TIMOTHY L. BAILEY
Senior Research Fellow
Division of Genomics and Computational Biology
Institute for Molecular Bioscience
University of Queensland
Brisbane, Qld 4072
Email: t.bailey@imb.uq.edu.au
WWW: http://research.imb.uq.edu.au/~tbailey

PUBLICATIONS

• Michael R. Tallack, Tom Whitington, Wai Shan Yuen, Elanor N. Wainwright, Janelle R. Keys, Brooke B. Gardiner, Ehsan Nourbakhsh, Nicole Cloonan, Sean M. Grimmond, Timothy L. Bailey, and Andrew C. Perkins, "KLF1/EKLF regulatory networks in primary erythroid cells", submitted, February 2010.

• Michael Piper, Guy Barry, John Hawkins, Sharon Mason, Charlotta Lindwall, Erica Little, Anindita Sarkar, Aaron Smith, Randal Moldrich, Glen Boyle, Shubha Tole, Richard Gronostajski, Timothy Bailey and Linda Richards, "NFIA Controls Telencephalic Progenitor Cell Differentiation through Repression of the Notch Effector Hes1'', submitted, 2009.

• Fabian A. Buske, Mikael Boden, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics'', Bioinformatics, accepted February 3, 2010.

• Robert McLeay and Timothy L. Bailey, "Motif Enrichment Analysis: A unified framework and method evaluation with ChIP data'', submitted, 2009.

• Timothy L. Bailey, Mikael Boden, Tom Whitington and Philip Machanick, "The value of position-specific priors in motif discovery using MEME'', submitted, 2009.

• Denis C. Bauer, Fabian A. Buske and Timothy L. Bailey, "Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster'', submitted, 2009.

• Denis C. Bauer, Fabian A. Buske, Timothy L. Bailey, Mikael Boden, "Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster'', Neurocomputing, accepted January 9, 2010.

• Mikael Boden, Graham Dellaire, Kevin Burrage, Timothy L. Bailey, "A Bayesian network model of proteins association with promyelocytic leukemia (PML) nuclear bodies'', accepted for publication, Journal of Computational Biology, November 14, 2009.

• Denis C Bauer and Timothy L. Bailey, "Optimizing static thermodynamic models of transcriptional regulation'', Bioinformatics, 25:1640-1646, 2009. [Abstract and Full Text]

• Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching'', Nucleic Acids Research, 37:W202-W208, 2009. [Abstract and Full Text]

• The Fantom Consortium, "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line'', Nature Genetics, 41:553-562, 2009. [Abstract and Full Text]

• John Hawkins, Charles Grant, William Noble and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites", Conference on Intelligent Systems for Molecular Biology (ISMB2009), Bioinformatics, 25:i339-i347, 2009. [Abstract and Full Text]

• T. Whitington, A. C. Perkins and T. L. Bailey, "High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites", Nucleic Acids Research, 37(1):14-25, 2009. [Abstract and Full Text]

• Denis C Bauer and Timothy L. Bailey, "STREAM: Static Thermodynamic REgulAtory Model of transcription", Bioinformatics, 24:2544-2525, 2008. [Abstract and Full Text]

• Mikael Bodén and Timothy L. Bailey, "Associating transcription factor binding site motifs with target GO terms and target genes", Nucleic Acids Research, 36(12):4108-4117, 2008. [Abstract and Full Text]

• Timothy L. Bailey, Chapter 12, "Discovering Sequence Motifs", Methods in Molecular Biology: Bioinformatics, Vol. 1, Data, Sequence Analysis and Evolution, pp. 231-251, edited by Jonathan M. Keith, Humana Press, Totowa, New Jersey, 2008.

• Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5), e1000071, 2008. [Abstract and Full Text]

• Denis C. Bauer and Timothy L. Bailey, "Studying the functional conservation of cis-regulatory modules and their transcriptional output", BMC Bioinformatics, 9:220, 2008. [Abstract and Full Text]

• John Hawkins and Timothy L. Bailey, "The statistical power of phylogenetic motif models", Twelfth Annual International Conference on Computational Biology, (RECOMB 2008), pp. 112-126, Springer-Verlag, Berlin, March, 2008. [Abstract and Full-text]

• Timothy L. Bailey, Chapter 17, "Discovering Sequence Motifs", Methods in Molecular Biology: Comparative Genomics, Vol. 1, pp. 271-292, edited by Nicholas H. Bergman, Humana Press, Totowa, New Jersey, 2007.

• Emma Redhead and Timothy L. Bailey, "Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm", BMC Bioinformatics, 8:385, 2007. [Abstract and Full Text]

• Martin C. Frith, Piero Carninci, Chikatoshi Kai, Jun Kawai, Timothy L. Bailey, Yoshihide Hayashizaki and John S Mattick, "Splicing bypasses 3' end formation signals to allow complex gene architectures", Gene, 403:188-193, 2007. [Abstract and Full Text]

• Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs'', Genome Biology, 8(2):R24, 2007. [Abstract and Full Text]

• Timothy L. Bailey, Nadya Williams, Chris Misleh, and Wilfred W. Li, "MEME: Discovering and analyzing DNA and protein sequence motifs", Nucleic Acids Research, 34:W369-W373, 2006. [Abstract and Full Text]

• Mikael Bodén and Timothy L. Bailey, "Identifying sequence regions undergoing conformational change via predicted continuum secondary structure", Bioinformatics, 22:1809-1814, 2006. [Abstract and Full Text]

• Stefan M Stanley, Timothy L Bailey and John S Mattick, "GONOME: measuring correlations between GO terms and genomic positions", BMC Bioinformatics, 7:94, 2006. [Abstract and Full Text]

• Mikael Bodén, Zheng Yuan and Timothy L Bailey, "Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures", BMC Bioinformatics, 7:68, 2006. [Abstract and Full Text]

• Martin C Frith, Timothy L Bailey, Takeya Kasukawa, Flavio Mignone, Sarah K Kummerfeld, Martin Madera, Sirisha Sunkara, Masaaki Furuno, John Quackenbush, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Graziano Pesole, and John S Mattick, "Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA", RNA Biology, 3:40-48, 2006. [Full-text PDF]

• Martin C Frith, Alistair R Forrest, Ehsan Nourbakhsh, Ken C Pang, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey and Sean M Grimmond, "The Abundance of Short Proteins in the Mammalian Proteome", PLoS Genetics, 2(4):e52, 2006. [Abstract and Full Text]

• Martin C Frith, Laurens G Wilming, Alistair Forrest, Hideya Kawaji, Sin Lam Tan, Claes Wahlestedt, Vladimir B Bajic, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey and Lukasz Huminiecki, "Pseudo-Messenger RNA: Phantoms of the Transcriptome", PLoS Genetics, 2(4):e23, 2006. [Abstract and Full Text]

• Piero Carninci et al., "The transcriptional landscape of the mammalian genome", Science, 309:1559-1563, 2005. [Abstract and Full Text]

• Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolov J. Makeev, Andrei A. Mironov, William Stafford Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolais Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye and Zhou Zhu, "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites", Nature Biotechnology, 23:137-144, 2005. [Abstract and Full Text]

• Zheng Yuan, Timothy L. Bailey and Rohan Teasdale, "Prediction of Protein B-factor Profiles", PROTEINS: Structure, Function, and Bioinformatics, 58:905-912, 2005. [ABSTRACT and Full Text]

• Zheng Yuan and Timothy L. Bailey, "Prediction of protein solvent profile using SVR", Proceedings of the 26th Annual International Conference of the IEEE EMBS, pp. 2889-2892, San Francisco, September, 2004. [Full-text PDF]

• Timothy L. Bailey and William Noble, "Searching for statistically significant regulatory modules", Bioinformatics, 19 Suppl 1:II16-II25, 2003. [Full-text PDF]

• Timothy L. Bailey, "Details of MCAST statistics", Technical report IMB-TR0001, Institute for Molecular Bioscience, University of Queensland, 2003. [Full-text PostScript] [Full-text PDF]

• Timothy L. Bailey, "Discovering Novel Sequence Motifs with MEME" Current Protocols in Bioinformatics, 2.4.1-2.4.32, edited by Andreas D. Baxevanis and Daniel B. Davison, John Wiley & Sons, Inc., 2002.

• Timothy L. Bailey and Michael Gribskov, "Estimating and evaluating the statistics of gapped local-alignment scores", Journal of Computational Biology, 9:575-593, 2002. [Full-text PDF]

• Timothy L. Bailey and Michael Gribskov, "Concerning the accuracy of MAST E-values", Bioinformatics, 16:488-489, 2000. [Full-text PDF]

• Timothy L. Bailey and Michael Gribskov, Chapter 69, "Evaluating homology search algorithms", Currents in Computational Molecular Biology, pp. 137-138, edited by Satoru Miyano, Ron Shamir and Toshihisa Takagi, Universal Academy Press, Inc., Tokyo, Japan, 2000. Postscript

• William Noble Grundy and Timothy L. Bailey, "Family pairwise search with embedded motif models", Bioinformatics, 15:463-470, 1999. Abstract/ [Full-text HTML] [Full-text PDF] [Full-text PostScript]

• Timothy L. Bailey and William Noble Grundy, "Classifying proteins by family using the product of correlated p-values", Third international conference on computational molecular biology (RECOMB99), pp. 10-14, Association for Computing Machinery, New York, April, 1999. Postscript

• Timothy L. Bailey and Michael Gribskov, "Methods and statistics for combining motif match scores", Journal of Computational Biology, 5:211-221, 1998. Postscript

• Timothy L. Bailey and Michael Gribskov, "Combining evidence using $p$-values: application to sequence homology searches", Bioinformatics, 14:48-54, 1998. Postscript

• William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker, "Hidden Markov model analysis of motifs in steroid dehydrogenases and their homologs", Biochemical and Biophysical Research Communications, 231:760-766, 1997. Postscript

• Timothy L. Bailey and Michael Gribskov, "Score distributions for simultaneous matching to multiple motifs", Journal of Computational Biology, 4:45-59, 1997. [Full-text PDF] [Full-text PostScript]

• Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases", Journal of steroid biochemistry and molecular biology, 62:29-44, 1997.

• William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker, "Meta-MEME: Motif-based hidden Markov models of protein families", Computer Applications in the Biological Sciences (CABIOS), 13:397-406, 1997. Postscript

• William N. Grundy, Timothy L. Bailey and Charles P. Elkan, "ParaMEME: A parallel implementation Computer Applications in the Biological Sciences (CABIOS), 12:303-310, 1996. Postscript

• Timothy L. Bailey and Michael Gribskov, "The megaprior heuristic for discovering protein sequence patterns", Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology (ISMB'96), pp. 14-24, AAAI Press, Menlo Park, California, June, 1996. [Full-text PostScript] [Full-text PDF]

• Timothy L. Bailey, "Discovering motifs in DNA and protein sequences: The approximate common substring problem", Ph.D. dissertation, University of California, San Diego, 1995. Postscript

• Timothy L. Bailey and Charles Elkan, "The value of prior knowledge in discovering motifs with MEME", Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB'95), pp. 21-29, AAAI Press, Menlo Park, California, July, 1995. [Full-text PostScript] [Full-text PDF]

• Timothy L. Bailey and Charles Elkan, "The value of prior knowledge in discovering motifs with MEME", Technical Report CS95-413, Department of Computer Science, University of California, San Diego, 1995. [Full-text PostScript] [Full-text PDF]

• Timothy L. Bailey and Charles Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers using EM'', Machine Learning, 21:1-2(51-80), October-November, 1995. Postscript

• Timothy L. Bailey and Charles Elkan, Chapter 18, "Cross-validation and Modal Theories", Computational Learning Theory and Natural Learning Systems, pp. 345-359, Vol. 3, MIT Press, 1995. Postscript

• Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (ISMB'94), pp. 28-36, AAAI Press, Menlo Park, California, August, 1994. [Full-text PostScript] [Full-text PDF]

• Timothy L. Bailey and Charles Elkan, "Estimating the Accuracy of Learned Concepts", Proceedings of the Thirteenth International Joint Conference on Artificial Intelligence, pp. 895-900, AAAI Press, 1993. Postscript

Posters

• Michael Tallack, Thomas Whitington, Brooke Gardinier, Eleanor Wainwright, Janelle Keys, Marion Monet, Ehsan Nourbakhsh, Nicole Cloonan, Sean Grimmond, Timothy Bailey, and Andrew Charles Perkins, "KLF1 regulatory networks in primary erythroid cells'', 51st American Society of Hematology Annual Meeting, (ASH), 2009.

• Fabian A. Buske, Mikael Boden, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", AMATA, 2009.

• Bauer, D.C., Bailey, T.L. "STREAM : A Practical Workbench for the Quantitative Modeling of Transcription", GIW 2008.

• Whitington, T, Perkin, A., Bailey T.L. "Predicting tissue-specific transcription factor binding sites with chromatin modification information", GIW 2008.

• Arieshanti, I., Boden, M., Maetschke, S., Buske F. "Similar sequence or structure: A kernel function that brings together the best of two worlds", GIW 2008.

• Buske, F., Boden, M., Bailey, T.L. "Using Comparative Genomics to Associate Transcription Factors with their Roles", GIW 2008.

• Maruyama, O., Bailey, T.L. "Predicting Ttranscription Factors Binding Sites through Parsimonious Composite Patterns", APBC 2008.