Timothy Bailey
Timothy Bailey
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MEME Suite: tools for motif discovery and searching
TL Bailey, M Boden, FA Buske, M Frith, CE Grant, L Clementi, J Ren, ...
Nucleic acids research 37 (suppl_2), W202-W208, 2009
Fitting a mixture model by expectation maximization to discover motifs in bipolymers
TL Bailey, C Elkan
Department of Computer Science and Engineering, University of California …, 1994
The transcriptional landscape of the mammalian genome
P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, ...
Science 309 (5740), 1559-1563, 2005
FIMO: scanning for occurrences of a given motif
CE Grant, TL Bailey, WS Noble
Bioinformatics 27 (7), 1017-1018, 2011
MEME: discovering and analyzing DNA and protein sequence motifs
TL Bailey, N Williams, C Misleh, WW Li
Nucleic acids research 34 (suppl_2), W369-W373, 2006
The MEME suite
TL Bailey, J Johnson, CE Grant, WS Noble
Nucleic acids research 43 (W1), W39-W49, 2015
Quantifying similarity between motifs
S Gupta, JA Stamatoyannopoulos, TL Bailey, WS Noble
Genome biology 8 (2), 1-9, 2007
MEME-ChIP: motif analysis of large DNA datasets
P Machanick, TL Bailey
Bioinformatics 27 (12), 1696-1697, 2011
Assessing computational tools for the discovery of transcription factor binding sites
M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, ...
Nature biotechnology 23 (1), 137-144, 2005
Combining evidence using p-values: application to sequence homology searches.
TL Bailey, M Gribskov
Bioinformatics (Oxford, England) 14 (1), 48-54, 1998
DREME: motif discovery in transcription factor ChIP-seq data
TL Bailey
Bioinformatics 27 (12), 1653-1659, 2011
Unsupervised learning of multiple motifs in biopolymers using expectation maximization
TL Bailey, C Elkan
Machine learning 21, 51-80, 1995
The value of prior knowledge in discovering motifs with MEME.
TL Bailey, C Elkan
Ismb 3, 21-29, 1995
Defining the RGG/RG motif
P Thandapani, TR O’Connor, TL Bailey, S Richard
Molecular cell 50 (5), 613-623, 2013
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
RC McLeay, TL Bailey
BMC bioinformatics 11 (1), 1-11, 2010
Inferring direct DNA binding from ChIP-seq
TL Bailey, P Machanick
Nucleic acids research 40 (17), e128-e128, 2012
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
F Ay, TL Bailey, WS Noble
Genome research 24 (6), 999-1011, 2014
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Nature genetics 41 (5), 553-562, 2009
Discovering sequence motifs with arbitrary insertions and deletions
MC Frith, NFW Saunders, B Kobe, TL Bailey
PLoS computational biology 4 (5), e1000071, 2008
Practical guidelines for the comprehensive analysis of ChIP-seq data
T Bailey, P Krajewski, I Ladunga, C Lefebvre, Q Li, T Liu, P Madrigal, ...
PLoS computational biology 9 (11), e1003326, 2013
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