Estimating the Accuracy of Learned Concepts. - Timothy L. Bailey; Charles Elkan (IJCAI, 1993)

Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer. - Timothy L. Bailey; Charles Elkan (ISMB, 1994)

The Value of Prior Knowledge in Discovering Motifs with MEME. - Timothy L. Bailey; Charles Elkan (ISMB, 1995)

Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. - Timothy L. Bailey; Charles Elkan (Mach. Learn., 1995)

The Megaprior Heuristic for Discovering Protein Sequence Patterns. - Timothy L. Bailey; Michael Gribskov (ISMB, 1996)

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. - William Noble Grundy; Timothy L. Bailey; Charles Elkan (Comput. Appl. Biosci., 1996)

Meta-MEME: motif-based hidden Markov models of protein families. - William Noble Grundy; Timothy L. Bailey; Charles Elkan; Michael E. Baker (Comput. Appl. Biosci., 1997)

Score Distributions for Simultaneous Matching to Multiple Motifs. - Timothy L. Bailey; Michael Gribskov (J. Comput. Biol., 1997)

Combining evidence using p-values: application to sequence homology searches. - Timothy L. Bailey; Michael Gribskov (Bioinform., 1998)

Methods and Statistics for Combining Motif Match Scores. - Timothy L. Bailey; Michael Gribskov (J. Comput. Biol., 1998)

MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences. - Timothy L. Bailey; Michael E. Baker; Charles Elkan; William Noble Grundy (Pattern Discovery in Biomolecular Data, 1999)

Classifying proteins by family using the product of correlated p-values. - Timothy L. Bailey; William Noble Grundy (RECOMB, 1999)

Family pairwise search with embedded motif models. - William Noble Grundy; Timothy L. Bailey (Bioinform., 1999)

Concerning the accuracy of MAST E-values. - Timothy L. Bailey; Michael Gribskov (Bioinform., 2000)

Searching for statistically significant regulatory modules. - Timothy L. Bailey; William Stafford Noble (ECCB, 2003)

Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores. - Timothy L. Bailey; Michael Gribskov (J. Comput. Biol., 2003)

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. - Mikael Bodén; Timothy L. Bailey (Bioinform., 2006)

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. - Mikael Bodén; Zheng Yuan; Timothy L. Bailey (BMC Bioinform., 2006)

GONOME: measuring correlations between GO terms and genomic positions. - Stefan M. Stanley; Timothy L. Bailey; John S. Mattick (BMC Bioinform., 2006)

MEME: discovering and analyzing DNA and protein sequence motifs. - Timothy L. Bailey; Nadya Williams; Chris Misleh; Wilfred W. Li (Nucleic Acids Res., 2006)

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. - Emma Redhead; Timothy L. Bailey (BMC Bioinform., 2007)

The Statistical Power of Phylogenetic Motif Models. - John Hawkins; Timothy L. Bailey (RECOMB, 2008)

STREAM: Static Thermodynamic REgulAtory Model of transcription. - Denis C. Bauer; Timothy L. Bailey (Bioinform., 2008)

Studying the functional conservation of cis-regulatory modules and their transcriptional output. - Denis C. Bauer; Timothy L. Bailey (BMC Bioinform., 2008)

Discovering Sequence Motifs with Arbitrary Insertions and Deletions. - Martin C. Frith; Neil F. W. Saunders; Bostjan Kobe; Timothy L. Bailey (PLoS Comput. Biol., 2008)

Optimizing static thermodynamic models of transcriptional regulation. - Denis C. Bauer; Timothy L. Bailey (Bioinform., 2009)

Assessing phylogenetic motif models for predicting transcription factor binding sites. - John Hawkins; Charles E. Grant; William Stafford Noble; Timothy L. Bailey (Bioinform., 2009)

MEME SUITE: tools for motif discovery and searching. - Timothy L. Bailey; Mikael Bodén; Fabian A. Buske; Martin C. Frith; Charles E. Grant; Luca Clementi; Jingyuan Ren; Wilfred W. Li; William Stafford Noble (Nucleic Acids Res., 2009)

Improved prediction of transcription binding sites from chromatin modification data. - Kengo Sato; Tom Whitington; Timothy L. Bailey; Paul Horton (CIBCB, 2010)

Assigning roles to DNA regulatory motifs using comparative genomics. - Fabian A. Buske; Mikael Bodén; Denis C. Bauer; Timothy L. Bailey (Bioinform., 2010)

The value of position-specific priors in motif discovery using MEME. - Timothy L. Bailey; Mikael Bodén; Tom Whitington; Philip Machanick (BMC Bioinform., 2010)

Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. - Denis C. Bauer; Fabian A. Buske; Timothy L. Bailey (BMC Bioinform., 2010)

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. - Robert C. McLeay; Timothy L. Bailey (BMC Bioinform., 2010)

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. - Denis C. Bauer; Fabian A. Buske; Timothy L. Bailey; Mikael Bodén (Neurocomputing, 2010)

A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies. - Mikael Bodén; Graham Dellaire; Kevin Burrage; Timothy L. Bailey (J. Comput. Biol., 2010)

DREME: motif discovery in transcription factor ChIP-seq data. - Timothy L. Bailey (Bioinform., 2011)

Sorting the nuclear proteome. - Denis C. Bauer; Kai Willadsen; Fabian A. Buske; Kim-Anh Lê Cao; Timothy L. Bailey; Graham Dellaire; Mikael Bodén (Bioinform., 2011)

FIMO: scanning for occurrences of a given motif. - Charles E. Grant; Timothy L. Bailey; William Stafford Noble (Bioinform., 2011)

MEME-ChIP: motif analysis of large DNA datasets. - Philip Machanick; Timothy L. Bailey (Bioinform., 2011)

Tissue-specific prediction of directly regulated genes. - Robert C. McLeay; Chris J. Leat; Timothy L. Bailey (Bioinform., 2011)

A probabilistic model of nuclear import of proteins. - Ahmed M. Mehdi; Muhammad Shoaib B. Sehgal; Bostjan Kobe; Timothy L. Bailey; Mikael Bodén (Bioinform., 2011)

Improved similarity scores for comparing motifs. - Emi Tanaka; Timothy L. Bailey; Charles E. Grant; William Stafford Noble; Uri Keich (Bioinform., 2011)

Epigenetic priors for identifying active transcription factor binding sites. - Gabriel Cuéllar-Partida; Fabian A. Buske; Robert C. McLeay; Tom Whitington; William Stafford Noble; Timothy L. Bailey (Bioinform., 2012)

Genome-wide in silico prediction of gene expression. - Robert C. McLeay; Tom Lesluyes; Gabriel Cuéllar-Partida; Timothy L. Bailey (Bioinform., 2012)

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. - Lei Sun; Zhihua Zhang 007; Timothy L. Bailey; Andrew C. Perkins; Michael R. Tallack; Zhao Xu; Hui Liu (BMC Bioinform., 2012)

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci. - Fabian A. Buske; Denis C. Bauer; John S. Mattick; Timothy L. Bailey (Bioinform., 2013)

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. - Ahmed M. Mehdi; Muhammad Shoaib B. Sehgal; Bostjan Kobe; Timothy L. Bailey; Mikael Bodén (Bioinform., 2013)

GT-Scan: identifying unique genomic targets. - Aidan O'Brien; Timothy L. Bailey (Bioinform., 2014)

Improving MEME via a two-tiered significance analysis. - Emi Tanaka; Timothy L. Bailey; Uri Keich (Bioinform., 2014)

The MEME Suite. - Timothy L. Bailey; James Johnson; Charles E. Grant; William S. Noble (Nucleic Acids Res., 2015)

MCAST: scanning for cis-regulatory motif clusters. - Charles E. Grant; James Johnson; Timothy L. Bailey; William Stafford Noble (Bioinform., 2016)

MoMo: discovery of statistically significant post-translational modification motifs. - Alice Cheng; Charles E. Grant; William S. Noble; Timothy L. Bailey (Bioinform., 2019)

T-Gene: improved target gene prediction. - Timothy O'Connor; Charles E. Grant; Mikael Bodén; Timothy L. Bailey (Bioinform., 2020)

STREME: accurate and versatile sequence motif discovery. - Timothy L. Bailey (Bioinform., 2021)