Sean R. Eddy

发表

Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs

Elena Rivas, Sean R. Eddy, S. Eddy, 2000, Bioinform..

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

Sean R. Eddy, Robin D. Dowell, S. Eddy, 2004, BMC Bioinformatics.

A genetic, genomic, and computational resource for exploring neural circuit function

Sean R. Eddy, Michael B. Reiser, Fred P. Davis, 2018, bioRxiv.

Profile hidden Markov models

Sean R. Eddy, S. Eddy, 1998, Bioinform..

A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas

Sean R. Eddy, Fred P. Davis, S. Eddy, 2009, Bioinform..

Rfam 12.0: updates to the RNA families database

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2014, Nucleic Acids Res..

Rfam: updates to the RNA families database

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2008, Nucleic Acids Res..

Remote homology search with hidden Potts models

Sean R. Eddy, Grey W. Wilburn, S. Eddy, 2020, bioRxiv.

HMMER web server: interactive sequence similarity searching

Robert D. Finn, Sean R. Eddy, Jody Clements, 2011, Nucleic Acids Res..

Rfam: Wikipedia, clans and the “decimal” release

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2010, Nucleic Acids Res..

The Pfam Protein Families Database

Sean R. Eddy, Ewan Birney, Erik L. L. Sonnhammer, 2002, Nucleic Acids Res..

Representation learning of genomic sequence motifs with convolutional neural networks

Sean R. Eddy, Peter K. Koo, Peter K. Koo, 2018, bioRxiv.

HMMER web server: 2018 update

Robert D. Finn, Sean R. Eddy, Rodrigo Lopez, 2018, Nucleic Acids Res..

The Pfam protein families database

Robert D. Finn, Sean R. Eddy, Stephen John Sammut, 2007, Nucleic Acids Res..

Multiple alignment and multiple sequence based searches

Sean R. Eddy, 1998 .

ATV: display and manipulation of annotated phylogenetic

Sean R. Eddy, Christian M. Zmasek, S. Eddy, 2001, Bioinform..

Probabilistic Phylogenetic Inference with Insertions and Deletions

Elena Rivas, Sean R. Eddy, S. Eddy, 2008, PLoS Comput. Biol..

The Pfam protein families database

Robert D. Finn, Sean R. Eddy, Lachlan James M. Coin, 2004, Nucleic Acids Res..

Accelerated Profile HMM Searches

Sean R. Eddy, S. Eddy, 2011, PLoS Comput. Biol..

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

Robert D. Finn, Elena Rivas, Sean R. Eddy, 2017, Nucleic Acids Res..

The Pfam protein families database

Robert D. Finn, Sean R. Eddy, Liisa Holm, 2014, Nucleic Acids Res..

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

Robert D. Finn, Sean R. Eddy, Alex Bateman, 1999, Nucleic Acids Res..

Multiple Alignment Using Hidden Markov Models

Sean R. Eddy, S. Eddy, 1995, ISMB.

Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks

Sean R. Eddy, Peter K. Koo, Praveen Anand, 2018, bioRxiv.

RSEARCH: Finding homologs of single structured RNA sequences

Sean R. Eddy, Robert J. Klein, S. Eddy, 2003, BMC Bioinformatics.

The Distributed Annotation System

Sean R. Eddy, Lincoln Stein, Robin D. Dowell, 2001, BMC Bioinformatics.

[Invited Lecture] Genome sequence analysis and profile hidden Markov models

Sean R. Eddy, S. Eddy, 1998, German Conference on Bioinformatics.

Dfam: a database of repetitive DNA based on profile hidden Markov models

Robert D. Finn, Sean R. Eddy, Thomas A. Jones, 2012, Nucleic Acids Res..

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Query-Dependent Banding (QDB) for Faster RNA Similarity Searches

Sean R. Eddy, Eric P. Nawrocki, S. Eddy, 2007, PLoS Comput. Biol..

Biological sequence analysis: Multiple sequence alignment methods

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

The Dfam database of repetitive DNA families

Robert D. Finn, Sean R. Eddy, Weidong Bao, 2015, Nucleic Acids Res..

Parameterizing sequence alignment with an explicit evolutionary model

Elena Rivas, Sean R. Eddy, S. Eddy, 2015, BMC Bioinformatics.

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

Sean R. Eddy, S. Eddy, 2002, BMC Bioinformatics.

Biological sequence analysis: RNA structure analysis

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Biological sequence analysis: Transformational grammars

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

“Antedisciplinary” Science

Sean R. Eddy, S. Eddy, 2005, PLoS Comput. Biol..

Biological sequence analysis: Contents

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Maximum Discrimination Hidden Markov Models of Sequence Consensus

Sean R. Eddy, Richard Durbin, Graeme J. Mitchison, 1995, J. Comput. Biol..

The Pfam protein families database in 2019

Silvio C. E. Tosatto, Robert D. Finn, Sean R. Eddy, 2018, Nucleic Acids Res..

HMMER web server: 2015 update

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2015, Nucleic Acids Res..

The Pfam protein families database

Sean R. Eddy, Ewan Birney, Erik L. L. Sonnhammer, 2007, Nucleic Acids Res..

Infernal 1.1: 100-fold faster RNA homology searches

Sean R. Eddy, Eric P. Nawrocki, S. Eddy, 2013, Bioinform..

Fast filtering for RNA homology search

Sean R. Eddy, Diana L. Kolbe, S. Eddy, 2011, Bioinform..

Hidden Markov model speed heuristic and iterative HMM search procedure

Sean R. Eddy, Elon Portugaly, Steve L. Johnson, 2010, BMC Bioinformatics.

Rfam: annotating non-coding RNAs in complete genomes

Sean R. Eddy, Alex Bateman, Sam Griffiths-Jones, 2004, Nucleic Acids Res..

Pfam: clans, web tools and services

Robert D. Finn, Sean R. Eddy, Alex Bateman, 2005, Nucleic Acids Res..

Local RNA structure alignment with incomplete sequence

Sean R. Eddy, Diana L. Kolbe, S. Eddy, 2009, Bioinform..

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

Sean R. Eddy, S. Eddy, 2008, PLoS Comput. Biol..

RNA structure alignment on a massively parallel computer

Sean R. Eddy, Henry Ellingworth, S. Eddy, 1995, HPCN Europe.

Infernal 1.0: inference of RNA alignments

Sean R. Eddy, Eric P. Nawrocki, Diana L. Kolbe, 2009, Bioinform..

Rfam: an RNA family database

Sean R. Eddy, Sam Griffiths-Jones, Alex Bateman, 2003, Nucleic Acids Res..

The language of RNA: a formal grammar that includes pseudoknots

Elena Rivas, Sean R. Eddy, S. Eddy, 2000, Bioinform..

Estimating the power of sequence covariation for detecting conserved RNA structure

Sean R. Eddy, Jody Clements, Elena Rivas, 2019, bioRxiv.

Pfam: multiple sequence alignments and HMM-profiles of protein domains

Sean R. Eddy, Alex Bateman, Ewan Birney, 1998, Nucleic Acids Res..

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

Sean R. Eddy, Robin D. Dowell, S. Eddy, 2006, BMC Bioinformatics.

A simple algorithm to infer gene duplication and speciation events on a gene tree

Sean R. Eddy, Christian M. Zmasek, S. Eddy, 2001, Bioinform..

The Pfam protein families database: towards a more sustainable future

Robert D. Finn, Sean R. Eddy, Marco Punta, 2015, Nucleic Acids Res..

Noncoding RNA gene detection using comparative sequence analysis

Elena Rivas, Sean R. Eddy, S. Eddy, 2001, BMC Bioinformatics.

Infernal 1.0: inference of RNA alignments

Sean R. Eddy, Eric P. Nawrocki, Diana L. Kolbe, 2009, Bioinform..

nhmmer: DNA homology search with profile HMMs

Sean R. Eddy, Travis J. Wheeler, S. Eddy, 2013, Bioinform..

Inside the black boxes Computer methods for macromolecular sequence analysis (Methods in enzymology vol. 266)

Sean R. Eddy, S. Eddy, 1997 .

RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

Sean R. Eddy, Christian M. Zmasek, S. Eddy, 2002, BMC Bioinformatics.

A genetic, genomic, and computational resource for exploring neural circuit function

Sean R. Eddy, Michael B. Reiser, Fred P. Davis, 2018, bioRxiv.

Rfam 11.0: 10 years of RNA families

Sean R. Eddy, Alex Bateman, Ruth Y. Eberhardt, 2012, Nucleic Acids Res..

Biological sequence analysis: Preface

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Pack-MULE transposable elements mediate gene evolution in plants

Sean R. Eddy, Zhirong Bao, Ning Jiang, 2004, Nature.

Biological sequence analysis: Building phylogenetic trees

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

HMMER User's Guide - Biological sequence analysis using profile hidden Markov models

Sean R. Eddy, S. Eddy, 1998 .

Computational identification of functional RNA homologs in metagenomic data

Sean R. Eddy, Eric P. Nawrocki, S. Eddy, 2013, RNA biology.

Rna structural alignment using stochastic context-free grammars

Sean R. Eddy, Robin D. Dowell, 2004 .

An active DNA transposon family in rice

Sean R. Eddy, Zhirong Bao, Hirohiko Hirochika, 2003, Nature.

Biological sequence analysis: Pairwise alignment

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Terrence S. Furey, Sean R. Eddy, Li Ding, 2005, Nature.

Response to Tavares et al., “Covariation analysis with improved parameters reveals conservation in lncRNA structures”

Sean R. Eddy, Elena Rivas, S. Eddy, 2020, bioRxiv.

Total Information Awareness for Worm Genetics

Sean R. Eddy, S. Eddy, 2006, Science.

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Terrence J. Sejnowski, Sean R. Eddy, Fred P. Davis, 2015, Neuron.

Biological sequence analysis: Pairwise alignment using HMMs

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Biological sequence analysis: Markov chains and hidden Markov models

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

19 RNA: The Shape of Things to Come

Sean R. Eddy, Dan Schneider, Larry Gold, 1993 .

Biological sequence analysis: Probabilistic approaches to phylogeny

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .

Biological Sequence Analysis by Richard Durbin

Sean R. Eddy, Anders Krogh, Richard Durbin, 1998 .