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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 174   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 81 72 81 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 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 49   7 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 134   680 Cited 757 times in Scopus757 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 70   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 53 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 35   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 13   0 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 84   24 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 26   18 Cited 18 times in Scopus18 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 21   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 80 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 58   66 Cited 73 times in Scopus73 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   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 49 33 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   103 Cited 98 times in Scopus98 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 36   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 156   12 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 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 82 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   171 Cited 169 times in Scopus169 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 62   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 20   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 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   12 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   35 Cited 32 times in Scopus32 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   153 Cited 150 times in Scopus150 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   559 Cited 655 times in Scopus655 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 87 2 727 Cited 755 times in Scopus755 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 18   2 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. 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   26 Cited 21 times in Scopus21 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 107 4 31 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 55   1 Cited 2 times in Scopus2 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 147   3 Cited 6 times in Scopus6 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 14   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 68   21 Cited 22 times in Scopus22 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

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