Accelerated Profile HMM Searches von Eddy, Sean R

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Infernal 1.1: 100-fold faster RNA homology searches von Nawrocki, Eric P, Eddy, Sean R

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Hidden Markov model speed heuristic and iterative HMM search procedure von Johnson, L Steven, Eddy, Sean R, Portugaly, Elon

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A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs von Rivas, Elena, Clements, Jody, Eddy, Sean R

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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain von Mo, Alisa, Mukamel, Eran A., Davis, Fred P., Luo, Chongyuan, Henry, Gilbert L., Picard, Serge, Urich, Mark A., Nery, Joseph R., Sejnowski, Terrence J., Lister, Ryan, Eddy, Sean R., Ecker, Joseph R., Nathans, Jeremy

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Many, but not all, lineage-specific genes can be explained by homology detection failure von Weisman, Caroline M., Murray, Andrew W., Eddy, Sean R.

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Mammalian cells repress random DNA that yeast transcribes von Eddy, Sean R.

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Estimating the power of sequence covariation for detecting conserved RNA structure von Rivas, Elena, Clements, Jody, Eddy, Sean R

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The C-value paradox, junk DNA and ENCODE von Eddy, Sean R.

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Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes von Eddy, Sean R

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HMMER web server: interactive sequence similarity searching von Finn, Robert D., Clements, Jody, Eddy, Sean R.

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HMMER web server: 2018 update von Potter, Simon C, Luciani, Aurélien, Eddy, Sean R, Park, Youngmi, Lopez, Rodrigo, Finn, Robert D

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nhmmer: DNA homology search with profile HMMs von Wheeler, Travis J, Eddy, Sean R

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Representation learning of genomic sequence motifs with convolutional neural networks von Koo, Peter K, Eddy, Sean R

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

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions von Mistry, Jaina, Finn, Robert D, Eddy, Sean R, Bateman, Alex, Punta, Marco

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A probabilistic model of local sequence alignment that simplifies statistical significance estimation von Eddy, Sean R

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Constructing benchmark test sets for biological sequence analysis using independent set algorithms von Petti, Samantha, Eddy, Sean R

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Remote homology search with hidden Potts models von Wilburn, Grey W., Eddy, Sean R.

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Rfam 14: expanded coverage of metagenomic, viral and microRNA families von Kalvari, Ioanna, Nawrocki, Eric P, Ontiveros-Palacios, Nancy, Argasinska, Joanna, Lamkiewicz, Kevin, Marz, Manja, Griffiths-Jones, Sam, Toffano-Nioche, Claire, Gautheret, Daniel, Weinberg, Zasha, Rivas, Elena, Eddy, Sean R, Finn, Robert D, Bateman, Alex, Petrov, Anton I

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