236,
  pmcid =        {PMC239628},
  reprinturl =   {https://doi.org/10.1371/journal.pcbi.1000069},
}

@Article{Eddy09,
  author = 	 {S. R. Eddy},
  title = 	 {Open Revolution},
  journal = 	 {PLOS Biology},
  year = 	 2009,
  volume = 	 7,
  pages = 	 {e1000078},
  reprinturl =   {https://doi.org/10.1371/journal.pbio.1000078},
}

@Article{Eddy91,
  author = 	{S. R. Eddy and L. Gold},
  title = 	{The Phage {T4} {nrdB} Intron: A Deletion Mutant
		 of a Version Found in the Wild},
  journal = 	GDEV,
  year = 	1991,
  volume = 	5,
  pages = 	{1032--1041},
  pmid =        2044951,
  reprinturl =  {https://doi.org/10.1101/gad.5.6.1032},
}

@PhdThesis{Eddy91b,
  author = 	 "Sean R. Eddy",
  title = 	 "Introns in the {T}-Even Bacteriophages",
  school = 	 "University of Colorado at Boulder",
  year = 	 1991,
  extranote =    {This electronic copy doesn't include all figures; the submitted thesis included many figures as photographs.}
}

@Article{Eddy92,
  author = 	 "S. R. Eddy and L. Gold",
  title = 	 "Artificial Mobile {DNA} Element Constructed from the
		  {EcoRI} Endonuclease Gene",
  journal = 	 PNAS,
  year = 	 1992,
  volume = 	 89,
  pages = 	 "1544--1547",
  pmid =         1311841,
  reprinturl =   {https://doi.org/10.1073/pnas.89.5.1544},
}

@Article{Eddy94,
  author = 	 {S. R. Eddy and R. Durbin},
  title = 	 {{RNA} Sequence Analysis Using Covariance Models},
  journal = 	 NAR,
  year = 	 1994,
  volume = 	 22,
  pages = 	 {2079--2088},
  pmid =         8029015,
  pmcid =        {PMC308124},
  reprinturl=    {https://doi.org/10.1093/nar/22.11.2079},
}

@InCollection{Eddy94b,
  author = 	 {S. R. Eddy},
  title = 	 {The \emph{{C}aenorhabditis elegans} Genome Project},
  booktitle = 	 {Advances in Plant Nematology},
  pages =	 {3--18},
  publisher =	 {Plenum Press},
  year =	 1994,
  editor = 	 "F. Lamberti and C. De Giorgi and D. McK Bird",
  address =	 {New York}
}

@Article{Eddy94c,
  author = 	 {S. R. Eddy},
  title = 	 {The Human Genome Project According to Los Alamos},
  journal = 	 TIBS,
  year = 	 1994,
  volume =	 20,
  pages =	 {91--92},
  mynote =	 {book review}
}

@Article{Eddy95,
  author = 	 {S. R. Eddy and G. Mitchison and R. Durbin},
  title = 	 {Maximum Discrimination Hidden {M}arkov Models of
		  Sequence Consensus},
  journal = 	 JCompB,
  year = 	 1995,
  volume = 	 2,
  pages = 	 "9--23",
  pmid =         7497123,
  pmcid =        {https://doi.org/10.1089/cmb.1995.2.9},                  
}

@InProceedings{Eddy95b,
  author = 	 "S. R. Eddy",
  title = 	 "Multiple Alignment Using Hidden {M}arkov Models",
  editor = 	 "Christopher Rawlings and Dominic Clark and Russ
		  Altman and Lawrence Hunter and Thomas Lengauer and
		  Shoshana Wodak",
  pages = 	 "114-120",
  booktitle =    "Proc. Third Int. Conf. Intelligent Systems for
		  Molecular Biology",
  year = 	 1995,
  publisher =    "AAAI Press",
  address = 	 "Menlo Park, CA",
  pmid =         7584426,
}

@Article{Eddy96,
  author = 	 {S. R. Eddy},
  title = 	 {Hidden {M}arkov Models},
  journal = 	 COSB,
  year = 	 1996,
  volume =	 6,
  pages =	 {361--365},
  pmid =         8804822,
  reprinturl =   {https://doi.org/10.1016/S0959-440X(96)80056-X},
}

@Article{Eddy96b,
  author = 	 {S. R. Eddy},
  title = 	 {Molecular Genetics \emph{in silico}: Fourth
                  International Conference on Intelligent Systems in
                  Molecular Biology},
  journal = 	 TIGS,
  year = 	 1996,
  volume =	 12,
  pages =	 372,
}

@Article{Eddy97,
  author = 	 {S. R. Eddy},
  title = 	 {Hidden {M}arkov Models and Large-Scale Genome Analysis},
  journal = 	 {Transactions of the American Crystallographic Association},
  year = 	 1997,
}

@TechReport{Eddy97b,
  author = 	 {S. R. Eddy},
  title = 	 {Maximum Likelihood Fitting of Extreme Value Distributions},
  institution =  {Washington University School of Medicine},
  year = 	 1997,
}

@Article{Eddy98,
  author = 	 {S. R. Eddy},
  title = 	 {Profile Hidden {M}arkov Models},
  journal = 	 {Bioinformatics},
  year = 	 1998,
  volume =	 14,
  pages =	 {755--763},
  pmid =         9918945,
  reprinturl =   {https://doi.org/10.1093/bioinformatics/14.9.755},
}

@Article{Eddy98b,
  author = 	 {S. R. Eddy},
  title = 	 {Multiple-alignment and -sequence searches},
  journal = 	 {Trends Guide to Bioinformatics},
  year = 	 1998,
  pages =	 {15--18},
}

@Article{Eddy99,
  author = 	 {S. R. Eddy},
  title = 	 {Noncoding {RNA} genes},
  journal = 	 COGD,
  year = 	 1999,
  volume =	 9,
  pages =	 {695--699},
  pmid =	 10607607,
  reprinturl =   {https://doi.org/10.1016/S0959-437X(99)00022-2},
}

@Article{Eddy99b,
  author = 	 {S. R. Eddy},
  title = 	 {Shotgun Coverage of Human Genome Computing},
  journal = 	 TIBS,
  year = 	 1999,
  volume =	 24,
  pages =	 124,
  reprinturl =   {https://doi.org/10.1016/S0968-0004(98)01308-5},                   
  note =	 {book review}
}

@Article{EddyMacKay96,
  author = 	 {S. R. Eddy and D. J. C. MacKay},
  title = 	 {Is the {P}ope the {P}ope?},
  journal = 	 {Nature},
  year = 	 1996,
  volume =	 382,
  pages =	 490,
  reprinturl =   {https://doi.org/10.1038/382490a0},
}

@InProceedings{Ellingworth95,
  author = 	 "H. Ellingworth and S. R. Eddy",
  title = 	 "{RNA} Structure Alignment on a Massively Parallel Computer",
  editor = 	 "Bob Hertzberger and Giuseppe Serazzi",
  pages = 	 "502--507",
  booktitle = "Lecture Notes in Computer Science 919: High
		  Performance Computing and Networking",
  year = 	 1995,
  publisher = "Springer",
  address = 	 "Berlin",
  reprinturl =   {https://doi.org/10.1007/BFb0046673},                  
}

@Article{Finn06,
  author =       {R. D. Finn and J. Mistry and B. Schuster-Bockler and
                  S. Griffiths-Jones and V. Hollich and T. Lassmann
                  and S. Moxon and M. Marshall and A. Khanna and
                  R. Durbin and S. R. Eddy and E. L. Sonnhammer and
                  A. Bateman},
  title =        {Pfam: Clans, Web Tools and Services},
  journal =      NAR,
  year =         2006,
  volume =       34,
  pages =        {D247--D251},
  pmid =	 16381856,
  pmcid =        {PMC1347511},
  reprinturl =   {https://doi.org/10.1093/nar/gkj149},
}

@Article{Finn08,
  author = 	 {R. D. Finn and J. Tate and J. Mistry and
                  P. C. Coggill and S. J. Sammut and H.-R. Hotz and
                  G. Ceric and K. Forslund and S. R. Eddy and
                  E. L. L. Sonnhammer and A. Bateman},
  title = 	 {The {P}fam Protein Families Database},
  journal = 	 NAR,
  year = 	 2008,
  volume =	 36,
  pages =	 {D281-D288},
  pmid =	 18039703,
  pmcid =        {PMC2238907},
  reprinturl =   {https://doi.org/10.1093/nar/gkm960},
}

@Article{Gardner09,
  author = 	 {P. P. Gardner and J. Daub and J. G. Tate and
                  E. P. Nawrocki and D. L. Kolbe and S. Lindgreen and
                  A. C. Wilkinson and R. D. Finn and
                  S. Griffiths-Jones and S. R. Eddy and A. Bateman},
  title = 	 {Rfam: Updates to the {RNA} Families Database},
  journal = 	 NAR,
  year = 	 2009,
  volume = 	 37,
  pages = 	 {D136--D140},
  pmid = 	 18953034,
  pmcid =        {PMC2686503},
  reprinturl =   {https://doi.org/10.1093/nar/gkn766},
}

@InCollection{Gold93,
  author = 	 {L. Gold and C. Tuerk and P. Allen and J. Binkley and
                  D. Brown and L. Green and S. MacDougal and
                  D. Schneider and D. Tasset and S. R. Eddy},
  title = 	 {{RNA}: The Shape of Things to Come},
  booktitle = 	 {The {RNA} World},
  pages =	 {497--509},
  publisher =	 {Cold Spring Harbor Laboratory Press},
  year =	 1993,
  editor =	 {R. F. Gesteland and J. F. Atkins},
  address =	 {New York},
  reprinturl =   {https://doi.org/10.1101/0.497-509},
}

@Article{Griffiths-Jones03,
  author =       {S. Griffiths-Jones and A. Bateman and M. Marshall
                  and A. Khanna and S. R. Eddy},
  title =        {Rfam: an {RNA} Family Database},
  journal =      NAR,
  year =         2003,
  volume =       31,
  pages =        {439--441},
  pmid =	 12520045,
  pmcid =        {PMC165453},
  reprinturl =   {https://doi.org/10.1093/nar/gkg006},
}

@Article{Griffiths-Jones05,
  author = 	 {S. Griffiths-Jones and S. Moxon and M. Marshall and
                  A. Khanna and S. R. Eddy and A. Bateman},
  title = 	 {Rfam: Annotating Non-Coding {RNAs} in Complete
                  Genomes},
  journal = 	 NAR,
  year = 	 2005,
  volume =	 33,
  pages =	 {D121-D141},
  pmid =	 15608160,
  pmcid =        {PMC540035},
  reprinturl =   {https://doi.org/10.1093/nar/gki081},
}

@Article{Hillier03,
  author =       {L. W. Hillier and R. S. Fulton and L. A. Fulton and
                  T. A. Graves and K. H. Pepin and C. Wagner-McPherson
                  and D. Layman and J. Maas and S. Jaeger and
                  R. Walker and K. Wylie and M. Sekhon and
                  M. C. Becker and M. D. O'Laughlin and M. E. Schaller
                  and G. A. Fewell and K. D. Delehaunty and
                  T. L. Miner and W. E. Nash and M. Cordes and H. Du
                  and H. Sun and J. Edwards and H. Bradshaw-Cordum and
                  J. Ali and S. Andrews and A. Isak and A. Vanbrunt
                  and C. Nguyen and F. Du and B. Lamar and L. Courtney
                  and J. Kalicki and P. Ozersky and L. Bielicki and
                  K. Scott and A. Holmes and R. Harkins and A. Harris
                  and C. M. Strong and S. Hou and C. Tomlinson and
                  S. Dauphin-Kohlberg and A. Kozlowicz-Reilly and
                  S. Leonard and T. Rohlfing and S. M. Rock and
                  A. M. Tin-Wollam and A. Abbott and P. Minx and
                  R. Maupin and C. Strowmatt and P. Latreille and
                  N. Miller and D. Johnson and J. Murray and
                  J. P. Woessner and M. C. Wendl and S. P. Yang and
                  B. R. Schultz and J. W. Wallis and J. Spieth and
                  T. A. Bieri and J. O. Nelson and N. Berkowicz and
                  P. E. Wohldmann and L. L. Cook and
                  M. T. Hickenbotham and J. Eldred and D. Williams and
                  J. A. Bedell and E. R. Mardis and S. W. Clifton and
                  S. L. Chissoe and M. A. Marra and C. Raymond and
                  E. Haugen and W. Gillett and Y. Zhou and R. James
                  and K. Phelps and S. Iadanoto and K. Bubb and
                  E. Simms and R. Levy and J. Clendenning and R. Kaul
                  and W. J. Kent and T. S. Furey and R. A. Baertsch
                  and M. R. Brent and E. Keibler and P. Flicek and
                  P. Bork and M. Suyama and J. A. Bailey and
                  M. E. Portnoy and D. Torrents and A. T. Chinwalla
                  and W. R. Gish and S. R. Eddy and J. D. McPherson
                  and M. V. Olson and E. E. Eichler and E. D. Green
                  and R. H. Waterston and R. K. Wilson},
  title =        {The {DNA} Sequence of Human Chromosome 7},
  journal =      {Nature},
  year =         2003,
  volume =       424,
  pages =        {157--164},
  pmid =	 12853948,
  reprinturl =   {https://doi.org/10.1038/nature01782},
}

@Article{Hillier05,
  author =       {L. W. Hillier and T. A. Graves and R. S. Fulton and
                  L. A. Fulton and K. H. Pepin and P. Minx and
                  C. Wagner-McPherson and D. Layman and K. Wylie and
                  M. Sekhon and M. C. Becker and G. A. Fewell and
                  K. D. Delehaunty and T. L. Miner and W. E. Nash and
                  C. Kremitzki and L. Oddy and H. Du and H. Sun and
                  H. Bradshaw-Cordum and J. Ali and J. Carter and
                  M. Cordes and A. Harris and A. Isak and A. van Brunt
                  and C. Nguyen and F. Du and L. Courtney and
                  J. Kalicki and P. Ozersky and S. Abbott and
                  J. Armstrong and E. A. Belter and L. Caruso and
                  M. Cedroni and M. Cotton and T. Davidson and
                  A. Desai and G. Elliott and T. Erb and C. Fronick
                  and T. Gaige and W. Haakenson and K. Haglund and
                  A. Holmes and R. Harkins and K. Kim and
                  S. S. Kruchowski and C. M. Strong and N. Grewal and
                  E. Goyea and S. Hou and A. Levy and S. Martinka and
                  K. Mead and M. D. McLellan and R. Meyer and
                  J. Randall-Maher and C. Tomlinson and
                  S. Dauphin-Kohlberg and A. Kozlowicz-Reilly and
                  N. Shah and S. Swearengen-Shahid and J. Snider and
                  J. T. Strong and J. Thompson and M. Yoakum and
                  S. Leonard and C. Pearman and L. Trani and
                  M. Radionenko and J. E. Waligorski and C. Wang and
                  S. M. Rock and A. M. Tin-Wollam and R. Maupin and
                  P. Latreille and M. C. Wendl and S. P. Yang and
                  C. Pohl and J. W. Wallis and J. Spieth and
                  T. A. Bieri and N. Berkowicz and J. O. Nelson and
                  J. Osborne and L. Ding and R. Meyer and A. Sabo and
                  Y. Shotland and P. Sinha and P. E. Wohldmann and
                  L. L. Cook and M. T. Hickenbotham and J. Eldred and
                  D. Williams and T. A. Jones and X. She and
                  F. D. Ciccarelli and E. Izaurralde and J. Taylor and
                  J. Schmutz and R. M. Myers and D. R. Cox and
                  X. Huang and J. D. McPherson and E. R. Mardis and
                  S. W. Clifton and W. C. Warren and A. T. Chinwalla
                  and S. R. Eddy and M. A. Marra and I. Ovcharenko and
                  T. S. Furey and W. Miller and E. E. Eichler and
                  P. Bork and M. Suyama and D. Torrents and
                  R. H. Waterston and R. K. Wilson},
  title = 	 {Generation and Annotation of the {DNA} Sequences of
                  Human Chromosomes 2 and 4},
  journal = 	 {Nature},
  year = 	 2005,
  volume =	 434,
  pages =	 {724--731},
  pmid =	 15815621,
  reprinturl =   {https://doi.org/10.1038/nature03466},
}

@Article{Jiang02,
  author =       {N. Jiang and Z. Bao and S. Temnykh and Z. Cheng and
                  J. Jiang and R. A. Wing and S. R. McCouch and
                  S. R. Wessler},
  title =        {Dasheng: a Recently Amplified Nonautonomous Long
                  Terminal Repeat Element That is a Major Component of
                  Pericentromeric Regions in Rice},
  journal =      {Genetics},
  year =         2002,
  volume =       161,
  pages =        {1293--1305},
  pmid =	 12136031,
  reprinturl =   {https://doi.org/10.1093/genetics/161.3.1293},
}

@Article{Jiang03,
  author = 	 {N. Jiang and Z. Bao and X. Zhang and H. Hirochika
                  and S. R. Eddy and S. R. McCouch and S. R. Wessler},
  title = 	 {An Active {DNA} Transposon Family in Rice},
  journal = 	 {Nature},
  year = 	 2003,
  volume =	 421,
  pmid =         12520302,
  pages =	 {163--167},
  reprinturl =   {https://doi.org/10.1038/nature01214},
}

@Article{Jiang04,
  author = 	 {N. Jiang and Z. Bao and X. Zhang and S. R. Eddy and
                  S. R. Wessler},
  title = 	 {Pack-{MULEs}: Transposon-Mediated Gene Evolution in Plants},
  journal = 	 {Nature},
  year =	 2004,
  volume =	 431,
  pages =	 {569-573},
  pmid =	 15457261,
  reprinturl =   {https://doi.org/10.1038/nature02953},
}

@PhdThesis{Johnson06,
  author = 	 {S. Johnson},
  title = 	 {Remote Protein Homology Detection Using Hidden {M}arkov Models},
  school = 	 {Washington University School of Medicine},
  year = 	 2006,
}

@Article{Jones01,
  author =       {S. J. Jones and D. L. Riddle and A. T. Pouzyrev and
                  V. E. Velculescu and L. Hillier and S. R. Eddy and
                  S. L. Stricklin and D. L. Baillie and R. Waterston
                  and M. A. Marra},
  title =        {Changes in Gene Expression Associated With
                  Developmental Arrest and Longevity in \emph{{C}aenorhabditis
                  elegans}},
  journal =      GR,
  year =         2001,
  volume =       11,
  pages =        {1346--1352},
  pmid =	 11483575,
  reprinturl =   {https://doi.org/10.1101/gr.184401},
}

@Article{Klein02,
  author =       {R. J. Klein and Z. Misulovin and S. R. Eddy},
  title =        {Noncoding {RNA} Genes Identified in {AT}-Rich Hyperthermophiles},
  journal =      PNAS,
  year =         2002,
  volume =       99,
  pages =        {7542--7547},
  pmid =	 12032319,
  pmcid =        {PMC124278},
  reprinturl =   {https://doi.org/10.1073/pnas.112063799},
}

@PhdThesis{Klein03,
  author = 	 {Robert J. Klein},
  title = 	 {Finding Noncoding {RNA} Genes in Genomic Sequences},
  school = 	 {Washington University School of Medicine},
  year = 	 2003,
}

@Article{KleinEddy03,
  author =       {R. J. Klein and S. R. Eddy},
  title =        {{RSEARCH:} Finding Homologs of Single Structured {RNA} Sequences},
  journal =      {BMC Bioinformatics},
  year =         2003,
  volume =       4,
  pages =        44,
  pmid =	 14499004,
  pmcid =        {PMC239859},
  reprinturl =   {https://doi.org/10.1186/1471-2105-4-44},
}

@InCollection{Kutter94,
  author = 	 "E. Kutter and E. Kellenberger and K.
		  C. and S. Eddy and J. Neitzel and L.
		  Messinger and J. North and B. Guttman",
  title = 	 "Effects of Bacterial Growth Conditions and
		  Physiology on T4 Infection",
  booktitle = "Molecular Biology of Bacteriophage T4",
  publisher = "American Society for Microbiology",
  year = 	 1994,
  editor = 	 "Jim D. Karam",
  chapter = 	 41,
  pages = 	 "406-418",
  address = 	 "Washington, D.C."
}

@Article{Lander01,
    author =      {{International Human Genome Sequencing Consortium}},
    old-author =     {E. S. Lander and L. M. Linton and B. Birren and
                  C. Nusbaum and M. C. Zody and J. Baldwin and
                  K. Devon and K. Dewar and M. Doyle and W. FitzHugh
                  and R. Funke and D. Gage and K. Harris and
                  A. Heaford and J. Howland and L. Kann and
                  J. Lehoczky and R. LeVine and P. McEwan and
                  K. McKernan and J. Meldrim and J. P. Mesirov and
                  C. Miranda and W. Morris and J. Naylor and
                  C. Raymond and M. Rosetti and R. Santos and
                  A. Sheridan and C. Sougnez and N. Stange-Thomann and
                  N. Stojanovic and A. Subramanian and D. Wyman and
                  J. Rogers and J. Sulston and R. Ainscough and
                  S. Beck and D. Bentley and J. Burton and C. Clee and
                  N. Carter and A. Coulson and R. Deadman and
                  P. Deloukas and A. Dunham and I. Dunham and
                  R. Durbin and L. French and D. Grafham and
                  S. Gregory and T. Hubbard and S. Humphray and
                  A. Hunt and M. Jones and C. Lloyd and A. McMurray
                  and L. Matthews and S. Mercer and S. Milne and
                  J. C. Mullikin and A. Mungall and R. Plumb and
                  M. Ross and R. Shownkeen and S. Sims and
                  R. H. Waterston and R. K. Wilson and L. W. Hillier
                  and J. D. McPherson and M. A. Marra and E. R. Mardis
                  and L. A. Fulton and A. T. Chinwalla and K. H. Pepin
                  and W. R. Gish and S. L. Chissoe and M. C. Wendl and
                  K. D. Delehaunty and T. L. Miner and A. Delehaunty
                  and J. B. Kramer and L. L. Cook and R. S. Fulton and
                  D. L. Johnson and P. J. Minx and S. W. Clifton and
                  T. Hawkins and E. Branscomb and P. Predki and
                  P. Richardson and S. Wenning and T. Slezak and
                  N. Doggett and J. F. Cheng and A. Olsen and S. Lucas
                  and C. Elkin and E. Uberbacher and M. Frazier and
                  R. A. Gibbs and D. M. Muzny and S. E. Scherer and
                  J. B. Bouck and E. J. Sodergren and K. C. Worley and
                  C. M. Rives and J. H. Gorrell and M. L. Metzker and
                  S. L. Naylor and R. S. Kucherlapati and D. L. Nelson
                  and G. M. Weinstock and Y. Sakaki and A. Fujiyama
                  and M. Hattori and T. Yada and A. Toyoda and T. Itoh
                  and C. Kawagoe and H. Watanabe and Y. Totoki and
                  T. Taylor and J. Weissenbach and R. Heilig and
                  W. Saurin and F. Artiguenave and P. Brottier and
                  T. Bruls and E. Pelletier and C. Robert and
                  P. Wincker and D. R. Smith and L. Doucette-Stamm and
                  M. Rubenfield and K. Weinstock and H. M. Lee and
                  J. Dubois and A. Rosenthal and M. Platzer and
                  G. Nyakatura and S. Taudien and A. Rump and H. Yang
                  and J. Yu and J. Wang and G. Huang and J. Gu and
                  L. Hood and L. Rowen and A. Madan and S. Qin and
                  R. W. Davis and N. A. Federspiel and A. P. Abola and
                  M. J. Proctor and R. M. Myers and J. Schmutz and
                  M. Dickson and J. Grimwood and D. R. Cox and
                  M. V. Olson and R. Kaul and C. Raymond and
                  N. Shimizu and K. Kawasaki and S. Minoshima and
                  G. A. Evans and M. Athanasiou and R. Schultz and
                  B. A. Roe and F. Chen and H. Pan and J. Ramser and
                  H. Lehrach and R. Reinhardt and W. R. McCombie and
                  M. de la Bastide and N. Dedhia and H. Blocker and
                  K. Hornischer and G. Nordsiek and R. Agarwala and
                  L. Aravind and J. A. Bailey and A. Bateman and
                  S. Batzoglou and E. Birney and P. Bork and
                  D. G. Brown and C. B. Burge and L. Cerutti and
                  H. C. Chen and D. Church and M. Clamp and
                  R. R. Copley and T. Doerks and S. R. Eddy and
                  E. E. Eichler and T. S. Furey and J. Galagan and
                  J. G. Gilbert and C. Harmon and Y. Hayashizaki and
                  D. Haussler and H. Hermjakob and K. Hokamp and
                  W. Jang and L. S. Johnson and T. A. Jones and
                  S. Kasif and A. Kaspryzk and S. Kennedy and
                  W. J. Kent and P. Kitts and E. V. Koonin and I. Korf
                  and D. Kulp and D. Lancet and T. M. Lowe and
                  A. McLysaght and T. Mikkelsen and J. V. Moran and
                  N. Mulder and V. J. Pollara and C. P. Ponting and
                  G. Schuler and J. Schultz and G. Slater and
                  A. F. Smit and E. Stupka and J. Szustakowski and
                  D. Thierry-Mieg and J. Thierry-Mieg and L. Wagner
                  and J. Wallis and R. Wheeler and A. Williams and
                  Y. I. Wolf and K. H. Wolfe and S. P. Yang and
                  R. F. Yeh and F. Collins and M. S. Guyer and
                  J. Peterson and A. Felsenfeld and K. A. Wetterstrand
                  and A. Patrinos and M. J. Morgan and J. Szustakowki
                  and P. de Jong and J. J. Catanese and K. Osoegawa
                  and H. Shizuya and S. Choi and Y. J. Chen},
  title = 	 {Initial Sequencing and Analysis of the Human Genome},
  journal = 	 {Nature},
  year = 	 2001,
  volume =	 409,
  pages =	 {860--921},
  pmid =	 11237011,
  reprinturl =   {https://doi.org/10.1038/35057062},
}

@PhdThesis{Lowe99,
  author = 	 {Todd M. J. Lowe},
  title = 	 {Combining New Computational and Traditional
                  Experimental Methods to Identify {tRNA} and {snoRNA}
                  Gene Families},
  school = 	 {Washington University School of Medicine},
  year = 	 1999,
}

@Article{LoweEddy97,
  author = 	 {T. M. Lowe and S. R. Eddy},
  title = 	 {{tRNAscan-SE}: A Program for Improved Detection of
                  Transfer {RNA} Genes in Genomic Sequence},
  journal = 	 NAR,
  year = 	 1997,
  volume =	 25,
  pages =	 {955--964},
  pmid =         9023104,
  pmcid =        {PMC146525},
  reprinturl =   {https://doi.org/10.1093/nar/25.5.955},
}

@Article{LoweEddy99,
  author = 	 {T. M. Lowe and S. R. Eddy},
  title = 	 {A Computational Screen for Methylation Guide {snoRNAs} in Yeast},
  journal =      {Science},
  volume =       283,
  pages =        {1168--1171},
  year =	 1999,
  pmid =         10024243,
  reprinturl =   {https://doi.org/10.1126/science.283.5405.1168},                  
}

@PhdThesis{McCutcheon06,
  author = 	 {J. P. McCutcheon},
  title = 	 {Screens for noncoding RNAs and strange lifeforms},
  school = 	 {Washington University School of Medicine},
  year = 	 2006
}

@Article{McCutcheonEddy03,
  author =       {J. P. McCutcheon and S. R. Eddy},
  title =        {Computational Identification of Non-Coding {RNAs} in
                  \emph{{S}accharomyces cerevisiae} by Comparative Genomics},
  journal =      NAR,
  year =         2003,
  volume =       31,
  pages =        {4119--4128},
  pmid =	 12853629,
  pmcid =        {PMC165953},
  reprinturl =   {https://doi.org/10.1093/nar/gkg438},
}

@Book{NAS03,
  author =	 {{Committee on Responsibilities of Authorship in the Biological Sciences}},
  title = 	 {Sharing Publication-Related Data and Materials:
                  Responsibilities of Authorship in the Life Sciences},
  publisher = 	 {National Academies Press},
  address =	 {Washington DC},
  year = 	 2003,
  isbn =         0309090407,
  reprinturl =   {https://doi.org/10.17226/10613},
}

@Article{NawrockiEddy07,
  author = 	 {E. P. Nawrocki and S. R. Eddy},
  title = 	 {Query-Dependent Banding ({QDB}) for Faster {RNA} Similarity Searches},
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2007,
  volume =	 3,
  pages =	 {e56},
  pmid =	 17397253,
  pmcid =        {PMC1847999},
  reprinturl =   {https://doi.org/10.1371/journal.pcbi.0030056},
}

@Article{Omer00,
  author = 	 {A. D. Omer and T. M. Lowe and A. G. Russell and
                  H. Ebhardt and S. R. Eddy and P. P. Dennis},
  title = 	 {Homologs of Small Nucleolar {RNAs} in {A}rchaea},
  journal = 	 {Science},
  year = 	 2000,
  volume =	 288,
  pages =	 {517--522},
  pmid =	 10775111,
  reprinturl =   {https://doi.org/10.1126/science.288.5465.517},
}

@Article{Rice85,
  author = 	 {C. M. Rice and E. M. Lenches and S. R. Eddy and S. J.
		  Shin and R. L. Sheets and J. H. Strauss},
  title = 	 {Nucleotide Sequence of Yellow Fever Virus:
		  Implications for Flavivirus Gene Expression and
		  Evolution},
  journal = 	 {Science},
  year = 	 1985,
  volume = 	 229,
  pages = 	 {726--733},
  pmid =         4023707,
  reprinturl =   {https://doi.org/10.1126/science.4023707},
}

@Article{Rivas01,
  author =       {E. Rivas and R. J. Klein and T. A. Jones and S. R. Eddy},
  title =        {Computational Identification of Noncoding {RNAs} in
                  \emph{{E.} coli} by Comparative Genomics},
  journal =      CURRB,
  year =         2001,
  volume =       11,
  pages =        {1369--1373},
  pmid =	 11553332,
  reprinturl =   {https://doi.org/10.1016/s0960-9822(01)00401-8},
}

@Article{Rivas05,
  author =       {E. Rivas},
  title =        {Evolutionary Models for Insertions and Deletions in a Probabilistic Modeling Framework},
  journal =      {BMC Bioinformatics.},
  year =         2005,
  volume =       6,
  pages =        63,
  pmid =	 15780137,
  reprinturl =   {https://doi.org/10.1186/1471-2105-6-63},
}

@Article{RivasEddy00a,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {The Language of {RNA}: A Formal Grammar That Includes Pseudoknots},
  journal = 	 {Bioinformatics},
  year = 	 2000,
  volume =	 16,
  pages =	 {326--333},
  pmid =         10869031,
  reprinturl =   {https://doi.org/10.1093/bioinformatics/16.4.334},
}

@Article{RivasEddy00b,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {Secondary Structure Alone is Generally Not Statistically Significant
                  for the Detection of Noncoding {RNAs}},
  journal = 	 {Bioinformatics},
  year = 	 2000,
  volume =	 6,
  pages =	 {583--605},
  pmid =         11038329,
  reprinturl =   {https://doi.org/10.1093/bioinformatics/16.7.583},
}

@Article{RivasEddy01,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {Noncoding {RNA} Gene Detection Using Comparative
                  Sequence Analysis},
  journal = 	 {BMC Bioinformatics},
  year =         2001,
  volume =       2,
  pages =        8,
  pmid =         11801179,
  pmcid =        {PMC64605},
  reprinturl =   {https://doi.org/10.1186/1471-2105-2-8},
}

@Article{RivasEddy08,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {Probabilistic Phylogenetic Inference with Insertions and Deletions},
  journal = 	 {PLOS Comput. Biol.},
  year = 	 2008,
  volume =	 4,
  pages =	 {e1000172},
  pmid =	 18787703,
  reprinturl =   {https://doi.org/10.1371/journal.pcbi.1000172},
}

@Article{RivasEddy99,
  author = 	 {E. Rivas and S. R. Eddy},
  title = 	 {A Dynamic Programming Algorithm for {RNA} Structure
                  Prediction Including Pseudoknots},
  journal =      JMB,
  year = 	 1999,
  volume =       285,
  pages =        {2053--2068},
  pmid =         9925784,
  reprinturl =   {https://doi.org/10.1006/jmbi.1998.2436},
}


@Article{Shendure05,
  author =       {J. Shendure and G. J. Porreca and N. B. Reppas and
                  X. Lin and J. P. McCutcheon and A. M. Rosenbaum and
                  M. D. Wang and K. Zhang and R. D. Mitra and
                  G. M. Church},
  title =        {Accurate Multiplex Polony Sequencing of an Evolved
                  Bacterial Genome},
  journal =      {Science},
  year =         2005,
  volume =       309,
  pages =        {1728--1732},
  pmid =	 16081699,
  reprinturl =   {https://doi.org/10.1126/science.1117389},
}

@Article{Shub94,
  author = 	 {D. A. Shub and H. Goodrich-Blair and S. R. Eddy},
  title = 	 {Amino Acid Sequence Motif of Group {I} Intron
		  Endonucleases is Conserved in Open Reading Frames of
		  Group {II} Introns},
  journal = 	 TIBS,
  year = 	 1994,
  volume = 	 19,
  pages = 	 {402--404},
  pmid =         7817395,
  reprinturl =   {https://doi.org/10.1016/0968-0004(94)90086-8},
}

@Article{Sonnhammer97,
  author = 	 {E. L. L. Sonnhammer and S. R. Eddy and R. Durbin},
  title = 	 {Pfam: A Comprehensive Database of Protein Families
                  Based on Seed Alignments},
  journal = 	 {Proteins},
  year = 	 1997,
  volume =	 28,
  pages =	 {405--420},
  pmid =         9223186,
  reprinturl =   {https://doi.org/10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L}
}

@Article{Sonnhammer98,
  author = 	 {E. L. L. Sonnhammer and S. R. Eddy and E. Birney and A. Bateman and R. Durbin},
  title = 	 {Pfam: Multiple Sequence Alignments and {HMM}-Profiles of Protein Domains},
  journal = 	 NAR,
  year = 	 1998,
  volume =	 26,
  pages =	 {320--322},
  pmid =         9399864,
  reprinturl =   {https://doi.org/10.1093/nar/26.1.320},
}

@Article{Speckmann02,
  author =       {W. A. Speckmann and Z. H. Li and T. M. Lowe and
                  S. R. Eddy and R. M. Terns and M. P. Terns},
  title =        {Archaeal Guide {RNAs} Function in {rRNA}
                  Modification in the Eukaryotic Nucleus},
  journal =      CURRB,
  year =         2002,
  volume =       12,
  pages =        {199--203},
  pmid =	 11839271,
  reprinturl =   {https://doi.org/10.1016/s0960-9822(02)00655-3},
}

@Article{Starostina04,
  author = 	 {N. G. Starostina and S. Marshburn and L. S. Johnson and S. R. Eddy and R. M. Terns and M. P. Terns},
  title = 	 {Circular Box {C/D} {RNAs} in \emph{{P}yrococcus furiosus}},
  journal = 	 PNAS,
  year =	 2004,
  volume =	 101,
  pages =	 {14097-14101},
  pmid =	 15375211,
  pmcid =        {PMC521125},
  reprinturl =   {https://doi.org/10.1073/pnas.0403520101},
}

@InCollection{Stricklin05,
  author = 	 {S. L. Stricklin and S. Griffiths-Jones and S. R. Eddy},
  title = 	 {\emph{{C.} elegans} Noncoding {RNA} Genes},
  booktitle = 	 {WormBook},
  publisher =	 {doi/10.1895/wormbook.1.7.1, http://www.wormbook.org},
  year =	 2005,
  editor =	 {{The \emph{C. elegans} Research Community}},
  reprinturl =   {http://www.wormbook.org/chapters/www_noncodingRNA/noncodingRNA.html},
}

@PhdThesis{Stricklin06,
  author = 	 {S. L. Stricklin},
  title = 	 {Noncoding {RNA} Genes in \emph{{C}aenorhabditis elegans}},
  school = 	 {Washington University School of Medicine},
  year = 	 2006
}

@Article{Tuerk90,
  author = 	{C. Tuerk and S. Eddy and D. Parma and L. Gold},
  title = 	{Autogenous Translational Operator Recognized by
		 Bacteriophage {T4} {DNA} Polymerase},
  journal = 	JMB,
  year = 	1990,
  volume = 	213,
  pages = 	{749--761},
  pmid =        2359122,
  reprinturl =  {https://doi.org/10.1016/S0022-2836(05)80261-X},
}

@Article{Waterston02,
  author     =   {{Mouse Genome Sequencing Consortium}},
  all-author =   {R. H. Waterston and K. Lindblad-Toh and E. Birney
                  and J. Rogers and J. F. Abril and P. Agarwal and
                  R. Agarwala and R. Ainscough and M. Alexandersson
                  and P. An and S. E. Antonarakis and J. Attwood and
                  R. Baertsch and J. Bailey and K. Barlow and S. Beck
                  and E. Berry and B. Birren and T. Bloom and P. Bork
                  and M. Botcherby and N. Bray and M. R. Brent and
                  D. G. Brown and S. D. Brown and C. Bult and
                  J. Burton and J. Butler and R. D. Campbell and
                  P. Carninci and S. Cawley and F. Chiaromonte and
                  A. T. Chinwalla and D. M. Church and M. Clamp and
                  C. Clee and F. S. Collins and L. L. Cook and
                  R. R. Copley and A. Coulson and O. Couronne and
                  J. Cuff and V. Curwen and T. Cutts and M. Daly and
                  R. David and J. Davies and K. D. Delehaunty and
                  J. Deri and E. T. Dermitzakis and C. Dewey and
                  N. J. Dickens and M. Diekhans and S. Dodge and
                  I. Dubchak and D. M. Dunn and S. R. Eddy and
                  L. Elnitski and R. D. Emes and P. Eswara and
                  E. Eyras and A. Felsenfeld and G. A. Fewell and
                  P. Flicek and K. Foley and W. N. Frankel and
                  L. A. Fulton and R. S. Fulton and T. S. Furey and
                  D. Gage and R. A. Gibbs and G. Glusman and S. Gnerre
                  and N. Goldman and L. Goodstadt and D. Grafham and
                  T. A. Graves and E. D. Green and S. Gregory and
                  R. Guigo and M. Guyer and R. C. Hardison and
                  D. Haussler and Y. Hayashizaki and L. W. Hillier and
                  A. Hinrichs and W. Hlavina and T. Holzer and F. Hsu
                  and A. Hua and T. Hubbard and A. Hunt and I. Jackson
                  and D. B. Jaffe and L. S. Johnson and M. Jones and
                  T. A. Jones and A. Joy and M. Kamal and
                  E. K. Karlsson and D. Karolchik and A. Kasprzyk and
                  J. Kawai and E. Keibler and C. Kells and W. J. Kent
                  and A. Kirby and D. L. Kolbe and I. Korf and
                  R. S. Kucherlapati and E. J. Kulbokas and D. Kulp
                  and T. Landers and J. P. Leger and S. Leonard and
                  I. Letunic and R. Levine and J. Li and M. Li and
                  C. Lloyd and S. Lucas and B. Ma and D. R. Maglott
                  and E. R. Mardis and L. Matthews and E. Mauceli and
                  J. H. Mayer and M. McCarthy and W. R. McCombie and
                  S. McLaren and K. McLay and J. D. McPherson and
                  J. Meldrim and B. Meredith and J. P. Mesirov and
                  W. Miller and T. L. Miner and E. Mongin and
                  K. T. Montgomery and M. Morgan and R. Mott and
                  J. C. Mullikin and D. M. Muzny and W. E. Nash and
                  J. O. Nelson and M. N. Nhan and R. Nicol and Z. Ning
                  and C. Nusbaum and M. J. O'Connor and Y. Okazaki and
                  K. Oliver and E. Overton-Larty and L. Pachter and
                  G. Parra and K. H. Pepin and J. Peterson and
                  P. Pevzner and R. Plumb and C. S. Pohl and
                  A. Poliakov and T. C. Ponce and C. P. Ponting and
                  S. Potter and M. Quail and A. Reymond and B. A. Roe
                  and K. M. Roskin and E. M. Rubin and A. G. Rust and
                  R. Santos and V. Sapojnikov and B. Schultz and
                  J. Schultz and M. S. Schwartz and S. Schwartz and
                  C. Scott and S. Seaman and S. Searle and T. Sharpe
                  and A. Sheridan and R. Shownkeen and S. Sims and
                  J. B. Singer and G. Slater and A. Smit and
                  D. R. Smith and B. Spencer and A. Stabenau and
                  N. Stange-Thomann and C. Sugnet and M. Suyama and
                  G. Tesler and J. Thompson and D. Torrents and
                  E. Trevaskis and J. Tromp and C. Ucla and
                  A. Ureta-Vidal and J. P. Vinson and A. C. Von
                  Niederhausern and C. M. Wade and M. Wall and
                  R. J. Weber and R. B. Weiss and M. C. Wendl and
                  A. P. West and K. Wetterstrand and R. Wheeler and
                  S. Whelan and J. Wierzbowski and D. Willey and
                  S. Williams and R. K. Wilson and E. Winter and
                  K. C. Worley and D. Wyman and S. Yang and S. P. Yang
                  and E. M. Zdobnov and M. C. Zody and E. S. Lander},
  title =        {Initial Sequencing and Comparative Analysis of the Mouse Genome},
  journal =      {Nature},
  year =         2002,
  volume =       420,
  pages =        {520--562},
  pmid =         12466850,
  reprinturl =   {https://doi.org/10.1038/nature01262},
}

@Article{Worm98,
  author = 	 {{The \emph{{C}. elegans} Genome Sequencing Consortium}},
  title = 	 {Genome Sequence of the Nematode \emph{{C}. elegans}:
                  A Platform for Investigating Biology},
  journal = 	 {Science},
  year = 	 1998,
  volume =	 282,
  pages =	 {2012--2018},
  pmid =         9851916,
  reprinturl =   {https://doi.org/10.1126/science.282.5396.2012},
}

@Article{Zmasek01a,
  author = 	 {C. M. Zmasek and S. R. Eddy},
  title = 	 {{ATV}: Display and Manipulation of Annotated Phylogenetic Trees},
  journal = 	 {Bioinformatics},
  year = 	 2001,
  volume =	 17,
  pages =	 {383--384},
  pmid =         11301314,
  reprinturl =   {https://doi.org/10.1093/bioinformatics/17.4.383},
}

@Article{Zmasek01b,
  author = 	 {C. M. Zmasek and S. R. Eddy},
  title = 	 {A Simple Algorithm to Infer Gene Duplication and Speciation Events on a Gene Tree},
  journal = 	 {Bioinformatics},
  year = 	 2001,
  volume =	 17,
  pages =	 {821--826},
  pmid =         11590098,
  reprinturl =   {https://doi.org/10.1093/bioinformatics/17.9.821},
}

@PhdThesis{Zmasek02,
  author = 	 {Christian M. Zmasek},
  title = 	 {Functional Analyses of Proteomes by Phylogenetic Methods},
  school = 	 {Washington University School of Medicine},
  year = 	 2002,
}

@Article{ZmasekEddy02,
  author = 	 {C. M. Zmasek and S. R. Eddy},
  title = 	 {{RIO}: Analyzing Proteomes by Automated Phylogenomics
                  Using Resampled Inference of Orthologs},
  journal = 	 {BMC Bioinformatics},
  year = 	 2002,
  volume =	 3,
  pages =	 14,
  pmid =	 12028595,
  reprinturl =   {https://doi.org/10.1186/1471-2105-3-14},
}