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Boden, Mikael, Dellaire, Graham, Burrage, Kevin and Bailey, Timothy L. (2010) A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies. Journal of Computational Biology, 17 4: 617-630. doi:10.1089/cmb.2009.0140 169   3 Cited 3 times in Scopus3 0
Tallack, Michael R., Whitington, Tom, Yuen, Wai Shan, Wainwright, Elanor N., Keys, Janelle R., Gardiner, Brooke B., Nourbakhsh, Ehsan, Cloonan, Nicole, Grimmond, Sean M., Bailey, Timothy L. and Perkins, Andrew C. (2010) A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells. Genome Research, 20 8: 1052-1063. doi:10.1101/gr.106575.110 80 68 79 Cited 81 times in Scopus81 1
Lin, Yuefeng, Li, Zhihua, Ozsolak, Fatih, Kim, Sang Woo, Arango-Argoty, Gustavo, Liu, Teresa T., Tenenbaum, Scott A., Bailey, Timothy, Monaghan, A. Paula, Milos, Patrice M. and John, Bino (2012) An in-depth map of polyadenylation sites in cancer. Nucleic Acids Research, 40 17: 8460-8471. doi:10.1093/nar/gks637 53   25 Cited 23 times in Scopus23 3
Lajoie, Mathieu, Hsu, Yu-Chih, Gronostajski, Richard M. and Bailey, Timothy L. (2014) An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation. BMC Genomics, 15 1: . doi:10.1186/1471-2164-15-231 16   1 Cited 0 times in Scopus0 1
Mehdi, Ahmed M., Sehgal, Muhammad Shoaib B., Kobe, Bostjan, Bailey, Timothy L. and Boden, Mikael (2011) A probabilistic model of nuclear import of proteins. Bioinformatics, 27 9: 1239-1246. doi:10.1093/bioinformatics/btr121 48   6 Cited 7 times in Scopus7 0
Tompa, Martin, Li, Nan, Bailey, Timothy L., Church, George M., De Moor, Bart, Eskin, Eleazar, Favorov, Alexander V., Frith, Martin C., Fu, Yutao, Kent, W.James, Makeev, Vsevolod J., Mironov, Andrei A., Noble, William Stafford, Pavesi, Giulio, Pesole, Graziano, Regnier, Mireille, Simonis, Nicolas, Sinha, Saurabh, Thijs, Gert, van Helden, Jacques, Vandenbogaert, Mathias, Weng, Zhiping, Workman, Christopher, Ye, Chun and Zhu, Zhou (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, 23 1: 137-144. doi:10.1038/nbt1053 134   675 Cited 755 times in Scopus755 6
Hawkins, John, Grant, Charles, Noble, William Stafford and Bailey, Timothy L. (2009). Assessing phylogenetic motif models for predicting transcription factor binding sites. In: Dan Gusfield and Anna Tramontano, ISMB/ECCB 2009 Conference Proceedings. ISMB/ECCB 2009: Joint 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden, (i339-i347). 27 June-2 July, 2009. doi:10.1093/bioinformatics/btp201 66   8 Cited 12 times in Scopus12 0
Buske, Fabian A., Boden, Mikael, Bauer, Denis C. and Bailey, Timothy L. (2010) Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics, 26 7: 860-866. doi:10.1093/bioinformatics/btq049 48   22 Cited 24 times in Scopus24 0
Boden, M. and Bailey, T. L. (2008) Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Research, 36 12: 4108-4117. doi:10.1093/nar/gkn374 34   12 Cited 13 times in Scopus13 0
Mylne, Joshua S., Chan, Lai Yue, Chanson, Aurelie H., Daly, Norelle L., Schaefer, Hanno, Bailey, Timothy L., Nguyencong, Philip, Cascales, Laura and Craik, David J. (2012) Cyclic peptides arising by evolutionary parallelism via asparaginyl-endopeptidase–mediated biosynthesis. Plant Cell, 24 7: 2765-2778. doi:10.1105/tpc.112.099085 84   23 Cited 21 times in Scopus21 2
Thandapani, Palaniraja, O'Connor, Timothy R., Bailey, Timothy L. and Richard, Stephane (2013) Defining the RGG/RG motif. Molecular Cell, 50 5: 613-623. doi:10.1016/j.molcel.2013.05.021 25   16 Cited 15 times in Scopus15 1
Lesluyes, Tom, Johnson, James, Machanick, Philip and Bailey, Timothy L. (2014) Differential motif enrichment analysis of paired ChIP-seq experiments. BMC Genomics, 15 752: 1-13. doi:10.1186/1471-2164-15-752 20   0 Cited 0 times in Scopus0 9
Bailey, Timothy L. (2008). Discovering Sequence Motifs. In Jonathan M. Keith (Ed.), Bioinformatics: Data, Sequence Analysis and Evolution 1 ed. (pp. 231-251) New Jersey: Humana Press. doi:10.1007/978-1-60327-159-2-12 76   Cited 15 times in Scopus15 0
Frith, Martin C., Saunders, Neil F. W., Kobe, Bostjan and Bailey, Timothy L. (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Computational Biology, 4 5: e1000071.1-e1000071.12. doi:10.1371/journal.pcbi.1000071 58   65 Cited 69 times in Scopus69 9
Frith, M. C., Bailey, T. L., Kasukawa, T., Mignone, F., Kummerfeld, S. K., Medera, M., Sunkara, S., Furuno, M., Bult, C. J., Quackenbush, J., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y, Pesole, G. and Mattick, J. S. (2006) Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA. RNA Biology, 3 1: 40-48. 75   Cited 36 times in Scopus36
Redhead, Emma and Bailey, Timothy L (2007) Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics, 8 Article Number: 385. doi:10.1186/1471-2105-8-385 68   39 Cited 48 times in Scopus48 0
Mehdi, Ahmed M., Sehgal, Muhammad Shoaib B., Kobe, Bostjan, Bailey, Timothy L. and Boden, Mikael (2013) DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. Bioinformatics, 29 1: 39-46. doi:10.1093/bioinformatics/bts654 46 29 2 Cited 2 times in Scopus2 3
Bailey, Timothy L. (2011) DREME: Motif discovery in transcription factor ChIP-seq data. Bioinformatics, 27 12: 1653-1659. doi:10.1093/bioinformatics/btr261 43   98 Cited 91 times in Scopus91 6
Bauer, Denis C., Buske, Fabian A. and Bailey, Timothy L. (2010) Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. BMC Bioinformatics, 11 . doi:10.1186/1471-2105-11-366 35   7 Cited 8 times in Scopus8 0
Cuellar-Partida, Gabriel, Buske, Fabian A., McLeay, Robert C., Whitington, Tom, Noble, William Stafford and Bailey, Timothy L. (2012) Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics, 28 1: 56-62. doi:10.1093/bioinformatics/btr614 155   12 Cited 12 times in Scopus12 0
Bailey, T. L. and Gribskov, M. (2002) Estimating and evaluating the statistics of gapped local-alignment scores. Journal of Computational Biology, 9 3: 575-593. doi:10.1089/106652702760138637 69   17 Cited 15 times in Scopus15 0
Plachez, Celine, Cato, Kathleen, McLeay, Robert C., Heng, Yee Hsieh Evelyn, Bailey, Timothy L., Gronostajski, Richard M., Richards, Linda J., Puche, Adam C. and Piper, Michael (2012) Expression of nuclear factor one A and -B in the olfactory bulb. The Journal of Comparative Neurology, 520 14: 3135-3149. doi:10.1002/cne.23081 81 1 1 Cited 1 times in Scopus1 0
Grant, Charles E., Bailey, Timothy L. and Noble, William S. (2011) FIMO: Scanning for occurrences of a given motif. Bioinformatics, 27 12: 1017-1018. doi:10.1093/bioinformatics/btr064 47   163 Cited 162 times in Scopus162 0
McLeay, Robert C., Lesluyes, Tom, Partida, Gabriel Cuellar and Bailey, Timothy L. (2012) Genome-wide in silico prediction of gene expression. Bioinformatics, 28 21: 2789-2796. doi:10.1093/bioinformatics/bts529 34   7 Cited 6 times in Scopus6 3
Stanley, Stefan M., Bailey, Timothy L. and Mattick, John S. (2006) GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinformatics, 7 94: 1-11. doi:10.1186/1471-2105-7-94 61   12 Cited 12 times in Scopus12 10
O'Brien, Aidan and Bailey, Timothy L. (2014) GT-Scan: identifying unique genomic targets. Bioinformatics, 30 18: 2673-2675. doi:10.1093/bioinformatics/btu354 19   2 Cited 2 times in Scopus2 17
Whitington, T, Perkins, A. C. and Bailey, T. L. (2009) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Research, 37 1: 14-25. doi:10.1093/nar/gkn866 73   34 Cited 41 times in Scopus41 0
Yu, Jing, Valerius, M. Todd, Duah, Mary, Staser, Karl, Hansard, Jennifer K., Guo, Jin-Jin, McMahon, Jill, Vaughan, Joe, Faria, Diane, Georgas, Kylie, Rumballe, Bree, Ren, Qun, Krautzberger, A. Michaela, Junker, Jan P., Thiagarajan, Rathi D., Machanick, Philip, Gray, Paul A., van Oudenaarden, Alexander, Rowitch, David H., Stiles, Charles D., Ma, Qiufu, Grimmond, Sean M., Bailey, Timothy L., Little, Melissa H. and McMahon, Andrew P. (2012) Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development, 139 10: 1863-1873. doi:10.1242/dev.074005 36   11 Cited 11 times in Scopus11 9
Boden, M. and Bailey, T. L. (2006) Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinformatics, 22 15: 1809-1814. doi:10.1093/bioinformatics/btl198 39   12 Cited 12 times in Scopus12 0
Sato, Kengo, Whitington, Tom, Bailey, Timothy L. and Horton, Paul (2010). Improved prediction of transcription binding sites from chromatin modification data. In: 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2010),, Montreal, Canada, (220-226). 2-5 May 2010. doi:10.1109/CIBCB.2010.5510323 41   Cited 0 times in Scopus0 0
Tanaka, Emi, Bailey, Timothy L., Grant, Charles E., Noble, William Stafford and Keich, Uri (2011) Improved similarity scores for comparing motifs. Bioinformatics, 27 12: 1603-1609. doi:10.1093/bioinformatics/btr257 53   15 Cited 15 times in Scopus15 0
Tanaka, Emi, Bailey, Timothy L. and Keich, Uri (2014) Improving MEME via a two-tiered significance analysis. Bioinformatics, 30 14: 1965-1973. doi:10.1093/bioinformatics/btu163 10   0 Cited 0 times in Scopus0 3
Bailey, Timothy L. and Machanick, P. (2012) Inferring direct DNA binding from ChIP-seq. Nucleic Acids Research, 40 17: e128-1-e128-10. doi:10.1093/nar/gks433 42   33 Cited 29 times in Scopus29 3
Whitington, Tom, Frith, Martin C., Johnson, James and Bailey, Timothy L. (2011) Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Research, 39 15: e98-1-e98-11. doi:10.1093/nar/gkr341 62   31 Cited 29 times in Scopus29 1
Tallack, M, Whitington, T, Gardiner, B, Wainwright, E, Keys, J, Monet, M, Nourbakhsh, E, Cloonan, N, Grimmond, S, Bailey, T and Perkins, AC (2009). Klf1 regulatory networks in primary erythroid cells. In: Blood. 51st Annual Meeting of the American-Society-of-Hematology, New Orleans, LA, U.S.A., (591-591). 5-8 December 2009. 58   0
Machanick, Philip and Bailey, Timothy L. (2011) MEME-ChIP: Motif analysis of large DNA datasets. Bioinformatics, 27 12: 1696-1697. doi:10.1093/bioinformatics/btr189 58   146 Cited 146 times in Scopus146 6
Bailey, T. L., Williams, N., Misleh, C. and Li, W. W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34 W369-W373. doi:10.1093/nar/gkl198 90   552 Cited 644 times in Scopus644 0
Bailey, T. L., Boden, M. B., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J. Y., Li, W. W. and Noble, W. S. (2009) MEME suite: Tools for motif discovery and searching. Nucleic Acids Research, 37 Suppl. 2: W202-W208. doi:10.1093/nar/gkp335 80   708 Cited 729 times in Scopus729 9
Ma, Wenxiu, Noble, William S. and Bailey, Timothy L. (2014) Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nature Protocols, 9 6: 1428-1450. doi:10.1038/nprot.2014.083 16   1 Cited 1 times in Scopus1 4
McLeay, Robert C. and Bailey, Timothy L. (2010) Motif Enrichment Analysis: A unified framework and an evaluation on ChIP data. BMC Bioinformatics, 11 165-1-165-11. doi:10.1186/1471-2105-11-165 177   21 Cited 21 times in Scopus21 3
Gillinder, Kevin R., Lajoie, Mathieu, Ilsley, Melissa, Tallack, Michael R., Magor, Graham, Landsberg, Michael, Bailey, Timothy L. and Perkins, Andrew C. (2013). Mutations In The Zinc Finger Domain Of Human and Mouse KLF1 Cause Congenital Dyserythropoietic Anemia (CDA) Via Promiscuous DNA Binding and Ectopic Target Gene Expression. In: Blood. 55th Annual Meeting of the American-Society-of-Hematology, New Orleans La, (). Dec 07-10, 2013. 6   0
Petersen, Kevin A., Nishi, Yuichi, Ma, Wenxiu, Vedenko, Anastasia, Shokri, Leila, Zhang, Xiaoxiao, McFarlane, Matthew, Baizabal, Jose-Manuel, Junker, Jan Philipp, van Oudenaarden, Alexander, Mikkelsen, Tarjei, Bernstein, Bradley E., Bailey, Timothy L., Bulyk, Martha L., Wong, Wing H. and McMahon, Andrew P. (2012) Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes & Development, 26 24: 2802-2816. doi:10.1101/gad.207142.112 26   24 Cited 19 times in Scopus19 0
Piper, Michael, Barry, Guy, Hawkins, John, Mason, Sharon, Lindwall, Charlotta, Little, Erica, Moldrich, Randal X., Boyle, Glen M., Gronostajski, Richard M., Bailey, Timothy L. and Richards, Linda (2010). NFIA controls progenitor cell differentiation through repression of the Notch effector Hes1. In: Faseb Journal. , , (). . 21   0
Piper, Michael, Barry, Guy, Hawkins, John, Mason, Sharon, Lindwall, Charlotta, Little, Erica, Sarkar, Anindita, Smith, Aaron G., Moldrich, Randal X., Boyle, Glen M., Tole, Shubjha, Gronostajski, Richard M., Bailey, Timothy L. and Richards, Linda J. (2010) NFIA controls telencephalic progenitor cell differentiation through repression of the Notch effector Hes1. Journal of Neuroscience, 30 27: 9127-9139. doi:10.1523/JNEUROSCI.6167-09.2010 105 4 30 Cited 30 times in Scopus30 0
Piper, Michael, Barry, Guy, Harvey, Tracey J., McLeay, Robert, Smith, Aaron G., Harris, Lachlan, Mason, Sharon, Stringer, Brett W., Day, Bryan W., Wray, Naomi R., Gronostajski, Richard M., Bailey, Timothy L., Boyd, Andrew W. and Richards, Linda J. (2014) NFIB-mediated repression of the epigenetic factor Ezh2 regulates cortical development. Journal of Neuroscience, 34 8: 2921-2930. doi:10.1523/JNEUROSCI.2319-13.2014 53   1 Cited 1 times in Scopus1 3
Heng, Yee Hsieh Evelyn, McLeay, Robert C., Harvey, Tracey J., Smith, Aaron G., Barry, Guy, Cato, Kathleen, Plachez, Celine, Little, Erica, Mason, Sharon, Dixon, Chantelle, Gronostajski, Richard M., Bailey, Timothy L., Richards, Linda J. and Piper, Michael (2014) NFIX regulates neural progenitor cell differentiation during hippocampal morphogenesis. Cerebral Cortex, 24 1: 261-279. doi:10.1093/cercor/bhs307 143   3 Cited 6 times in Scopus6 0
Tallack, Michael, Magor, Graham W., Dartigues, Benjamin, Sun, Lei, Huang, Stephen, Fittock, Jessica M., Fry, Sally V., Glazov, Evgeny A., Bailey, Timothy L. and Perkins, Andrew C. (2012) Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq. Genome Research, 22 12: 2385-2398. doi:10.1101/gr.135707.111 67   21 Cited 20 times in Scopus20 14
Dixon, Chantelle, Harvey, Tracey, Smith, Aaron G., Gronostajski, Richard M., Bailey, Timothy L. and Piper, Michael (2013) Nuclear factor one X regulates Bobby Sox during development of the mouse forebrain. Cellular and Molecular Neurobiology, 33 7: 867-873. doi:10.1007/s10571-013-9961-4 51   2 Cited 1 times in Scopus1 0
Bauer, D. C. and Bailey, T. L. (2009) Optimizing static thermodynamic models of transcriptional regulation. BIOINFORMATICS, 25 13: 1640-1646. doi:10.1093/bioinformatics/btp283 50   5 Cited 5 times in Scopus5 0
Buske, Fabian A., Mattick, John S. and Bailey, Timothy L. (2011) Potential in vivo roles of nucleic acid triple-helices. RNA Biology, 8 3: 427-439. doi:10.4161/rna.8.3.14999 41   33 Cited 36 times in Scopus36 0

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