Timothy L. Bailey

Bioinform., 2021

2020

T-Gene: improved target gene prediction.

[BibT_eX]

[DOI]

Bioinform., 2020

2019

MoMo: discovery of statistically significant post-translational modification motifs.

[BibT_eX]

[DOI]

Bioinform., 2019

2016

MCAST: scanning for cis-regulatory motif clusters.

[BibT_eX]

[DOI]

James Johnson

Bioinform., 2016

2015

The MEME Suite.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2015

2014

Improving MEME via a two-tiered significance analysis.

[BibT_eX]

[DOI]

Emi Tanaka

Uri Keich

Bioinform., 2014

GT-Scan: identifying unique genomic targets.

[BibT_eX]

[DOI]

Aidan O'Brien

Muhammad Shoaib B. Sehgal

Bioinform., 2014

2013

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.

[BibT_eX]

[DOI]

Ahmed M. Mehdi

Bostjan Kobe

Bioinform., 2013

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

[BibT_eX]

[DOI]

Bioinform., 2013

2012

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Genome-wide in silico prediction of gene expression.

[BibT_eX]

[DOI]

Tom Lesluyes

Gabriel Cuéllar-Partida

Bioinform., 2012

Epigenetic priors for identifying active transcription factor binding sites.

[BibT_eX]

[DOI]

Gabriel Cuéllar-Partida

Fabian A. Buske

Tom Whitington

Bioinform., 2012

2011

Improved similarity scores for comparing motifs.

[BibT_eX]

[DOI]

Emi Tanaka

Muhammad Shoaib B. Sehgal

Uri Keich

Bioinform., 2011

A probabilistic model of nuclear import of proteins.

[BibT_eX]

[DOI]

Ahmed M. Mehdi

Bostjan Kobe

Bioinform., 2011

Tissue-specific prediction of directly regulated genes.

[BibT_eX]

[DOI]

Chris J. Leat

Bioinform., 2011

MEME-ChIP: motif analysis of large DNA datasets.

[BibT_eX]

[DOI]

Philip Machanick

Bioinform., 2011

FIMO: scanning for occurrences of a given motif.

[BibT_eX]

[DOI]

Bioinform., 2011

Sorting the nuclear proteome.

[BibT_eX]

[DOI]

Bioinform., 2011

DREME: motif discovery in transcription factor ChIP-seq data.

[BibT_eX]

[DOI]

Bioinform., 2011

2010

A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies.

[BibT_eX]

[DOI]

J. Comput. Biol., 2010

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster.

[BibT_eX]

[DOI]

Neurocomputing, 2010

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster.

[BibT_eX]

[DOI]

Fabian A. Buske

BMC Bioinform., 2010

The value of position-specific priors in motif discovery using MEME.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Assigning roles to DNA regulatory motifs using comparative genomics.

[BibT_eX]

[DOI]

Bioinform., 2010

Improved prediction of transcription binding sites from chromatin modification data.

[BibT_eX]

[DOI]

Proceedings of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2010

2009

MEME SUITE: tools for motif discovery and searching.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2009

Assessing phylogenetic motif models for predicting transcription factor binding sites.

[BibT_eX]

[DOI]

John Hawkins

Bioinform., 2009

Optimizing static thermodynamic models of transcriptional regulation.

[BibT_eX]

[DOI]

Bioinform., 2009

2008

Discovering Sequence Motifs with Arbitrary Insertions and Deletions.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2008

Studying the functional conservation of cis-regulatory modules and their transcriptional output.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

STREAM: Static Thermodynamic REgulAtory Model of transcription.

[BibT_eX]

[DOI]

Bioinform., 2008

The Statistical Power of Phylogenetic Motif Models.

[BibT_eX]

[DOI]

John Hawkins

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

[BibT_eX]

[DOI]

Emma Redhead

BMC Bioinform., 2007

2006

MEME: discovering and analyzing DNA and protein sequence motifs.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2006

GONOME: measuring correlations between GO terms and genomic positions.

[BibT_eX]

[DOI]

Stefan M. Stanley

John S. Mattick

BMC Bioinform., 2006

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures.

[BibT_eX]

[DOI]

Zheng Yuan

BMC Bioinform., 2006

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure.

[BibT_eX]

[DOI]

Bioinform., 2006

2003

Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores.

[BibT_eX]

[DOI]

J. Comput. Biol., 2003

Searching for statistically significant regulatory modules.

[BibT_eX]

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2000

Concerning the accuracy of MAST E-values.

[BibT_eX]

[DOI]

Bioinform., 2000

1999

Family pairwise search with embedded motif models.

[BibT_eX]

[DOI]

William Noble Grundy

Bioinform., 1999

Classifying proteins by family using the product of correlated p-values.

[BibT_eX]

[DOI]

William Noble Grundy

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences.

[BibT_eX]

Proceedings of the Pattern Discovery in Biomolecular Data: Tools, 1999

1998

Methods and Statistics for Combining Motif Match Scores.

[BibT_eX]

[DOI]

J. Comput. Biol., 1998

Combining evidence using p-values: application to sequence homology searches.

[BibT_eX]

[DOI]

Bioinform., 1998

1997

Score Distributions for Simultaneous Matching to Multiple Motifs.

[BibT_eX]

[DOI]

J. Comput. Biol., 1997

Meta-MEME: motif-based hidden Markov models of protein families.

[BibT_eX]

[DOI]

Comput. Appl. Biosci., 1997

1996

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.

[BibT_eX]

[DOI]

William Noble Grundy

Comput. Appl. Biosci., 1996

The Megaprior Heuristic for Discovering Protein Sequence Patterns.

[BibT_eX]

[DOI]

Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

1995

Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization.

[BibT_eX]

[DOI]

Mach. Learn., 1995

The Value of Prior Knowledge in Discovering Motifs with MEME.

[BibT_eX]

[DOI]

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

1994

Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer.

[BibT_eX]

[DOI]

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

1993

Estimating the Accuracy of Learned Concepts.

[BibT_eX]

[DOI]