Sean R. Eddy

PLoS Comput. Biol., March, 2023

Codetta: predicting the genetic code from nucleotide sequence.

[BibT_eX]

[DOI]

Yekaterina Shulgina

Bioinform., January, 2023

2022

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

[BibT_eX]

[DOI]

Samantha Petti

PLoS Comput. Biol., 2022

2021

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

[BibT_eX]

[DOI]

Ioanna Kalvari

Nancy Ontiveros-Palacios

Claire Toffano-Nioche

Nucleic Acids Res., 2021

2020

Remote homology search with hidden Potts models.

[BibT_eX]

[DOI]

Grey W. Wilburn

PLoS Comput. Biol., 2020

Estimating the power of sequence covariation for detecting conserved RNA structure.

[BibT_eX]

[DOI]

Jody Clements

Bioinform., 2020

2019

Representation learning of genomic sequence motifs with convolutional neural networks.

[BibT_eX]

[DOI]

Peter K. Koo

PLoS Comput. Biol., 2019

The Pfam protein families database in 2019.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2019

2018

HMMER web server: 2018 update.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2018

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

[BibT_eX]

[DOI]

Ioanna Kalvari

Joanna Argasinska

Natalia Quinones-Olvera

Nucleic Acids Res., 2018

2016

The Dfam database of repetitive DNA families.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2016

The Pfam protein families database: towards a more sustainable future.

[BibT_eX]

[DOI]

Amaia Sangrador-Vegas

Gustavo A. Salazar

John G. Tate

Nucleic Acids Res., 2016

2015

Rfam 12.0: updates to the RNA families database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2015

HMMER web server: 2015 update.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2015

Parameterizing sequence alignment with an explicit evolutionary model.

[BibT_eX]

[DOI]

BMC Bioinform., 2015

2014

Pfam: the protein families database.

[BibT_eX]

[DOI]

John G. Tate

Marco Punta

Nucleic Acids Res., 2014

2013

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

[BibT_eX]

[DOI]

Nucleic Acids Res., 2013

Rfam 11.0: 10 years of RNA families.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2013

nhmmer: DNA homology search with profile HMMs.

[BibT_eX]

[DOI]

Travis J. Wheeler

Bioinform., 2013

Infernal 1.1: 100-fold faster RNA homology searches.

[BibT_eX]

[DOI]

Bioinform., 2013

2012

The Pfam protein families database.

[BibT_eX]

[DOI]

Robert D. Finn

Nucleic Acids Res., 2012

2011

Accelerated Profile HMM Searches.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2011

Rfam: Wikipedia, clans and the "decimal" release.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2011

HMMER web server: interactive sequence similarity searching.

[BibT_eX]

[DOI]

Robert D. Finn

Jody Clements

Nucleic Acids Res., 2011

Fast filtering for RNA homology search.

[BibT_eX]

[DOI]

Diana L. Kolbe

Bioinform., 2011

2010

The Pfam protein families database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2010

Hidden Markov model speed heuristic and iterative HMM search procedure.

[BibT_eX]

[DOI]

L. Steven Johnson

Elon Portugaly

BMC Bioinform., 2010

2009

Rfam: updates to the RNA families database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2009

Infernal 1.0: inference of RNA alignments.

[BibT_eX]

[DOI]

Diana L. Kolbe

Bioinform., 2009

Local RNA structure alignment with incomplete sequence.

[BibT_eX]

[DOI]

Diana L. Kolbe

Bioinform., 2009

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

[BibT_eX]

[DOI]

Fred P. Davis

Bioinform., 2009

2008

Probabilistic Phylogenetic Inference with Insertions and Deletions.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2008

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

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2008

The Pfam protein families database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2008

2007

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

[BibT_eX]

[DOI]

Benjamin Schuster-Böckler

PLoS Comput. Biol., 2007

2006

Pfam: clans, web tools and services.

[BibT_eX]

[DOI]

Robert D. Finn

Jaina Mistry

Nucleic Acids Res., 2006

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.

[BibT_eX]

[DOI]

Robin D. Dowell

BMC Bioinform., 2006

2005

"Antedisciplinary" Science.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2005

Rfam: annotating non-coding RNAs in complete genomes.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2005

2004

The Pfam protein families database.

[BibT_eX]

[DOI]

Lachlan James M. Coin

David J. Studholme

Corin Yeats

Nucleic Acids Res., 2004

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

[BibT_eX]

[DOI]

Robin D. Dowell

BMC Bioinform., 2004

2003

Rfam: an RNA family database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2003

RSEARCH: Finding homologs of single structured RNA sequences.

[BibT_eX]

[DOI]

Robert J. Klein

BMC Bioinform., 2003

2002

The Pfam Protein Families Database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2002

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

[BibT_eX]

[DOI]

Christian M. Zmasek

BMC Bioinform., 2002

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

[BibT_eX]

[DOI]

BMC Bioinform., 2002

2001

Noncoding RNA gene detection using comparative sequence analysis.

[BibT_eX]

[DOI]

BMC Bioinform., 2001

The Distributed Annotation System.

[BibT_eX]

[DOI]

BMC Bioinform., 2001

ATV: display and manipulation of annotated phylogenetic.

[BibT_eX]

[DOI]

Christian M. Zmasek

Bioinform., 2001

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

[BibT_eX]

[DOI]

Christian M. Zmasek

Bioinform., 2001

2000

The Pfam Protein Families Database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2000

The language of RNA: a formal grammar that includes pseudoknots.

[BibT_eX]

[DOI]

Bioinform., 2000

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

[BibT_eX]

[DOI]

Bioinform., 2000

1999

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

[BibT_eX]

[DOI]

Nucleic Acids Res., 1999

1998

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

[BibT_eX]

[DOI]

Nucleic Acids Res., 1998

Profile hidden Markov models.

[BibT_eX]

[DOI]

Bioinform., 1998

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

[BibT_eX]

Proceedings of the German Conference on Bioinformatics, 1998

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

[BibT_eX]

[DOI]

Cambridge University Press, ISBN: 9780511790492, 1998

1995

Maximum Discrimination Hidden Markov Models of Sequence Consensus.

[BibT_eX]

[DOI]

Graeme J. Mitchison

Richard Durbin

J. Comput. Biol., 1995

Multiple Alignment Using Hidden Markov Models.

[BibT_eX]

[DOI]

Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

RNA structure alignment on a massively parallel computer.

[BibT_eX]

[DOI]

Henry Ellingworth