TIMOTHY L. BAILEY, Ph.D.
Department of Pharmacology
School of Medicine
University of Nevada, Reno
(775)-784-4651
timothybailey@unr.edu
https://tlbailey.bitbucket.io
.
Last updated: December 27, 2021.




CURRENT POSITIONS

Professor
Department of Pharmacology
School of Medicine
University of Nevada, Reno
.
Honorary Principal Research Fellow
Institute for Molecular Bioscience
The University of Queensland
Brisbane, Australia




PUBLICATIONS

  1. Charles E. Grant and Timothy L. Bailey, “XSTREME: Comprehensive motif analysis of biological sequence datasets”, bioRxiv, September 3, 2021. [Abstract and Full Text]
  2. Timothy L. Bailey and Charles E. Grant, “SEA: Simple Enrichment Analysis of motifs”, bioRxiv, August 24, 2021. [Abstract and Full Text]
  3. Timothy L. Bailey, “STREME: Accurate and versatile sequence motif discovery”, Bioinformatics, 37:2834-2840, 2021. [Abstract and Full Text]
  4. Timothy O’Connor, Charles E. Grant, Mikael Bodén and Timothy L. Bailey, “T-Gene: Improved target gene prediction”, Bioinformatics, 36(12):3902-3904, 2020. [Abstract and Full Text]
  5. Timothy O’Connor, Charles E. Grant, Mikael Bodén and Timothy L. Bailey, “T-Gene: Improved target gene prediction”, bioRxiv, preprint, 2019. [Abstract and Full Text]
  6. Alice Cheng, Charles E. Grant, William S. Noble and Timothy L. Bailey, “MoMo: Discovery of statistically significant post-translational modification motifs”, Bioinformatics, 35(16):2774-2782, 2019. [Abstract and Full Text]
  7. Mehdi Moustaqil, Frank Fontaine, Jeroen Overman, Alex McCann, Timothy L Bailey, Akshay Bhumkar, Dominic J B Hunter, Paulina Rudolffi, Yong-Heng Huang, Ralf Jauch, Yann Gambin, Mathias Francois, Nicole Giles, “Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor”, Nucleic Acids Research, 46:11381–11395, 2018. [Abstract and Full Text]
  8. A. Cheng, C. E. Grant, T. L. Bailey and W. S. Noble, “MoMo: Discovery of post-translational modification motifs”, bioRxiv, preprint, 2017. [Abstract and Full Text]
  9. Melissa D. Ilsley, Kevin R. Gillinder, Graham W. Magor, Sthephen Huang, Timothy Bailey, Merlin Crosley, Andrew C. Perkins, “Krüppel-like factors compete for promoters and enhancers to fine-tune transcription”, Nucleic Acids Research, 45:6572–6588, 2017. [Abstract and Full Text]
  10. Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril Robertson, Kelly Holmes, Angela Salim, Sreeman Mamidyala, Mark Butler, Ashley Robinson, Wayne Johnston, Kirill Alexandrov, Brian Black, Benjamin Hogan, Sarah De Val, Robert Capon, Jason Carroll, Timothy Bailey, Peter Koopman, Ralf Jauch, Mark Smyth, Matthew Cooper, Yann Gambin, and Mathias Francois, “Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice”, eLIFE, 6:e21221, 2017. [Abstract and Full Text]
  11. Kevin R. Gillinder, Melissa D. Ilsley, Danitza Nebor, Ravi Sachidanandam, Mathieu Lajoie, Graham W. Magor, Michael R. Tallack, Timothy Bailey, Michael J. Landsberg, Joel Mackay, Michael W. Parker, Luke A. Miles, Joel H. Graber, Luanne L. Peters, James J. Bieker, Andrew C. Perkins, “Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and derails differentiation”, Nucleic Acids Research, 45(3):1130–1143, 2017. [Abstract and Full Text]
  12. Timothy O’Connor, Mikael Bodén, Timothy L. Bailey, “CisMapper: Predicting regulatory interactions from transcription factor ChIP-seq data”, Nucleic Acids Research, 45:e19, 2017. [Abstract and Full Text]
  13. Coby Viner, James Johnson, Nicolas Walker, Hui Shi, Marcela Sjöberg, David J. Adams, Anne C. Ferguson-Smith, Timothy L. Bailey, and Michael M. Hoffman, “Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet”, bioRxiv, preprint, 2016. [Abstract and Full Text]
  14. Charles E. Grant, James Johnson, Timothy L. Bailey, William S. Noble, “MCAST: Scanning for cis-regulatory motif clusters”, Bioinformatics, 32(8):1217–1219, 2016. [Abstract and Full Text]
  15. Jonathan WC Lim, Amber-Lee S Donahoo, Jens Bunt, Timothy J Edwards, Laura R Fenlon, Ying Liu, Jing Zhou, Randal X Moldrich, Michael Piper, Ilan Gobius, Timothy L Bailey, Naomi R Wray, Nicoletta Kessaris, Mu-Ming Poo, John LR Rubenstein, and Linda J Richards, “EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex”, Development, 142(21):3746–3757, 2015. [Abstract and Full Text]
  16. Christian Larney, Timothy Bailey, and Peter Koopman, “Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species”, BMC Developmental Biology, 15:34, 2015. [Abstract and Full Text]
  17. Timothy L. Bailey, James Johnson, Charles E. Grant and William S. Noble, “The MEME Suite”, Nucleic Acids Research, W1:W39–W49, 2015. [Abstract and Full Text]
  18. Diana Vidovic, Lachlan Harris, Tracey Harvey, Yee Hsieh Evelyn Heng, Aaron Smith, Jason Osinski, James Hughes, Paul Thomas, Richard M. Gronostajski, Timothy L. Bailey and Michael Piper, “Expansion of the lateral ventricles underlies the hydrocephalus evident in mice lacking the transcription factor NFIX”, Brain Research, 1616:71–87, 2015.
  19. Timothy R. O’Connor and Timothy L. Bailey, “Creating and validating cis-regulatory maps of tissue-specific gene expression regulation”, Nucleic Acids Research, 42:11000–11010, 2015. [Abstract and Full Text]
  20. Tom Lesluyes, James Johnson, Philip Machanick and Timothy L. Bailey, “Differential motif enrichment analysis of paired ChIP-seq experiments”, BMC Genomics, 15:752, 2014. [Abstract and Full Text]
  21. Christian Larney, Timothy Bailey, and Peter Koopman, “Switching on Sex: Transcriptional Regulation of the Testis-Determining Gene”, Development, 141:2195–2205, 2014. [IF 6.2] [Abstract and Full Text]
  22. Aidan O’Brien and Timothy L. Bailey, “GT-Scan: identifying unique genomic targets”, Bioinformatics, 30:2673–2675, 2014. [Abstract and Full Text]
  23. Emi Tanaka, Timothy L. Bailey and Uri Keich, “Improving MEME via a two-tiered significance analysis”, Bioinformatics, 30:1965–1973, 2014. [IF 5.3] [Abstract and Full Text]
  24. Mathieu Lajoie, Yu-chih Hsu, Richard M Gronostajski and Timothy L. Bailey, “An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation”, BMC Genomics, 15:231, 2014. [IF 4.4] [Abstract and Full Text]
  25. Ahmed M. Mehdi, Ralph Patrick, Timothy L. Bailey and Mikael Bodén, “Predicting the dynamics of protein abundance”, Molecular and Cellular Proteomics, 13:1330–1340, 2014. [IF 7.4] [Abstract and Full Text]
  26. Ferhat Ay, Timothy L. Bailey and William S. Noble, “Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts”, Genome Research, 24:999–1011, 2014. [IF 14.4] [Abstract and Full Text]
  27. Wenxiu Ma, William S. Noble, Timothy L. Bailey, “Motif-based analysis of large nucleotide datasets using MEME-ChIP”, Nature Protocols, 9:1428–1450, 2014. [IF 9.9] [Abstract and Full Text]
  28. Michael Piper, Guy Barry, Tracey Harvey, Robert McLeay, Aaron Smith, Lachlan Harris, Sharon Mason, Brett Stringer, Bryan Day, Naomi Wray, Richard Gronostajski, Timothy Bailey, Andrew Boyd, and Linda Richards, “NFIB-mediated repression of the epigenetic factor Ezh2 regulates cortical development”, Journal of Neuroscience, 34:2921–2930, 2014. [IF 7.1] [Abstract and Full Text]
  29. Yee Hsieh Evelyn Heng, Robert McLeay, Guy Barry, Kathleen Cato, Celine Plachez, Erica Little, Sharon Mason, Chantelle Reid, Richard M. Gronostajski, Timothy L. Bailey, Linda J. Richards and Michael Piper, “NFIX Regulates Neural Progenitor Cell Differentiation During Hippocampal Morphogenesis”, Cerebral Cortex, 24:261–279, 2014. [Abstract and Full Text]
  30. Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim and Jie Zhang, “Practical guidelines for the comprehensive analysis of ChIP-seq data”, PLoS Computational Biology, 9(11):e1003326, 2013. [IF 4.9] [Abstract and Full Text]
  31. Chantelle Dixon, Tracey J. Harvey, Aaron G. Smith, Richard M. Gronostajski, Timothy L. Bailey, Linda J. Richards and Michael Piper, “Nuclear factor one X regulates Bobby Sox during development of the mouse forebrain”, Cellular and Molecular Neurobiology, 33(7):867–873, 2013. [IF 2.3] [Abstract and Full Text]
  32. Emily S.W. Wong, Margaret Hardy, David Wood, Timothy Bailey and Glenn F. King, “SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula”, PLoSOne, 8:e66279, 2013. [IF 4.1] [Abstract and Full Text]
  33. Fabian A. Buske, Denis C. Bauer, John S. Mattick and Timothy L. Bailey, “Triplex-Inspector: An analysis tool for triplex-mediated targeting of genomic loci”, Bioinformatics, 29:1895–1897, 2013. [IF 5.3] [Abstract and Full Text]
  34. Palaniraja Thandapani, Tim O’Connor, Timothy L. Bailey and Stéphane Richard, “Defining the RGG/RG motif”, Molecular Cell, 50:613–623, 2013. [IF 14.2] [Abstract and Full Text]
  35. Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey and Mikael Bodén, “DLocalMotif: A discriminative approach for discovering local motifs in protein sequences”, Bioinformatics, 29:39–46, 2013. [IF 5.3] [Abstract and Full Text]
  36. Lei Sun, Zhihua Zhang, Timothy L Bailey, Andrew C Perkins, Michael R Tallack, Zhao Xu and Hui Liu, “Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study”, BMC Bioinformatics, 13:331, 2012. [Abstract and Full Text]
  37. Kevin A. Peterson, Yuichi Nishi, Wenxiu Ma, Anastasia Vedenko, Leila Shokri, Xiao Xiao Zhang, Matthew McFarlane, Jan Philipp Junker, Alexander van Oudenaarden, Tarjei Mikkelsen, Bradley E. Bernstein, Timothy L. Bailey, Martha L. Bulyk, Wing H. Wong, and Andrew P. McMahon, “Neural-specific Sox2 input and differential Gli binding affinity provide context and positional information in Shh-directed neural patterning”, Genes and Development, 26:2802–2816, 2012. [Abstract and Full Text]
  38. Robert C. McLeay, Tom Lesluyes, Gabriel Cuellar Partida and Timothy L. Bailey, “Genome-wide in silico prediction of gene expression”, Bioinformatics, 28:2789–2796, 2012. [Abstract and Full Text]
  39. Michael R. Tallack, Graham W. Magor, Benjamin Dartigues, Lei Sun, Stephen Huang, Jessica M. Fittock, Sally V. Fry, Evgeny A. Glazov, Timothy L. Bailey and Andrew C. Perkins, “Novel roles for Klf1 in erythropoiesis revealed by mRNA-seq”, Genome Research, 22:2385–2398, 2012. [Abstract and Full Text]
  40. Yuefeng Lin, Zhihua Li, Fatih Ozsolak, Sang Woo Kim, Gustavo Arango-Argoty, Teresa T. Liu, Scott A. Tenenbaum, Timothy Bailey, A. Paula Monaghan, Patrice M. Milos and Bino John, “An in-depth map of polyadenylation sites in cancer”, Nucleic Acids Research, 40:8460–8471, 2012. [Abstract and Full Text]
  41. Joshua S. Mylne, Lai Yue Chan, Aurelie H. Chanson, Norelle L. Daly, Hanno Schaefer, Timothy L. Bailey, Philip Nguyencong, Laura Cascales and David J. Craik, “Cyclic peptides arising by parallelism via asparaginyl-endopeptidase mediated biosynthesis”, The Plant Cell, 24:2765-2778, 2012. [Abstract and Full Text]
  42. Timothy L. Bailey and Philip Machanick, “Inferring direct DNA binding from ChIP-seq”, Nucleic Acids Research, 40:e128, 2012. [Abstract and Full Text]
  43. Fabian A. Buske, Denis C. Bauer, John S. Mattick and Timothy L. Bailey, “TRIPLEXATOR: Detecting nucleic acid triple helices in genomic and transcriptomic data”, Genome Research, 22:1372-1381, 2012. [Abstract and Full Text]
  44. Jing Yu, M. Todd Valerius, Mary Duah, Karl Staser, Jennifer K Hansard, Jin-jin Guo, Jill McMahon, Joe Vaughan, Diane Faria, Kylie Georgas, Bree Rumballe, Qun Ren, A. Michaela Mayer, Jan P Junker, Rathi D Thiagarajan, Philip Machanick, Paul A Gray, Alexander van Oudenaarden, David H Rowitch, Charles D Stiles, Qiufu Ma, Sean M Grimmond, Timothy Bailey, Melissa H Little, and Andrew P McMahon, “Identification of molecular compartments and genetic circuitry in the developing mammalian kidney”, Development, 139:1863-1873, 2012. [Abstract and Full Text]
  45. Céline Plachez, Kathleen Cato, Robert McLeay, Yee Hsieh Evelyn Heng, Timothy L. Bailey, Richard M. Gronostajski, Linda J. Richards, Adam C. Puche and Michael Piper, “Expression of Nuclear Factor One A and B in the Olfactory Bulb”, Journal of Comparative Neurology, 520:3135-3149, 2012. [Abstract and Full Text]
  46. Gabriel Cuellar Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble and Timothy L. Bailey, “Epigenetic priors for identifying active transcription factor binding sites”, Bioinformatics, 28:56-62, 2012. [Abstract and Full Text]
  47. Robert C. McLeay, Chris J. Leat and Timothy L. Bailey, “Tissue-specific prediction of directly regulated genes”, Bioinformatics, 27:2354-2360, 2011. [Abstract and Full Text]
  48. Thomas Whitington, Martin Frith, James Johnson and Timothy L. Bailey, “Inferring transcription factor complexes from ChIP-seq data”, Nucleic Acids Research, 39(15):e98, 2011. [Abstract and Full Text]
  49. Timothy L. Bailey, “DREME: Motif discovery in transcription factor ChIP-seq data”, Bioinformatics, 27:1653–1659, 2011. [Abstract and Full Text]
  50. Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble and Uri Keich, “Analysis of the similarity measures between motifs”, Bioinformatics, 27:1603–1609, 2011. [Abstract and Full Text]
  51. Philip Machanick and Timothy L. Bailey, “MEME-ChIP: motif analysis of large DNA datasets”, Bioinformatics, 27:1696–1697, 2011. [Abstract and Full Text]
  52. Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire and Mikael Bodén “Sorting the nuclear proteome”, Bioinformatics, 27(13):i7–i14, 2011. [Abstract and Full Text]
  53. Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén, “A probabilistic model of nuclear import of proteins”, Bioinformatics, 27:1239–1246, 2011. [Abstract and Full Text]
  54. Charles E. Grant, Timothy L. Bailey and William S. Noble, “FIMO: Scanning for occurrences of a given motif”, Bioinformatics, 27:1017–1018, 2011. [Abstract and Full Text]
  55. Fabian A. Buske, John S. Mattick and Timothy L. Bailey, “Potential in vivo roles of nucleic acid triple-helices”, RNA Biology, 8:427-439, 2011. [Abstract and Full Text]
  56. Denis C. Bauer, Fabian A. Buske and Timothy L. Bailey, “Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster”, BMC Bioinformatics, 11:366, 2010. [Abstract and Full Text]
  57. Mikael Bóden, Graham Dellaire, Kevin Burrage, Timothy L. Bailey, “A Bayesian network model of proteins association with promyelocytic leukemia (PML) nuclear bodies”, Journal of Computational Biology, 17, 617–630, 2010. [Abstract and Full Text]
  58. Robert McLeay and Timothy L. Bailey, “Motif Enrichment Analysis: A unified framework and evaluation on ChIP data”, BMC Bioinformatics, 11:165, 2010. [Abstract and Full Text]
  59. Kengo Sato, Tom Whitington, Timothy L. Bailey and Paul Horton, “Improved Prediction of Transcription Binding Sites from Chromatin Modification Data”, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2010), pp. 1–7, May, 2010. [Full Text]
  60. Michael R Tallack, Tom Whitington, Wai Shan Yuen, Elanor Wainwright, Janelle R Keys, Brooke Gardiner, Ehsan Nourbaksh, Nicole Cloonan, Sean M Grimmond, Timothy L Bailey and Andrew C Perkins, “A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells”, Genome Research, 20:1052–1063, 2010. [Abstract and Full Text]
  61. 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”, Journal of Neuroscience, 30:9127–9139, 2010. [Abstract and Full Text]
  62. Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, “Assigning roles to DNA regulatory motifs using comparative genomics”, Bioinformatics, 26(7):860–866, 2010. [Abstract and Full Text] [Supplementary Data]
  63. Timothy L. Bailey, Mikael Bóden, Tom Whitington and Philip Machanick, “The value of position-specific priors in motif discovery using MEME”, BMC Bioinformatics, 11:179, 2010. [Abstract and Full Text] [Supplementary Data (yeast_suppl_data.tgz)]
  64. Denis C. Bauer, Fabian A. Buske, Timothy L. Bailey and Mikael Bodén, “Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster”, Neurocomputing, 73, 2300–2307, 2010. [Abstract and Full Text]
  65. Denis C Bauer and Timothy L. Bailey, “Optimizing static thermodynamic models of transcriptional regulation”, Bioinformatics, 25:1640–1646, 2009. [Abstract and Full Text]
  66. 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]
  67. 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]
  68. 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]
  69. 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]
  70. Denis C Bauer and Timothy L. Bailey, “STREAM: Static Thermodynamic REgulAtory Model of transcription”, Bioinformatics, 24:2544–2525, 2008. [Abstract and Full Text]
  71. 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]
  72. 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.
  73. 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]
  74. 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]
  75. 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]
  76. 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.
  77. 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]
  78. Martin C. Frith, Piero Carninci, Chikatoshi Kai, Jun Kawai, Timothy L. Bailey, Yoshihide Hayashizaki, John S Mattick, “Splicing bypasses 3’ end formation signals to allow complex gene architectures”, Gene, 403:188–193, 2007. [Abstract and Full Text]
  79. Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, “Quantifying similarity between motifs”, Genome Biology, 8(2):R24, 2007. [Abstract and Full Text]
  80. 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]
  81. 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]
  82. 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]
  83. 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]
  84. 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, John S Mattick, “Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA”, RNA Biology, 3:40–48, 2006. [Full-text PDF]
  85. 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]
  86. 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]
  87. Piero Carninci et al., “The transcriptional landscape of the mammalian genome”, Science, 309:1559–1563, 2005. [Abstract and Full Text]
  88. 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]
  89. 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]
  90. 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]
  91. Timothy L. Bailey and William Noble, “Searching for statistically significant regulatory modules”, Bioinformatics, 19 Suppl 1:II16–II25, 2003. [Full-text PDF]
  92. 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]
  93. 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.
  94. 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]
  95. Timothy L. Bailey and Michael Gribskov, “Concerning the accuracy of MAST E-values”, Bioinformatics, 16:488–489, 2000. [Full-text PDF]
  96. 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
  97. William Noble Grundy and Timothy L. Bailey, “Family pairwise search with embedded motif models”, Bioinformatics, 15:463–470, 1999. [Abstract] [Full-text PDF]
  98. 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
  99. Timothy L. Bailey and Michael Gribskov, “Methods and statistics for combining motif match scores”, Journal of Computational Biology, 5:211–221, 1998. Postscript
  100. Timothy L. Bailey and Michael Gribskov, “Combining evidence using p-values: application to sequence homology searches”, Bioinformatics, 14:48–54, 1998. Postscript
  101. 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
  102. 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]
  103. 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.
  104. 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
  105. 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
  106. 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]
  107. 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
  108. 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]
  109. 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]
  110. 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
  111. 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
  112. 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]
  113. 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
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