Timothy L. Bailey

Publication Activity (10 Years)

Years Active: 1993-2021
Publications (10 Years): 5

Top Topics

Pearson Correlation

Motif Discovery

Top Venues

Nucleic Acids Res.

Publications

Timothy L. Bailey
STREME: accurate and versatile sequence motif discovery. Bioinform. 37 (18) (2021)
Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey
T-Gene: improved target gene prediction. Bioinform. 36 (12) (2020)
Alice Cheng, Charles E. Grant, William S. Noble, Timothy L. Bailey
MoMo: discovery of statistically significant post-translational modification motifs. Bioinform. 35 (16) (2019)
Charles E. Grant, James Johnson, Timothy L. Bailey, William Stafford Noble
-regulatory motif clusters. Bioinform. 32 (8) (2016)
Timothy L. Bailey, James Johnson, Charles E. Grant, William S. Noble
The MEME Suite. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Aidan O'Brien, Timothy L. Bailey
GT-Scan: identifying unique genomic targets. Bioinform. 30 (18) (2014)
Emi Tanaka, Timothy L. Bailey, Uri Keich
Improving MEME via a two-tiered significance analysis. Bioinform. 30 (14) (2014)
Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. Bioinform. 29 (1) (2013)
Fabian A. Buske, Denis C. Bauer, John S. Mattick, Timothy L. Bailey
Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci. Bioinform. 29 (15) (2013)
Lei Sun, Zhihua Zhang, Timothy L. Bailey, Andrew C. Perkins, Michael R. Tallack, Zhao Xu, Hui Liu
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. BMC Bioinform. 13 (2012)
Gabriel Cuéllar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey
Epigenetic priors for identifying active transcription factor binding sites. Bioinform. 28 (1) (2012)
Robert C. McLeay, Tom Lesluyes, Gabriel Cuéllar-Partida, Timothy L. Bailey
prediction of gene expression. Bioinform. 28 (21) (2012)
Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble, Uri Keich
Improved similarity scores for comparing motifs. Bioinform. 27 (12) (2011)
Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén
A probabilistic model of nuclear import of proteins. Bioinform. 27 (9) (2011)
Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire, Mikael Bodén
Sorting the nuclear proteome. Bioinform. 27 (13) (2011)
Robert C. McLeay, Chris J. Leat, Timothy L. Bailey
Tissue-specific prediction of directly regulated genes. Bioinform. 27 (17) (2011)
Timothy L. Bailey
DREME: motif discovery in transcription factor ChIP-seq data. Bioinform. 27 (12) (2011)
Charles E. Grant, Timothy L. Bailey, William Stafford Noble
FIMO: scanning for occurrences of a given motif. Bioinform. 27 (7) (2011)
Philip Machanick, Timothy L. Bailey
MEME-ChIP: motif analysis of large DNA datasets. Bioinform. 27 (12) (2011)
Mikael Bodén, Graham Dellaire, Kevin Burrage, Timothy L. Bailey
A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies. J. Comput. Biol. 17 (4) (2010)
Timothy L. Bailey, Mikael Bodén, Tom Whitington, Philip Machanick
The value of position-specific priors in motif discovery using MEME. BMC Bioinform. 11 (2010)
Kengo Sato, Tom Whitington, Timothy L. Bailey, Paul Horton
Improved prediction of transcription binding sites from chromatin modification data. CIBCB (2010)
Denis C. Bauer, Fabian A. Buske, Timothy L. Bailey, Mikael Bodén
Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. Neurocomputing 73 (13-15) (2010)
Denis C. Bauer, Fabian A. Buske, Timothy L. Bailey
. BMC Bioinform. 11 (2010)
Fabian A. Buske, Mikael Bodén, Denis C. Bauer, Timothy L. Bailey
Assigning roles to DNA regulatory motifs using comparative genomics. Bioinform. 26 (7) (2010)
Robert C. McLeay, Timothy L. Bailey
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinform. 11 (2010)
Denis C. Bauer, Timothy L. Bailey
Optimizing static thermodynamic models of transcriptional regulation. Bioinform. 25 (13) (2009)
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin C. Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William Stafford Noble
MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
John Hawkins, Charles E. Grant, William Stafford Noble, Timothy L. Bailey
Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinform. 25 (12) (2009)
Denis C. Bauer, Timothy L. Bailey
Studying the functional conservation of cis-regulatory modules and their transcriptional output. BMC Bioinform. 9 (2008)
Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey
Discovering Sequence Motifs with Arbitrary Insertions and Deletions. PLoS Comput. Biol. 4 (5) (2008)
Denis C. Bauer, Timothy L. Bailey
STREAM: Static Thermodynamic REgulAtory Model of transcription. Bioinform. 24 (21) (2008)
John Hawkins, Timothy L. Bailey
The Statistical Power of Phylogenetic Motif Models. RECOMB (2008)
Emma Redhead, Timothy L. Bailey
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinform. 8 (2007)
Stefan M. Stanley, Timothy L. Bailey, John S. Mattick
GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinform. 7 (2006)
Timothy L. Bailey, Nadya Williams, Chris Misleh, Wilfred W. Li
MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Mikael Bodén, Timothy L. Bailey
Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinform. 22 (15) (2006)
Mikael Bodén, Zheng Yuan, Timothy L. Bailey
Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. BMC Bioinform. 7 (2006)
Timothy L. Bailey, William Stafford Noble
Searching for statistically significant regulatory modules. ECCB (2003)
Timothy L. Bailey, Michael Gribskov
Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores. J. Comput. Biol. 9 (3) (2003)
Timothy L. Bailey, Michael Gribskov
Concerning the accuracy of MAST E-values. Bioinform. 16 (5) (2000)
William Noble Grundy, Timothy L. Bailey
Family pairwise search with embedded motif models. Bioinform. 15 (6) (1999)
Timothy L. Bailey, William Noble Grundy
-values. RECOMB (1999)
Timothy L. Bailey, Michael Gribskov
Methods and Statistics for Combining Motif Match Scores. J. Comput. Biol. 5 (2) (1998)
Timothy L. Bailey, Michael Gribskov
Combining evidence using p-values: application to sequence homology searches. Bioinform. 14 (1) (1998)
William Noble Grundy, Timothy L. Bailey, Charles Elkan, Michael E. Baker
Meta-MEME: motif-based hidden Markov models of protein families. Comput. Appl. Biosci. 13 (4) (1997)
Timothy L. Bailey, Michael Gribskov
Score Distributions for Simultaneous Matching to Multiple Motifs. J. Comput. Biol. 4 (1) (1997)
Timothy L. Bailey, Michael Gribskov
The Megaprior Heuristic for Discovering Protein Sequence Patterns. ISMB (1996)
William Noble Grundy, Timothy L. Bailey, Charles Elkan
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput. Appl. Biosci. 12 (4) (1996)
Timothy L. Bailey, Charles Elkan
Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. Mach. Learn. 21 (1-2) (1995)
Timothy L. Bailey, Charles Elkan
The Value of Prior Knowledge in Discovering Motifs with MEME. ISMB (1995)
Timothy L. Bailey, Charles Elkan
Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer. ISMB (1994)
Timothy L. Bailey, Charles Elkan
Estimating the Accuracy of Learned Concepts. IJCAI (1993)