Book Chapter
Bailey, Timothy L. (2008). Discovering Sequence Motifs. Bioinformatics: Data, Sequence Analysis and Evolution. (pp. 231-251) edited by Jonathan M. Keith. New Jersey: Humana Press. doi: 10.1007/978-1-60327-159-2_12
Journal Articles
Overman, Jeroen, Fontaine, Frank, Moustaqil, Mehdi, Mittal, Deepak, Sierecki, Emma, Sacilotto, Natalia, Zuegg, Johannes, Robertson, Avril AB, Holmes, Kelly, Salim, Angela A, Mamidyala, Sreeman, Butler, Mark S, Robinson, Ashley S, Lesieur, Emmanuelle, Johnston, Wayne, Alexandrov, Kirill, Black, Brian L, Hogan, Benjamin M, De Val, Sarah, Capon, Robert J, Carroll, Jason S, Bailey, Timothy L, Koopman, Peter, Jauch, Ralf, Cooper, Matthew A, Gambin, Yann and Francois, Mathias (2023). Correction: Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice. eLife, 12 e90408. doi: 10.7554/elife.90408
Ilsley, Melissa D., Gillinder, Kevin R., Magor, Graham W., Huang, Stephen, Bailey, Timothy L., Crossley, Merlin and Perkins, Andrew C. (2017). Kruppel-like factors compete for promoters and enhancers to fine-tune transcription. Nucleic Acids Research, 45 (11), 6572-6588. doi: 10.1093/nar/gkx441
Overman, Jeroen, Fontaine, Frank, Moustaqil, Mehdi, Mittal, Deepak, Sierecki, Emma, Sacilotto, Natalia, Zuegg, Johannes, Robertson, Avril A. B., Holmes, Kelly, Salim, Angela A., Mamidyala, Sreeman, Butler, Mark S., Robinson, Ashley S., Lesieur, Emmanuelle, Johnston, Wayne, Alexandrov, Kirill, Black, Brian L., Hogan, Benjamin M., De Val, Sarah, Capon, Robert J., Carroll, Jason S., Bailey, Timothy L., Koopman, Peter, Jauch, Ralf, Smyth, Mark J., Cooper, Matthew A., Gambin, Yann and Francois, Mathias (2017). Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice. eLife, 6 e21221. doi: 10.7554/eLife.21221
Gillinder, Kevin R., Ilsley, Melissa D., Nébor, Danitza, Sachidanandam, Ravi, Lajoie, Mathieu, Magor, Graham W., Tallack, Michael R., Bailey, Timothy, Landsberg, Michael J., Mackay, Joel P., Parker, Michael W., Miles, Luke A., Graber,Joel H., Peters, Luanne L., Bieker, James J. and Perkins, Andrew C. (2016). Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability. Nucleic Acids Research, 45 (3), 1130-1143. doi: 10.1093/nar/gkw1014
O'Connor, Timothy, Boden, Mikael and Bailey, Timothy L. (2016). CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data. Nucleic Acids Research, 45 (4), e19. doi: 10.1093/nar/gkw956
Grant, Charles E., Johnson, James, Bailey, Timothy L. and Noble, William Stafford (2016). MCAST: scanning for cis-regulatory motif clusters. Bioinformatics, 32 (8), 1217-1219. doi: 10.1093/bioinformatics/btv750
Larney, Christian, Bailey, Timothy L. and Koopman, Peter (2015). Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species Gametogenesis and fertilization. BMC Developmental Biology, 15 (1) 34, 34.1-34.14. doi: 10.1186/s12861-015-0085-6
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 (2015). NFIX regulates proliferation and migration within the murine SVZ neurogenic niche. Cerebral Cortex, 25 (10), 3758-3778. doi: 10.1093/cercor/bhu253
Lim, Jonathan W. C., Donahoo, Amber-Lee S., Bunt, Jens, Edwards, Timothy J., Fenlon, Laura R., Liu, Ying, Zhou, Jing, Moldrich, Randal X., Piper, Michael, Gobius, Ilan, Bailey, Timothy L., Wray, Naomi R., Kessaris, Nicoletta, Poo, Mu-Ming, Rubenstein, John L. R. and Richards, Linda J. (2015). EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex. Development, 142 (21), 3746-3757. doi: 10.1242/dev.119909
Vidovic, Diana, Harris, Lachlan, Harvey, Tracey J., Heng, Yee Hsieh Evelyn, Smith, Aaron G., Osinski, Jason, Hughes, James, Thomas, Paul, Gronostajski, Richard M., Bailey, Timothy L. and Piper, Michael (2015). Expansion of the lateral ventricles and ependymal deficits underlie the hydrocephalus evident in mice lacking the transcription factor NFIX. Brain Research, 1616, 71-87. doi: 10.1016/j.brainres.2015.04.057
Bailey, Timothy L., Johnson, James, Grant, Charles E. and Noble, William S. (2015). The MEME Suite. Nucleic Acids Research, 43 (W1), W39-W49. doi: 10.1093/nar/gkv416
O'Brien, Aidan and Bailey, Timothy L. (2014). GT-Scan: identifying unique genomic targets. Bioinformatics, 30 (18), 2673-2675. doi: 10.1093/bioinformatics/btu354
Lesluyes, Tom, Johnson, James, Machanick, Philip and Bailey, Timothy L. (2014). Differential motif enrichment analysis of paired ChIP-seq experiments. BMC Genomics, 15 (752) 752, 1-13. doi: 10.1186/1471-2164-15-752
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
Plachez, C., Cato, K., McLeay, R. C., Heng, Y. H. E., Bailey, T. L., Gronostajski, Richard M., Richards, L. J., Puche, A. C. and Piper, M. (2014). Expression of Nuclear Factor One A and -B in the Olfactory Bulb (vol 520, pg 3135, 2012). Journal of Comparative Neurology, 522 (11), 2688-2688. doi: 10.1002/cne.23574
Larney, Christian, Bailey, Timothy L. and Koopman, Peter (2014). Switching on sex: transcriptional regulation of the testis-determining gene Sry. Development (Cambridge), 141 (11), 2195-2205. doi: 10.1242/dev.107052
Mehdi, Ahmed M., Patrick, Ralph, Bailey, Timothy L. and Boden, Mikael (2014). Predicting the dynamics of protein abundance. Molecular and Cellular Proteomics, 13 (5), 1330-1340. doi: 10.1074/mcp.M113.033076
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) 231, 231. doi: 10.1186/1471-2164-15-231
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
Ferhat, Ay, Bailey, Timothy L. and Noble, William Stafford (2014). Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Research, 24 (6), 999-1011. doi: 10.1101/gr.160374.113
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
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
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
Buske, Fabian A., Bauer, Denis C., Mattick, John S. and Bailey, Timothy L. (2013). Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci. Bioinformatics, 29 (15), 1895-1897. doi: 10.1093/bioinformatics/btt315
Wong, Emily S. W., Hardy, Margaret C., Wood, David, Bailey, Timothy and King, Glenn F. (2013). SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula. PLoS ONE, 8 (7) e66279, e66279.1-e66279.11. doi: 10.1371/journal.pone.0066279
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
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
Bailey, Timothy, Krajewski, Pawel, Ladunga, Istvan, Lefebvre, Celine, Li,Qunhua, Liu, Tao, Madrigal, Pedro, Taslim, Cenny and Zhang, Jie (2013). Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Computational Biology, 9 (11) e1003326, e1003326.1-e1003326.7. doi: 10.1371/journal.pcbi.1003326
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
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
Sun, Lei, Zhang, Zhihua, Bailey, Timothy L., Perkins, Andrew C., Tallack, Michael R., Xu, Zhao and Liu, Hui (2012). Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. BMC Bioinformatics, 13 (1) 331, 331.1-331.25. doi: 10.1186/1471-2105-13-331
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
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
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
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
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
Buske, Fabian A., Bauer, Denis C., Mattick, John S. and Bailey, Timothy L. (2012). Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Research, 22 (7), 1372-1381. doi: 10.1101/gr.130237.111
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
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
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) btr614, 56-62. doi: 10.1093/bioinformatics/btr614
McLeay, Robert C., Leat, Chris J. and Bailey, Timothy L. (2011). Tissue-specific prediction of directly regulated genes. Bioinformatics, 27 (17) btr399, 2354-2360. doi: 10.1093/bioinformatics/btr399
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
Bauer, Denis C., Willadsen, Kai, Buske, Fabian A., Lê Cao, Kim-Anh, Bailey, Timothy L., Dellaire, Graham and Bodén, Mikael (2011). Sorting the nuclear proteome. Bioinformatics, 27 (13) btr217, i7-i14. doi: 10.1093/bioinformatics/btr217
Bailey, Timothy L. (2011). DREME: Motif discovery in transcription factor ChIP-seq data. Bioinformatics, 27 (12) btr261, 1653-1659. doi: 10.1093/bioinformatics/btr261
Machanick, Philip and Bailey, Timothy L. (2011). MEME-ChIP: Motif analysis of large DNA datasets. Bioinformatics, 27 (12) btr189, 1696-1697. doi: 10.1093/bioinformatics/btr189
Tanaka, Emi, Bailey, Timothy L., Grant, Charles E., Noble, William Stafford and Keich, Uri (2011). Improved similarity scores for comparing motifs. Bioinformatics, 27 (12) btr257, 1603-1609. doi: 10.1093/bioinformatics/btr257
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
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) btr121, 1239-1246. doi: 10.1093/bioinformatics/btr121
Grant, Charles E., Bailey, Timothy L. and Noble, William S. (2011). FIMO: Scanning for occurrences of a given motif. Bioinformatics, 27 (12) btr064, 1017-1018. doi: 10.1093/bioinformatics/btr064
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 (vol 20, pg 1052, 2010). Genome Research, 20 (12), 1748-1748.
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
Bauer, Denis C., Buske, Fabian A., Bailey, Timothy L. and Boden, Mikael (2010). Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. Neurocomputing, 73 (13-15), 2300-2307. doi: 10.1016/j.neucom.2010.01.022
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 (1) 366, 366. doi: 10.1186/1471-2105-11-366
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
Bailey, Timothy L., Bodén, Mikael, Whitington, Tom and Machanick, Philip (2010). The value of position-specific priors in motif discovery using MEME. BMC Bioinformatics, 11 (179) 179, 1-14. doi: 10.1186/1471-2105-11-179
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
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) btq049, 860-866. doi: 10.1093/bioinformatics/btq049
McLeay, Robert C. and Bailey, Timothy L. (2010). Motif Enrichment Analysis: A unified framework and an evaluation on ChIP data. BMC Bioinformatics, 11 (1) 165, 165-1-165-11. doi: 10.1186/1471-2105-11-165
Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A, Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Bjorkegren, J, Brombacher, F, Bulger, E ... Riken Omics Science Center (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 (5), 553-562. doi: 10.1038/ng.375
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
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
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
Bauer, Denis C. and Bailey, Timothy L. (2008). STREAM: Static Thermodynamic regulatory model of transcription. Bioinformatics, 24 (21), 2544-2545. doi: 10.1093/bioinformatics/btn467
Bailey, Timothy L (2008). Discovering sequence motifs. Methods in molecular biology (Clifton, N.J.), 452, 231-251. doi: 10.1007/978-1-60327-159-2_12
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
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, e1000071.1-e1000071.12. doi: 10.1371/journal.pcbi.1000071
Bauer, Denis C. and Bailey, Timothy L. (2008). Studying the functional conservation of cis-regulatory modules and their transcriptional output. BMC Bioinformatics, 9 (1) 220, Article Number: 220. doi: 10.1186/1471-2105-9-220
Frith, M. C., Carninci, P., Kai, C., Kawai, J., Bailey, T. L., Hayashizaki, Y. and Mattick, J. S. (2007). Splicing bypasses 3' end formation signals to allow complex gene architectures. Gene, 403 (1-2), 188-193. doi: 10.1016/j.gene.2007.08.012
Redhead, Emma and Bailey, Timothy L (2007). Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics, 8 (1) 385, Article Number: 385. doi: 10.1186/1471-2105-8-385
Gupta, Shobhit, Stamatoyannopoulos, John A., Bailey, Timothy L. and Noble, William Stafford (2007). Quantifying similarity between motifs. Genome Biology, 8 (2) R24, R24.1-R24.9. doi: 10.1186/gb-2007-8-2-r24
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. doi: 10.4161/rna.3.1.2789
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
Stanley, Stefan M., Bailey, Timothy L. and Mattick, John S. (2006). GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinformatics, 7 (94) 94, 1-11. doi: 10.1186/1471-2105-7-94
Boden, M., Yuan, Z. and Bailey, T. L. (2006). Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. Bmc Bioinformatics, 7 (68) 68, 1-12. doi: 10.1186/1471-2105-7-68
Frith, Martin C., Wilming, Laurens G., Forrest, Alistair, Kawaji, Hideya, Tan, Sin Lam, Wahlestedt, Claes, Bajic, Vladimir B., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L. and Huminiecki, Lukasz (2006). Pseudo-messenger RNA: Phantoms of the transcriptome. PLOS Genetics, 2 (4) e23, 504-514. doi: 10.1371/journal.pgen.0020023
Frith, Martin C., Forrest, Alistair R., Nourbakhsh, Ehsan, Pang, Ken C., Kai, Chikatoshi, Kawai, Jun, Carnici, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L. and Grimmond, Sean M. (2006). The abundance of short proteins in the mammalian proteome. Plos Genetics, 2 (4) e52, 515-528. doi: 10.1371/journal.pgen.0020052
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 (WEB. SERV. ISS.), W369-W373. doi: 10.1093/nar/gkl198
The FANTOM Consortium, Gough, J., Frith, M. C., Ravasi, T., Wells, C., Forrest, A. R. R., Davis, M. J., Aturaliya, R. N., Bailey, T. L., Crowe, M. L., Faulkner, G., Pang, K. C., Teasdale, R. D., Grimmond, S. M., Mattick, J. S., Hume, D. A. and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Core Team) (2005). The transcriptional landscape of the mammalian genome. Science, 309 (5740), 1559-1563. doi: 10.1126/science.1112014
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
Yuan, Z., Bailey, T. L. and Teasdale, R. D. (2005). Prediction of protein B-factor profiles. Proteins-structure Function And Bioinformatics, 58 (4), 905-912. doi: 10.1002/prot.20375
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
Conference Papers
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. 56th Annual Meeting of the American Society of Hematology, San Francisco, CA United States, 06-09 December 2014. Washington, DC United States: American Society of Hematology.
Viner, Coby, Johnson, James, Grant, Charles E., Bailey, Timothy L., Noble, William Stafford and Hoffman, Michael M. (2014). Transcription factor motif discovery and prediction in an expanded epigenetic alphabet. Genomics: the Power and the Promise 2014, Ottawa Convention Centre, Ottawa, Canada, 24-26 November 2014. Ottawa, ON Canada: N R C Research Press. doi: 10.1139/gen-2014-0153
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. 55th Annual Meeting of the American-Society-of-Hematology, New Orleans La, Dec 07-10, 2013. WASHINGTON: AMER SOC HEMATOLOGY.
Sato, Kengo, Whitington, Tom, Bailey, Timothy L. and Horton, Paul (2010). Improved prediction of transcription binding sites from chromatin modification data. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2010),, Montreal, Canada, 2-5 May 2010. United States: IEEE - Institute for Electrical and Electronic Engineers. doi: 10.1109/CIBCB.2010.5510323
Hawkins, John, Grant, Charles, Noble, William Stafford and Bailey, Timothy L. (2009). Assessing phylogenetic motif models for predicting transcription factor binding sites. ISMB/ECCB 2009: Joint 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden, 27 June-2 July, 2009. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/bioinformatics/btp201
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. 51st Annual Meeting of the American-Society-of-Hematology, New Orleans, LA, U.S.A., 5-8 December 2009. Washington, D.C., U. S. A.: American Society of Hematology.
Hawkins, John and Bailey, Timothy L. (2008). The statistical power of phylogenetic motif models. 12th Annual International Conference, RECOMB 2008, Singapore, 30 March – 2 April 2008. Berlin, Germany: Springer. doi: 10.1007/978-3-540-78839-3_10
Yuan, Zheng and Bailey, Timothy L. (2004). Prediction of protein solvent profile using SVR. Conference Proceedings - 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2004, , , September 1, 2004-September 5, 2004.
Yuan, Zheng and Bailey, Timothy Lawrence (2004). Prediction of protein solvent profile using SVR. 26th Annual International Conference of the IEEE EMBS, San Francisco, 1-5 September 2004. IEEE. doi: 10.1109/IEMBS.2004.1403822
Bailey, Timothy L. and Noble, William Stafford (2003). Searching for statistically significant regulatory modules. Oxford: Oxford University Press. doi: 10.1093/bioinformatics/btg1054