Honorary Professor Timothy Bailey

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

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

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

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.

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.

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

Honorary Professor Timothy Bailey

Publications

Book Chapter

Journal Articles

Conference Papers