RNA structure alignment on a massively parallel computer. - Henry Ellingworth; Sean R. Eddy (HPCN Europe, 1995)

Multiple Alignment Using Hidden Markov Models. - Sean R. Eddy (ISMB, 1995)

Maximum Discrimination Hidden Markov Models of Sequence Consensus. - Sean R. Eddy; Graeme J. Mitchison; Richard Durbin (J. Comput. Biol., 1995)

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids - Richard Durbin; Sean R. Eddy; Anders Krogh; Graeme J. Mitchison (Cambridge University Press, 1998)

[Invited Lecture] Genome sequence analysis and profile hidden Markov models. - Sean R. Eddy (German Conference on Bioinformatics, 1998)

Profile hidden Markov models. - Sean R. Eddy (Bioinform., 1998)

Pfam: multiple sequence alignments and HMM-profiles of protein domains. - Erik L. L. Sonnhammer; Sean R. Eddy; Ewan Birney; Alex Bateman; Richard Durbin (Nucleic Acids Res., 1998)

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. - Alex Bateman; Ewan Birney; Richard Durbin; Sean R. Eddy; Robert D. Finn; Erik L. L. Sonnhammer (Nucleic Acids Res., 1999)

Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. - Elena Rivas; Sean R. Eddy (Bioinform., 2000)

The language of RNA: a formal grammar that includes pseudoknots. - Elena Rivas; Sean R. Eddy (Bioinform., 2000)

The Pfam Protein Families Database. - Alex Bateman; Ewan Birney; Richard Durbin; Sean R. Eddy; Kevin L. Howe; Erik L. L. Sonnhammer (Nucleic Acids Res., 2000)

A simple algorithm to infer gene duplication and speciation events on a gene tree. - Christian M. Zmasek; Sean R. Eddy (Bioinform., 2001)

ATV: display and manipulation of annotated phylogenetic. - Christian M. Zmasek; Sean R. Eddy (Bioinform., 2001)

The Distributed Annotation System. - Robin D. Dowell; Rodney M. Jokerst; Allen Day; Sean R. Eddy; Lincoln Stein (BMC Bioinform., 2001)

Noncoding RNA gene detection using comparative sequence analysis. - Elena Rivas; Sean R. Eddy (BMC Bioinform., 2001)

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. - Sean R. Eddy (BMC Bioinform., 2002)

RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. - Christian M. Zmasek; Sean R. Eddy (BMC Bioinform., 2002)

The Pfam Protein Families Database. - Alex Bateman; Ewan Birney; Lorenzo Cerutti; Richard Durbin; Laurence Ettwiller; Sean R. Eddy; Sam Griffiths-Jones; Kevin L. Howe; Mhairi Marshall; Erik L. L. Sonnhammer (Nucleic Acids Res., 2002)

RSEARCH: Finding homologs of single structured RNA sequences. - Robert J. Klein; Sean R. Eddy (BMC Bioinform., 2003)

Rfam: an RNA family database. - Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R. Eddy (Nucleic Acids Res., 2003)

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. - Robin D. Dowell; Sean R. Eddy (BMC Bioinform., 2004)

The Pfam protein families database. - Alex Bateman; Lachlan James M. Coin; Richard Durbin; Robert D. Finn; Volker Hollich; Sam Griffiths-Jones; Ajay Khanna; Mhairi Marshall; Simon Moxon; Erik L. L. Sonnhammer; David J. Studholme; Corin Yeats; et al. (Nucleic Acids Res., 2004)

Rfam: annotating non-coding RNAs in complete genomes. - Sam Griffiths-Jones; Simon Moxon; Mhairi Marshall; Ajay Khanna; Sean R. Eddy; Alex Bateman (Nucleic Acids Res., 2005)

"Antedisciplinary" Science. - Sean R. Eddy (PLoS Comput. Biol., 2005)

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. - Robin D. Dowell; Sean R. Eddy (BMC Bioinform., 2006)

Pfam: clans, web tools and services. - Robert D. Finn; Jaina Mistry; Benjamin Schuster-Böckler; Sam Griffiths-Jones; Volker Hollich; Timo Lassmann; Simon Moxon; Mhairi Marshall; Ajay Khanna; Richard Durbin; Sean R. Eddy; Erik L. L. Sonnhammer; et al. (Nucleic Acids Res., 2006)

Query-Dependent Banding (QDB) for Faster RNA Similarity Searches. - Eric P. Nawrocki; Sean R. Eddy (PLoS Comput. Biol., 2007)

The Pfam protein families database. - Robert D. Finn; John G. Tate; Jaina Mistry; Penny C. Coggill; Stephen John Sammut; Hans-Rudolf Hotz; Goran Ceric; Kristoffer Forslund; Sean R. Eddy; Erik L. L. Sonnhammer; Alex Bateman (Nucleic Acids Res., 2008)

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation. - Sean R. Eddy (PLoS Comput. Biol., 2008)

Probabilistic Phylogenetic Inference with Insertions and Deletions. - Elena Rivas; Sean R. Eddy (PLoS Comput. Biol., 2008)

A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas. - Fred P. Davis; Sean R. Eddy (Bioinform., 2009)

Local RNA structure alignment with incomplete sequence. - Diana L. Kolbe; Sean R. Eddy (Bioinform., 2009)

Infernal 1.0: inference of RNA alignments. - Eric P. Nawrocki; Diana L. Kolbe; Sean R. Eddy (Bioinform., 2009)

Rfam: updates to the RNA families database. - Paul P. Gardner; Jennifer Daub; John G. Tate; Eric P. Nawrocki; Diana L. Kolbe; Stinus Lindgreen; Adam C. Wilkinson; Robert D. Finn; Sam Griffiths-Jones; Sean R. Eddy; Alex Bateman (Nucleic Acids Res., 2009)

Hidden Markov model speed heuristic and iterative HMM search procedure. - L. Steven Johnson; Sean R. Eddy; Elon Portugaly (BMC Bioinform., 2010)

The Pfam protein families database. - Robert D. Finn; Jaina Mistry; John G. Tate; Penny C. Coggill; Andreas Heger; Joanne E. Pollington; O. Luke Gavin; Prasad Gunasekaran; Goran Ceric; Kristoffer Forslund; Liisa Holm; Erik L. L. Sonnhammer; et al. (Nucleic Acids Res., 2010)

Fast filtering for RNA homology search. - Diana L. Kolbe; Sean R. Eddy (Bioinform., 2011)

HMMER web server: interactive sequence similarity searching. - Robert D. Finn; Jody Clements; Sean R. Eddy (Nucleic Acids Res., 2011)

Rfam: Wikipedia, clans and the "decimal" release. - Paul P. Gardner; Jennifer Daub; John G. Tate; Benjamin L. Moore; Isabelle H. Osuch; Sam Griffiths-Jones; Robert D. Finn; Eric P. Nawrocki; Diana L. Kolbe; Sean R. Eddy; Alex Bateman (Nucleic Acids Res., 2011)

Accelerated Profile HMM Searches. - Sean R. Eddy (PLoS Comput. Biol., 2011)

The Pfam protein families database. - Marco Punta; Penny C. Coggill; Ruth Y. Eberhardt; Jaina Mistry; John G. Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; et al. (Nucleic Acids Res., 2012)

Infernal 1.1: 100-fold faster RNA homology searches. - Eric P. Nawrocki; Sean R. Eddy (Bioinform., 2013)

nhmmer: DNA homology search with profile HMMs. - Travis J. Wheeler; Sean R. Eddy (Bioinform., 2013)

Rfam 11.0: 10 years of RNA families. - Sarah W. Burge; Jennifer Daub; Ruth Y. Eberhardt; John G. Tate; Lars Barquist; Eric P. Nawrocki; Sean R. Eddy; Paul P. Gardner; Alex Bateman (Nucleic Acids Res., 2013)

Dfam: a database of repetitive DNA based on profile hidden Markov models. - Travis J. Wheeler; Jody Clements; Sean R. Eddy; Robert Hubley; Thomas A. Jones; Jerzy Jurka; Arian F. A. Smit; Robert D. Finn (Nucleic Acids Res., 2013)

Pfam: the protein families database. - Robert D. Finn; Alex Bateman; Jody Clements; Penelope Coggill; Ruth Y. Eberhardt; Sean R. Eddy; Andreas Heger; Kirstie Hetherington; Liisa Holm; Jaina Mistry; Erik L. L. Sonnhammer; John G. Tate; et al. (Nucleic Acids Res., 2014)

Parameterizing sequence alignment with an explicit evolutionary model. - Elena Rivas; Sean R. Eddy (BMC Bioinform., 2015)

HMMER web server: 2015 update. - Robert D. Finn; Jody Clements; William Arndt; Benjamin L. Miller; Travis J. Wheeler; Fabian Schreiber; Alex Bateman; Sean R. Eddy (Nucleic Acids Res., 2015)

Rfam 12.0: updates to the RNA families database. - Eric P. Nawrocki; Sarah W. Burge; Alex Bateman; Jennifer Daub; Ruth Y. Eberhardt; Sean R. Eddy; Evan W. Floden; Paul P. Gardner; Thomas A. Jones; John G. Tate; Robert D. Finn (Nucleic Acids Res., 2015)

The Pfam protein families database: towards a more sustainable future. - Robert D. Finn; Penelope Coggill; Ruth Y. Eberhardt; Sean R. Eddy; Jaina Mistry; Alex L. Mitchell; Simon C. Potter; Marco Punta; Matloob Qureshi; Amaia Sangrador-Vegas; Gustavo A. Salazar; John G. Tate; et al. (Nucleic Acids Res., 2016)

The Dfam database of repetitive DNA families. - Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao 004; Arian F. A. Smit; Travis J. Wheeler (Nucleic Acids Res., 2016)

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. - Ioanna Kalvari; Joanna Argasinska; Natalia Quinones-Olvera; Eric P. Nawrocki; Elena Rivas; Sean R. Eddy; Alex Bateman; Robert D. Finn; Anton I. Petrov (Nucleic Acids Res., 2018)

HMMER web server: 2018 update. - Simon C. Potter; Aurelien Luciani; Sean R. Eddy; Young Mi Park; Rodrigo Lopez; Robert D. Finn (Nucleic Acids Res., 2018)

The Pfam protein families database in 2019. - Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R. Eddy; Aurelien Luciani; Simon C. Potter; Matloob Qureshi; Lorna J. Richardson; Gustavo A. Salazar; Alfredo Smart; Erik L. L. Sonnhammer; Layla Hirsh; et al. (Nucleic Acids Res., 2019)

Representation learning of genomic sequence motifs with convolutional neural networks. - Peter K. Koo; Sean R. Eddy (PLoS Comput. Biol., 2019)

Estimating the power of sequence covariation for detecting conserved RNA structure. - Elena Rivas; Jody Clements; Sean R. Eddy (Bioinform., 2020)

Remote homology search with hidden Potts models. - Grey W. Wilburn; Sean R. Eddy (PLoS Comput. Biol., 2020)

Rfam 14: expanded coverage of metagenomic, viral and microRNA families. - Ioanna Kalvari; Eric P. Nawrocki; Nancy Ontiveros-Palacios; Joanna Argasinska; Kevin Lamkiewicz; Manja Marz; Sam Griffiths-Jones; Claire Toffano-Nioche; Daniel Gautheret; Zasha Weinberg; Elena Rivas; Sean R. Eddy; et al. (Nucleic Acids Res., 2021)

Constructing benchmark test sets for biological sequence analysis using independent set algorithms. - Samantha Petti; Sean R. Eddy (PLoS Comput. Biol., 2022)

Codetta: predicting the genetic code from nucleotide sequence. - Yekaterina Shulgina; Sean R. Eddy (Bioinform., 2023)

Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms. - Samantha Petti; Sean R. Eddy (PLoS Comput. Biol., 2023)