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Methods and statistics for combining motif match scores.
Bailey TL, Gribskov M. Bailey TL, et al. J Comput Biol. 1998 Summer;5(2):211-21. doi: 10.1089/cmb.1998.5.211. J Comput Biol. 1998. PMID: 9672829
Discovering sequence motifs.
Bailey TL. Bailey TL. Methods Mol Biol. 2008;452:231-51. doi: 10.1007/978-1-60327-159-2_12. Methods Mol Biol. 2008. PMID: 18566768 Review.
MEME SUITE: tools for motif discovery and searching.
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. Bailey TL, et al. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335. Epub 2009 May 20. Nucleic Acids Res. 2009. PMID: 19458158 Free PMC article.
Discovering sequence motifs with arbitrary insertions and deletions.
Frith MC, Saunders NF, Kobe B, Bailey TL. Frith MC, et al. PLoS Comput Biol. 2008 May 9;4(4):e1000071. doi: 10.1371/journal.pcbi.1000071. PLoS Comput Biol. 2008. PMID: 18437229 Free PMC article.
Quantifying similarity between motifs.
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Gupta S, et al. Genome Biol. 2007;8(2):R24. doi: 10.1186/gb-2007-8-2-r24. Genome Biol. 2007. PMID: 17324271 Free PMC article.
Discovering sequence motifs.
Bailey TL. Bailey TL. Methods Mol Biol. 2007;395:271-92. doi: 10.1007/978-1-59745-514-5_17. Methods Mol Biol. 2007. PMID: 17993680 Review.
The value of position-specific priors in motif discovery using MEME.
Bailey TL, Bodén M, Whitington T, Machanick P. Bailey TL, et al. BMC Bioinformatics. 2010 Apr 9;11:179. doi: 10.1186/1471-2105-11-179. BMC Bioinformatics. 2010. PMID: 20380693 Free PMC article.
Estimating and evaluating the statistics of gapped local-alignment scores.
Bailey TL, Gribskov M. Bailey TL, et al. J Comput Biol. 2002;9(3):575-93. doi: 10.1089/106652702760138637. J Comput Biol. 2002. PMID: 12162893
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