Timothy L. Bailey

发表

Assigning roles to DNA regulatory motifs using comparative genomics

Mikael Bodén, Fabian A. Buske, Denis C. Bauer, 2010, Bioinform..

Epigenetic priors for identifying active transcription factor binding sites

William Stafford Noble, Fabian A. Buske, Timothy L. Bailey, 2012, Bioinform..

GONOME: measuring correlations between GO terms and genomic positions

Timothy L. Bailey, Stefan M. Stanley, John S. Mattick, 2006, BMC Bioinformatics.

The Statistical Power of Phylogenetic Motif Models

John Hawkins, Timothy L. Bailey, T. Bailey, 2008, RECOMB.

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

Mikael Bodén, Fabian A. Buske, Denis C. Bauer, 2010, Neurocomputing.

Improved prediction of transcription binding sites from chromatin modification data

Paul Horton, Timothy L. Bailey, Tom Whitington, 2010, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

MoMo: Discovery of post-translational modification motifs

William Stafford Noble, Timothy L. Bailey, Alice Cheng, 2017, bioRxiv.

Family pairwise search with embedded motif models

William Noble Grundy, Timothy L. Bailey, 1999, Bioinform..

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

Denis C. Bauer, Timothy L. Bailey, T. Bailey, 2008, BMC Bioinformatics.

MEME: discovering and analyzing DNA and protein sequence motifs

Wilfred W. Li, Timothy L. Bailey, Nadya Williams, 2006, Nucleic Acids Res..

Concerning the accuracy of MAST E-values

Michael Gribskov, Timothy L. Bailey, M. Gribskov, 2000, Bioinform..

STREME: Accurate and versatile sequence motif discovery

Timothy L. Bailey, T. Bailey, 2020, bioRxiv.

Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores

Michael Gribskov, Timothy L. Bailey, M. Gribskov, 2003, J. Comput. Biol..

Tissue-specific prediction of directly regulated genes

Timothy L. Bailey, Robert C. McLeay, Chris J. Leat, 2011, Bioinform..

Proceedings of the 2006 workshop on Intelligent systems for bioinformatics - Volume 73

Mikael Bodén, Timothy L. Bailey, M. Bodén, 2006 .

Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data

Timothy L. Bailey, T. Bailey, 2011 .

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

Zhihua Zhang, Hui Liu, Lei Sun, 2012, BMC Bioinformatics.

T-Gene: Improved target gene prediction

Mikael Bodén, Timothy L. Bailey, Charles E. Grant, 2019, bioRxiv.

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

Timothy L. Bailey, Emma Redhead, T. Bailey, 2007, BMC Bioinformatics.

Discovering motifs in dna and protein sequences: the approximate common substring problem

Charles Elkan, Timothy L. Bailey, C. Elkan, 1995 .

MEME-ChIP: motif analysis of large DNA datasets

Philip Machanick, Timothy L. Bailey, T. Bailey, 2011, Bioinform..

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

Michael Gribskov, Timothy L. Bailey, M. Gribskov, 1998, Bioinform..

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

Fabian A. Buske, Denis C. Bauer, Timothy L. Bailey, 2013, Bioinform..

Optimizing static thermodynamic models of transcriptional regulation

Denis C. Bauer, Timothy L. Bailey, T. Bailey, 2009, Bioinform..

Proceedings of the A1 2006 Workshop on Intelligent Systems of Bioinformatics (WISB 2006)

Mikael Bodén, Timothy L. Bailey, M. Bodén, 2006 .

GT-Scan: identifying unique genomic targets

Timothy L. Bailey, Aidan O'Brien, T. Bailey, 2014, Bioinform..

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure

Mikael Bodén, Timothy L. Bailey, M. Bodén, 2006, Bioinform..

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

Mikael Bodén, Zheng Yuan, Timothy L. Bailey, 2006, BMC Bioinformatics.

Methods and Statistics for Combining Motif Match Scores

Michael Gribskov, Timothy L. Bailey, M. Gribskov, 1998, J. Comput. Biol..

Score Distributions for Simultaneous Matching to Multiple Motifs

Michael Gribskov, Timothy L. Bailey, M. Gribskov, 1997, J. Comput. Biol..

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

Charles Elkan, Timothy L. Bailey, C. Elkan, 1994, ISMB.

MoMo: Discovery of statistically significant post-translational modification motifs

William Stafford Noble, Timothy L. Bailey, Charles E. Grant, 2018 .

Genome-wide in silico prediction of gene expression

Timothy L. Bailey, Gabriel Cuellar-Partida, Robert C. McLeay, 2012, Bioinform..

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

Mikael Bodén, Bostjan Kobe, Timothy L. Bailey, 2013, Bioinform..

William Stafford Noble, Emi Tanaka, Uri Keich, 2011, Bioinform..

MEME Suite: tools for motif discovery and searching

Mikael Bodén, William Stafford Noble, Martin C. Frith, 2009, Nucleic Acids Res..

STREAM: Static Thermodynamic REgulAtory Model of transcription

Denis C. Bauer, Timothy L. Bailey, 2008, Bioinform..

A probabilistic model of nuclear import of proteins

Mikael Bodén, Bostjan Kobe, Timothy L. Bailey, 2011, Bioinform..

The Megaprior Heuristic for Discovering Protein Sequence Patterns

Michael Gribskov, Timothy L. Bailey, M. Gribskov, 1996, ISMB.

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

Timothy L. Bailey, Robert C. McLeay, T. Bailey, 2010, BMC Bioinformatics.

Sorting the nuclear proteome

Mikael Bodén, Kim-Anh Lê Cao, Fabian A. Buske, 2011, Bioinform..

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

William Noble Grundy, Charles Elkan, Timothy L. Bailey, 1996, Comput. Appl. Biosci..

Improving MEME via a two-tiered significance analysis

Emi Tanaka, Uri Keich, Timothy L. Bailey, 2014, Bioinform..

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

Philip Machanick, Mikael Bodén, Timothy L. Bailey, 2010, BMC Bioinformatics.

Assessing phylogenetic motif models for predicting transcription factor binding sites

John Hawkins, William Stafford Noble, Timothy L. Bailey, 2009, Bioinform..

Unsupervised learning of multiple motifs in biopolymers using expectation maximization

Charles Elkan, Timothy L. Bailey, C. Elkan, 1995, Mach. Learn..

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

William Noble Grundy, Charles Elkan, Timothy L. Bailey, 1997, Comput. Appl. Biosci..

The MEME Suite

William Stafford Noble, Timothy L. Bailey, William S. Noble, 2015, Nucleic Acids Res..

FIMO: scanning for occurrences of a given motif

William Stafford Noble, Timothy L. Bailey, Charles E. Grant, 2011, Bioinform..

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

William Noble Grundy, Timothy L. Bailey, W. Grundy, 1999, RECOMB.

The Value of Prior Knowledge in Discovering Motifs with MEME

Charles Elkan, Timothy L. Bailey, C. Elkan, 1995, ISMB.

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

Fabian A. Buske, Denis C. Bauer, Timothy L. Bailey, 2010, BMC Bioinformatics.

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

William Noble Grundy, Charles Elkan, Timothy L. Bailey, 1999, Pattern Discovery in Biomolecular Data.

MCAST: scanning for cis-regulatory motif clusters

William Stafford Noble, Timothy L. Bailey, James Johnson, 2016, Bioinform..

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

Mikael Bodén, Kevin Burrage, Timothy L. Bailey, 2010, J. Comput. Biol..

Estimating the Accuracy of Learned Concepts

Charles Elkan, Timothy L. Bailey, C. Elkan, 1993, IJCAI.

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

Martin C. Frith, Bostjan Kobe, Neil F. W. Saunders, 2008, PLoS Comput. Biol..

Searching for statistically significant regulatory modules

William Stafford Noble, Timothy L. Bailey, T. Bailey, 2003, ECCB.

STREME: accurate and versatile sequence motif discovery

Timothy L. Bailey, 2021, Bioinform..

Inferring transcription factor complexes from ChIP-seq data

Martin C. Frith, Timothy L. Bailey, James Johnson, 2011, Nucleic acids research.

An artificial intelligence approach to motif discovery in protein sequences: Application to steroid dehydrogenases

Timothy L. Bailey, Michael E. Baker, C. Elkan, 1997, The Journal of Steroid Biochemistry and Molecular Biology.