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%   C-c C-e C-u  for Unpublished, including preprints                 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@Unpublished{ChenHoekstra24,
  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},
  note =         {eLife, in press},
  year =      2024,
  reprinturl = {https://doi.org/10.1101/2024.08.22.608850},
}

@Unpublished{Sarkar24,
  author = 	 {A. Sarkar and K. Krishnan and S. R. Eddy},
  title = 	 {Protein Sequence Domain Annotation using Language Models},
  note = 	 {bioRxiv preprint and manuscript submitted},
  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,
  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,
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  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},
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  volume = 	 42,
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@Article{Nawrocki13c,
  author = 	 {E. P. Nawrocki and S. R. Eddy},
  title = 	 {Infernal 1.1: 100-fold Faster {RNA} Homology Searches},
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  year = 	 2013,
  volume = 	 29,
  pages = 	 {2933-2935},
  pmid =         24008419,
  pmcid =        {PMC3810854},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btt509},
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@Article{Wheeler13b,
  author = 	 {T. J. Wheeler and S. R. Eddy},
  title = 	 {{nhmmer}: {DNA} Homology Search With Profile {HMMs}},
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  volume =       29,
  pages =        {2487-2489},
  pmid =         23842809,
  pmcid =        {PMC3777106},
  reprinturl =   {https://doi.org/10.1093/bioinformatics/btt403},
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@Article{Nawrocki13d,
  author = 	 {E. P. Nawrocki and S. W. Burge},
  title = 	 {Special Focus: Bioinformatics},
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@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,
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  pmid = 	 23598997,
  pmcid =        {PMC3695513},
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@Article{Nawrocki13b,
  author = 	 {E. P. Nawrocki and S. R. Eddy},
  title = 	 {Computational Identification of Functional {RNA}
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  volume =       10,
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  pmid =         23722291,
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@Article{Rivas13,
  author = 	 {E. Rivas},
  title = 	 {The Four Ingredients of Single-Sequence {RNA}
                  Secondary Structure Prediction: A Unifying
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  volume =       10,
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  pmid =         23695796,
  pmcid =        {PMC3849167},                   
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@Article{Eddy13,
  author = 	 {S. R. Eddy},
  title = 	 {The {ENCODE} Project: Mistakes Overshadowing a Success},
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@Article{Davis13,
  author = 	 {F. P. Davis and S. R. Eddy},
  title = 	 {Transcription Factors that Convert Adult Cell
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  year = 	 2013,
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@Article{Swart13,
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                  L. F. Landweber},
  title =        {The \emph{{O}xytricha trifallax} Macronuclear Genome: A
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@Article{BurgeBateman13,
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  title = 	 {Rfam 11.0: 10 Years of {RNA} Families},
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  pmid = 	 23125362,
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@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},
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@Article{HenryEddy12,
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  pmcid =        {PMC3479168},                 
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@Article{Punta12,
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                  A. Heger and L. Holm and E. L. Sonnhammer and
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  title =        {The {P}fam Protein Families Database},
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  author = 	 {D. L. Bernick and P. P. Dennis and M. H{\"o}chsmann and T. M. Lowe},
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  reprinturl =   {https://doi.org/10.1261/rna.031385.111},
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  author =       {D. L. Bernick and C. L. Cox and P. P. Dennis and T. M. Lowe},
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  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}
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  author = 	 {E. Rivas and R. Lang and S. R. Eddy},
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  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
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@Article{Zmasek01a,
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@Article{Zmasek01b,
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@PhdThesis{Zmasek02,
  author = 	 {Christian M. Zmasek},
  title = 	 {Functional Analyses of Proteomes by Phylogenetic Methods},
  school = 	 {Washington University School of Medicine},
  year = 	 2002,
}

@Article{ZmasekEddy02,
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