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2020 – today
- 2023
[j58]Yekaterina Shulgina
, Sean R. Eddy:
Codetta: predicting the genetic code from nucleotide sequence. Bioinform. 39(1) (2023)- [j57]Samantha Petti, Sean R. Eddy:
Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms. PLoS Comput. Biol. 19(3) (2023) - 2022
- [j56]Samantha Petti, Sean R. Eddy:
Constructing benchmark test sets for biological sequence analysis using independent set algorithms. PLoS Comput. Biol. 18(3) (2022) - 2021
- [j55]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): D192-D200 (2021) - 2020
- [j54]Elena Rivas, Jody Clements, Sean R. Eddy:
Estimating the power of sequence covariation for detecting conserved RNA structure. Bioinform. 36(10): 3072-3076 (2020) - [j53]Grey W. Wilburn, Sean R. Eddy:
Remote homology search with hidden Potts models. PLoS Comput. Biol. 16(11) (2020)
2010 – 2019
- 2019
- [j52]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): D427-D432 (2019) - [j51]Peter K. Koo, Sean R. Eddy:
Representation learning of genomic sequence motifs with convolutional neural networks. PLoS Comput. Biol. 15(12) (2019) - 2018
- [j50]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): D335-D342 (2018) - [j49]Simon C. Potter, Aurelien Luciani, Sean R. Eddy, Young Mi Park, Rodrigo Lopez, Robert D. Finn:
HMMER web server: 2018 update. Nucleic Acids Res. 46(Webserver-Issue): W200-W204 (2018) - 2016
- [j48]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): 81-89 (2016) - [j47]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): 279-285 (2016) - 2015
- [j46]Elena Rivas, Sean R. Eddy:
Parameterizing sequence alignment with an explicit evolutionary model. BMC Bioinform. 16: 406:1-406:23 (2015) - [j45]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): 130-137 (2015) - [j44]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): W30-W38 (2015) - 2014
- [j43]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): 222-230 (2014) - 2013
- [j42]Travis J. Wheeler, Sean R. Eddy:
nhmmer: DNA homology search with profile HMMs. Bioinform. 29(19): 2487-2489 (2013) - [j41]Eric P. Nawrocki, Sean R. Eddy:
Infernal 1.1: 100-fold faster RNA homology searches. Bioinform. 29(22): 2933-2935 (2013) - [j40]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): 70-82 (2013) - [j39]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): 226-232 (2013) - 2012
- [j38]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): 290-301 (2012) - 2011
- [j37]Diana L. Kolbe, Sean R. Eddy:
Fast filtering for RNA homology search. Bioinform. 27(22): 3102-3109 (2011) - [j36]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): 141-145 (2011) - [j35]Robert D. Finn, Jody Clements, Sean R. Eddy:
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39(Web-Server-Issue): 29-37 (2011) - [j34]Sean R. Eddy:
Accelerated Profile HMM Searches. PLoS Comput. Biol. 7(10) (2011) - 2010
- [j33]L. Steven Johnson, Sean R. Eddy, Elon Portugaly:
Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinform. 11: 431 (2010) - [j32]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): 211-222 (2010)
2000 – 2009
- 2009
- [j31]Diana L. Kolbe, Sean R. Eddy:
Local RNA structure alignment with incomplete sequence. Bioinform. 25(10): 1236-1243 (2009) - [j30]Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy:
Infernal 1.0: inference of RNA alignments. Bioinform. 25(10): 1335-1337 (2009) - [j29]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): 1647-1654 (2009) - [j28]Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy:
Infernal 1.0: inference of RNA alignments. Bioinform. 25(13): 1713 (2009) - [j27]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): 136-140 (2009) - 2008
- [j26]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): 281-288 (2008) - [j25]Sean R. Eddy:
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation. PLoS Comput. Biol. 4(5) (2008) - [j24]Elena Rivas, Sean R. Eddy:
Probabilistic Phylogenetic Inference with Insertions and Deletions. PLoS Comput. Biol. 4(9) (2008) - 2007
- [j23]Eric P. Nawrocki, Sean R. Eddy:
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches. PLoS Comput. Biol. 3(3) (2007) - 2006
- [j22]Robin D. Dowell, Sean R. Eddy:
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinform. 7: 400 (2006) - [j21]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): 247-251 (2006) - 2005
- [j20]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): 121-124 (2005) - [j19]Sean R. Eddy:
"Antedisciplinary" Science. PLoS Comput. Biol. 1(1) (2005) - 2004
- [j18]Robin D. Dowell, Sean R. Eddy:
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinform. 5: 71 (2004) - [j17]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): 138-141 (2004) - 2003
- [j16]Robert J. Klein, Sean R. Eddy:
RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinform. 4: 44 (2003) - [j15]Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy:
Rfam: an RNA family database. Nucleic Acids Res. 31(1): 439-441 (2003) - 2002
- [j14]Christian M. Zmasek, Sean R. Eddy:
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinform. 3: 14 (2002) - [j13]Sean R. Eddy:
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinform. 3: 18 (2002) - [j12]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): 276-280 (2002) - 2001
- [j11]Christian M. Zmasek, Sean R. Eddy:
ATV: display and manipulation of annotated phylogenetic. Bioinform. 17(4): 383-384 (2001) - [j10]Christian M. Zmasek, Sean R. Eddy:
A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinform. 17(9): 821-828 (2001) - [j9]Robin D. Dowell, Rodney M. Jokerst, Allen Day, Sean R. Eddy, Lincoln Stein:
The Distributed Annotation System. BMC Bioinform. 2: 7 (2001) - [j8]Elena Rivas, Sean R. Eddy:
Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinform. 2: 8 (2001) - 2000
- [j7]Elena Rivas, Sean R. Eddy:
The language of RNA: a formal grammar that includes pseudoknots. Bioinform. 16(4): 334-340 (2000) - [j6]Elena Rivas, Sean R. Eddy:
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinform. 16(7): 583-605 (2000) - [j5]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): 263-266 (2000)
1990 – 1999
- 1999
- [j4]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): 260-262 (1999) - 1998
- [b1]Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme J. Mitchison:
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998, ISBN 0-521-62971-3 - [j3]Sean R. Eddy:
Profile hidden Markov models. Bioinform. 14(9): 755-763 (1998) - [j2]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): 320-322 (1998) - [c3]Sean R. Eddy:
[Invited Lecture] Genome sequence analysis and profile hidden Markov models. German Conference on Bioinformatics 1998 - 1995
- [j1]Sean R. Eddy, Graeme J. Mitchison, Richard Durbin:
Maximum Discrimination Hidden Markov Models of Sequence Consensus. J. Comput. Biol. 2(1): 9-23 (1995) - [c2]Henry Ellingworth, Sean R. Eddy:
RNA structure alignment on a massively parallel computer. HPCN Europe 1995: 502-507 - [c1]Sean R. Eddy:
Multiple Alignment Using Hidden Markov Models. ISMB 1995: 114-120
Coauthor Index
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