Search filters

List of works by Sean Eddy

"Antedisciplinary" science

scientific article

A computational screen for alternative genetic codes in over 250,000 genomes

scientific article published on 9 November 2021

A dynamic programming algorithm for RNA structure prediction including pseudoknots

scientific article

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

scientific article published on 15 January 2020

A member of the immunoglobulin superfamily in bacteriophage T4

scientific article published in 1997

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

scientific article published on 2 July 2002

A model of the statistical power of comparative genome sequence analysis

scientific article

A new generation of homology search tools based on probabilistic inference

scientific article (publication date: October 2009)

A probabilistic model of local sequence alignment that simplifies statistical significance estimation

scientific article published in May 2008

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

scientific article (publication date: February 2012)

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

scientific article published in September 2001

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

scientific article published on 7 November 2016

A survey of nematode SmY RNAs

scientific article

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

scientific article

A uniform system for microRNA annotation

scientific article

ATV: display and manipulation of annotated phylogenetic trees

scientific article

Accelerated Profile HMM Searches ⬇️

scientific article (publication date: October 2011)

Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns

scientific article published on October 1994

An active DNA transposon family in rice

scientific article published on January 2003

Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus

scientific article

Artificial mobile DNA element constructed from the EcoRI endonuclease gene

scientific article published on March 1992

Autogenous translational operator recognized by bacteriophage T4 DNA polymerase

scientific article

Automated de novo identification of repeat sequence families in sequenced genomes

scientific article (publication date: August 2002)

C. elegans noncoding RNA genes

scientific article

Cell type-specific genomics of Drosophila neurons

scientific article

Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice

scientific article published on 26 August 2024

Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans.

scientific article

Circular box C/D RNAs in Pyrococcus furiosus

scholarly article

Codetta: predicting the genetic code from nucleotide sequence

scientific article published in January 2023

Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates

scientific article published on 2 September 2015

Computational analysis of RNAs

scientific article published in January 2006

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes

scientific article published on January 2014

Computational genomics of noncoding RNA genes

scientific article

Computational identification of functional RNA homologs in metagenomic data

scientific article

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics

scientific article

Computational identification of noncoding RNAs in E. coli by comparative genomics

scientific article (publication date: 4 September 2001)

Constructing benchmark test sets for biological sequence analysis using independent set algorithms

scientific article published on 07 March 2022

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

scientific article (publication date: 2013)

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

scientific article

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

scientific article published on June 2015

Epigenomic landscapes of retinal rods and cones

scientific article

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

scientific article

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

scientific article

Fast filtering for RNA homology search

scientific article (publication date: 15 November 2011)

Free circular introns with an unusual branchpoint in neuronal projections

scientific article published on 07 November 2019

GENETICS: Total Information Awareness for Worm Genetics

scientific article published in Science

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

scientific article

Genome maps. VI. Caenorhabditis elegans. Wall chart

scientific article

Group I introns are widespread in archaea

article published in 2018

HMMER web server: 2015 update

scientific article published on 5 May 2015

HMMER web server: 2018 update.

scientific article published in July 2018

HMMER web server: interactive sequence similarity searching ⬇️

scientific article published on May 18, 2011

Hidden Markov model speed heuristic and iterative HMM search procedure

scientific article

Hidden Markov models

scientific article (publication date: June 1996)

Homologs of small nucleolar RNAs in Archaea

scientific article (publication date: 21 April 2000)

Homology searches for structural RNAs: from proof of principle to practical use.

scientific article published on April 2015

How do RNA folding algorithms work?

scientific article

Infernal 1.0: inference of RNA alignments

scientific article

Infernal 1.0: inference of RNA alignments

scientific article published on 15 June 2009

Infernal 1.1: 100-fold faster RNA homology searches

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes

scientific article

Local RNA structure alignment with incomplete sequence

scientific article published on 20 March 2009

Many, but not all, lineage-specific genes can be explained by homology detection failure

scientific article published on 02 November 2020

Maximum discrimination hidden Markov models of sequence consensus

scientific article

Multiple alignment using hidden Markov models

scientific article published on January 1, 1995

Noncoding RNA gene detection using comparative sequence analysis

scientific article

Noncoding RNA genes

scientific article

Noncoding RNA genes identified in AT-rich hyperthermophiles

scientific article

Non–coding RNA genes and the modern RNA world ⬇️

scientific article published on December 1, 2001

Open Revolution.

scientific article published on 24 March 2009

Pack-MULE transposable elements mediate gene evolution in plants

scientific article published on September 2004

Pfam: clans, web tools and services

scientific article

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

scientific article published in January 1998

Pfam: the protein families database

scientific article (publication date: 2014)

Prepublication data sharing

scientific article

Probabilistic phylogenetic inference with insertions and deletions

scientific article

Profile hidden Markov models

scientific article (publication date: 1998)

Query-dependent banding (QDB) for faster RNA similarity searches

scientific article

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

scientific article

RNA sequence analysis using covariance models

scientific article

RSEARCH: finding homologs of single structured RNA sequences

scientific article

Remote homology search with hidden Potts models

scientific article published on 30 November 2020

Representation learning of genomic sequence motifs with convolutional neural networks

scientific article published on 19 December 2019

Rfam 11.0: 10 years of RNA families

scientific article

Rfam 12.0: updates to the RNA families database

scientific article

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

scientific article published on 3 November 2017

Rfam: Wikipedia, clans and the "decimal" release

scientific article

Rfam: an RNA family database

scientific article

Rfam: annotating non-coding RNAs in complete genomes

scientific article

Rfam: updates to the RNA families database

scientific article

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

scientific article published in July 2000

Sharing publication-related data and materials: responsibilities of authorship in the life sciences

scientific article

The C-value paradox, junk DNA and ENCODE ⬇️

scientific article published on November 6, 2012

The DNA sequence of human chromosome 7

scientific article

The Dfam database of repetitive DNA families

scientific article

The ENCODE project: missteps overshadowing a success

scientific article published in April 2013

The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

scientific article

The Pfam protein families database

scientific article (publication date: 2004)

The Pfam protein families database

scientific article (publication date: 2012)

The Pfam protein families database

scientific article (published 2010-01-01)

The Pfam protein families database ⬇️

scientific article

The Pfam protein families database

scientific article (publication date: 2002)

The Pfam protein families database in 2019

scholarly article by Sara El-Gebali et al published 24 October 2018 in Nucleic Acids Research

The Pfam protein families database.

scientific article

The Pfam protein families database: towards a more sustainable future

scientific article

The distributed annotation system

scientific article

The language of RNA: a formal grammar that includes pseudoknots

scientific article published in April 2000

The phage T4 nrdB intron: a deletion mutant of a version found in the wild

scientific article

Transcription factors that convert adult cell identity are differentially polycomb repressed

scientific article

Unrestricted free access works and must continue

scientific article published in Nature

What is Bayesian statistics?

scientific article published in September 2004

What is a hidden Markov model?

scientific article

What is dynamic programming?

Where did the BLOSUM62 alignment score matrix come from?

scientific article

nhmmer: DNA homology search with profile HMMs ⬇️

scientific article (publication date: October 2013)

Paulina is supported by:

About Paulina

Help