Sean R. Eddy

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 12

Top Topics

Protein Families

Independent Set

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Samantha Petti, Sean R. Eddy
Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms. PLoS Comput. Biol. 19 (3) (2023)
Yekaterina Shulgina, Sean R. Eddy
Codetta: predicting the genetic code from nucleotide sequence. Bioinform. 39 (1) (2023)
Samantha Petti, Sean R. Eddy
Constructing benchmark test sets for biological sequence analysis using independent set algorithms. PLoS Comput. Biol. 18 (3) (2022)
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, Robert D. Finn, Alex Bateman, Anton I. Petrov
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 49 (Database-Issue) (2021)
Grey W. Wilburn, Sean R. Eddy
Remote homology search with hidden Potts models. PLoS Comput. Biol. 16 (11) (2020)
Elena Rivas, Jody Clements, Sean R. Eddy
Estimating the power of sequence covariation for detecting conserved RNA structure. Bioinform. 36 (10) (2020)
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, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn
The Pfam protein families database in 2019. Nucleic Acids Res. 47 (Database-Issue) (2019)
Peter K. Koo, Sean R. Eddy
Representation learning of genomic sequence motifs with convolutional neural networks. PLoS Comput. Biol. 15 (12) (2019)
Simon C. Potter, Aurelien Luciani, Sean R. Eddy, Youngmi Park, Rodrigo Lopez, Robert D. Finn
HMMER web server: 2018 update. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P. Nawrocki, Elena Rivas, Sean R. Eddy, Alex Bateman, Robert D. Finn, Anton I. Petrov
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 46 (Database-Issue) (2018)
Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler
The Dfam database of repetitive DNA families. Nucleic Acids Res. 44 (Database-Issue) (2016)
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, Alex Bateman
The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44 (Database-Issue) (2016)
Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy
HMMER web server: 2015 update. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Elena Rivas, Sean R. Eddy
Parameterizing sequence alignment with an explicit evolutionary model. BMC Bioinform. 16 (2015)
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
Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43 (Database-Issue) (2015)
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, Marco Punta
Pfam: the protein families database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Sarah W. Burge, Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Lars Barquist, Eric P. Nawrocki, Sean R. Eddy, Paul P. Gardner, Alex Bateman
Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41 (Database-Issue) (2013)
Eric P. Nawrocki, Sean R. Eddy
Infernal 1.1: 100-fold faster RNA homology searches. Bioinform. 29 (22) (2013)
Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn
Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 41 (Database-Issue) (2013)
Travis J. Wheeler, Sean R. Eddy
nhmmer: DNA homology search with profile HMMs. Bioinform. 29 (19) (2013)
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, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn
The Pfam protein families database. Nucleic Acids Res. 40 (Database-Issue) (2012)
Robert D. Finn, Jody Clements, Sean R. Eddy
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Sean R. Eddy
Accelerated Profile HMM Searches. PLoS Comput. Biol. 7 (10) (2011)
Diana L. Kolbe, Sean R. Eddy
Fast filtering for RNA homology search. Bioinform. 27 (22) (2011)
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
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res. 39 (Database-Issue) (2011)
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, Sean R. Eddy, Alex Bateman
The Pfam protein families database. Nucleic Acids Res. 38 (Database-Issue) (2010)
L. Steven Johnson, Sean R. Eddy, Elon Portugaly
Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinform. 11 (2010)
Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy
Infernal 1.0: inference of RNA alignments. Bioinform. 25 (13) (2009)
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
Rfam: updates to the RNA families database. Nucleic Acids Res. 37 (Database-Issue) (2009)
Diana L. Kolbe, Sean R. Eddy
Local RNA structure alignment with incomplete sequence. Bioinform. 25 (10) (2009)
Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy
Infernal 1.0: inference of RNA alignments. Bioinform. 25 (10) (2009)
Fred P. Davis, Sean R. Eddy
A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas. Bioinform. 25 (13) (2009)
Elena Rivas, Sean R. Eddy
Probabilistic Phylogenetic Inference with Insertions and Deletions. PLoS Comput. Biol. 4 (9) (2008)
Sean R. Eddy
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation. PLoS Comput. Biol. 4 (5) (2008)
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
The Pfam protein families database. Nucleic Acids Res. 36 (Database-Issue) (2008)
Eric P. Nawrocki, Sean R. Eddy
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches. PLoS Comput. Biol. 3 (3) (2007)
Robin D. Dowell, Sean R. Eddy
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinform. 7 (2006)
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, Alex Bateman
Pfam: clans, web tools and services. Nucleic Acids Res. 34 (Database-Issue) (2006)
Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33 (Database-Issue) (2005)
Sean R. Eddy
"Antedisciplinary" Science. PLoS Comput. Biol. 1 (1) (2005)
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, Sean R. Eddy
The Pfam protein families database. Nucleic Acids Res. 32 (Database-Issue) (2004)
Robin D. Dowell, Sean R. Eddy
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinform. 5 (2004)
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy
Rfam: an RNA family database. Nucleic Acids Res. 31 (1) (2003)
Robert J. Klein, Sean R. Eddy
RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinform. 4 (2003)
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
The Pfam Protein Families Database. Nucleic Acids Res. 30 (1) (2002)
Sean R. Eddy
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinform. 3 (2002)
Christian M. Zmasek, Sean R. Eddy
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinform. 3 (2002)
Elena Rivas, Sean R. Eddy
Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinform. 2 (2001)
Robin D. Dowell, Rodney M. Jokerst, Allen Day, Sean R. Eddy, Lincoln Stein
The Distributed Annotation System. BMC Bioinform. 2 (2001)
Christian M. Zmasek, Sean R. Eddy
ATV: display and manipulation of annotated phylogenetic. Bioinform. 17 (4) (2001)
Christian M. Zmasek, Sean R. Eddy
A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinform. 17 (9) (2001)
Elena Rivas, Sean R. Eddy
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinform. 16 (7) (2000)
Elena Rivas, Sean R. Eddy
The language of RNA: a formal grammar that includes pseudoknots. Bioinform. 16 (4) (2000)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer
The Pfam Protein Families Database. Nucleic Acids Res. 28 (1) (2000)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27 (1) (1999)
Sean R. Eddy
Profile hidden Markov models. Bioinform. 14 (9) (1998)
Sean R. Eddy
[Invited Lecture] Genome sequence analysis and profile hidden Markov models. German Conference on Bioinformatics (1998)
Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26 (1) (1998)
Sean R. Eddy
Multiple Alignment Using Hidden Markov Models. ISMB (1995)
Sean R. Eddy, Graeme J. Mitchison, Richard Durbin
Maximum Discrimination Hidden Markov Models of Sequence Consensus. J. Comput. Biol. 2 (1) (1995)
Henry Ellingworth, Sean R. Eddy
RNA structure alignment on a massively parallel computer. HPCN Europe (1995)