Sean R. Eddy - RankMe

63 papers A 1Journal 59Unranked 2

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