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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 177   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 83 74 83 Cited 84 times in Scopus84 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 54   28 Cited 27 times in Scopus27 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 20   2 Cited 1 times in Scopus1 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 51   8 Cited 8 times in Scopus8 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 136   682 Cited 764 times in Scopus764 9
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 73   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 55 2 23 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 36   12 Cited 13 times in Scopus13 0
O'Connor, Timothy R. and Bailey, Timothy L. (2014) Creating and validating cis-regulatory maps of tissue-specific gene expression regulation. Nucleic Acids Research, 42 17: 11000-11010. doi:10.1093/nar/gku801 14   1 3
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 85   28 Cited 24 times in Scopus24 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 27   22 Cited 19 times in Scopus19 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 25   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 82 2 Cited 15 times in Scopus15 6
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 59   68 Cited 77 times in Scopus77 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. 76   Cited 38 times in Scopus38
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 70   40 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 52 36 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 45   112 Cited 108 times in Scopus108 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 37   7 Cited 9 times in Scopus9 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 158   13 Cited 12 times in Scopus12 3
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 70   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 83 1 2 Cited 2 times in Scopus2 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 49   179 Cited 178 times in Scopus178 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 36   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 64   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 23   3 Cited 2 times in Scopus2 20
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 74   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 38   13 Cited 15 times in Scopus15 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 41   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 42   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 55   17 Cited 17 times in Scopus17 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 13   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 43   41 Cited 36 times in Scopus36 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 63   31 Cited 30 times in Scopus30 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. 59   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 60   162 Cited 161 times in Scopus161 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 93   575 Cited 672 times in Scopus672 3
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 91 2 779 Cited 809 times in Scopus809 7
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 24   3 Cited 2 times in Scopus2 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:10.1186/1471-2105-11-165 181 2 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. 9   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 27   28 Cited 26 times in Scopus26 0
Perkins, Andrew C., Gillinder, Kevin R., Magor, Graham, Lajoie, Mathieu, Bailey, Timothy L., Tallack, Michael R., Ilsley, Melissa, Landsberg, Michael, Mackay, Joel P., Bieker, James J. and Peters, Luanne L. (2014). New Insights into the Mechanism of Dominant Anemia Caused By Zinc Finger Mutations in KLF1. In: Blood. 56th Annual Meeting of the American-Society-of-Hematology, San Francisco Ca, (). Dec 06-09, 2014. 31   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. , , (). . 24   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 109 4 34 Cited 35 times in Scopus35 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 60   3 Cited 3 times in Scopus3 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 158   4 Cited 8 times in Scopus8 0
Heng, Yee Hsieh Evelyn, Zhou, Bo, Harris, Lachlan, Harvey, Tracey, Smith, Aaron, Horne, Elise, Martynoga, Ben, Andersen, Jimena, Achimastou, Angeliki, Cato, Kathleen, Richards, Linda J., Gronostajski, Richard M., Yeo, Giles S., Guillemot, François, Bailey, Timothy L. and Piper, Michael (2014) NFIX regulates proliferation and migration within the murine SVZ neurogenic niche. Cerebral Cortex, . doi:10.1093/cercor/bhu253 22   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 69   23 Cited 23 times in Scopus23 13

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