Timothy L Bailey

Summary

Affiliation: University of Queensland
Country: Australia

Publications

  1. pmc Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
    Lei Sun
    School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221008, PR China
    BMC Bioinformatics 13:331. 2012
  2. pmc Inferring direct DNA binding from ChIP-seq
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Nucleic Acids Res 40:e128. 2012
  3. pmc Quantifying similarity between motifs
    Shobhit Gupta
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
    Genome Biol 8:R24. 2007
  4. pmc MEME: discovering and analyzing DNA and protein sequence motifs
    Timothy L Bailey
    Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    Nucleic Acids Res 34:W369-73. 2006
  5. pmc The value of position-specific priors in motif discovery using MEME
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    BMC Bioinformatics 11:179. 2010
  6. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
  7. pmc Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
    Genome Res 22:1372-81. 2012
  8. pmc Genome-wide in silico prediction of gene expression
    Robert C McLeay
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 28:2789-96. 2012
  9. pmc MEME-ChIP: motif analysis of large DNA datasets
    Philip Machanick
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Bioinformatics 27:1696-7. 2011
  10. pmc Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
    Michael R Tallack
    Mater Medical Research Institute, Mater Hospital, Brisbane, Queensland 4101, Australia
    Genome Res 22:2385-98. 2012

Detail Information

Publications49

  1. pmc Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
    Lei Sun
    School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221008, PR China
    BMC Bioinformatics 13:331. 2012
    ..Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions...
  2. pmc Inferring direct DNA binding from ChIP-seq
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Nucleic Acids Res 40:e128. 2012
    ..CentriMo is now part of the MEME Suite software package available at http://meme.nbcr.net. All data and output files presented here are available at: http://research.imb.uq.edu.au/t.bailey/sd/Bailey2011a...
  3. pmc Quantifying similarity between motifs
    Shobhit Gupta
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
    Genome Biol 8:R24. 2007
    ..Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs...
  4. pmc MEME: discovering and analyzing DNA and protein sequence motifs
    Timothy L Bailey
    Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    Nucleic Acids Res 34:W369-73. 2006
    ..This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance...
  5. pmc The value of position-specific priors in motif discovery using MEME
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    BMC Bioinformatics 11:179. 2010
    ....
  6. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net...
  7. pmc Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
    Genome Res 22:1372-81. 2012
    ..With focus on biotechnological applications, we screen mammalian genomes for high-affinity triplex target sites that can be used to target genomic loci specifically and find that triplex formation offers a resolution of ~1300 nt...
  8. pmc Genome-wide in silico prediction of gene expression
    Robert C McLeay
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 28:2789-96. 2012
    ..ChIP-seq TF binding data, however, are tissue-specific and relatively difficult to obtain. This limits the applicability of gene expression models that rely on ChIP-seq TF binding data...
  9. pmc MEME-ChIP: motif analysis of large DNA datasets
    Philip Machanick
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Bioinformatics 27:1696-7. 2011
    ..While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets...
  10. pmc Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
    Michael R Tallack
    Mater Medical Research Institute, Mater Hospital, Brisbane, Queensland 4101, Australia
    Genome Res 22:2385-98. 2012
    ..Our study has identified two novel lncRNAs that are dynamically expressed during erythroid differentiation, and discovered a role for KLF1 in directing apoptotic gene expression to drive the terminal stages of erythroid maturation...
  11. pmc Sorting the nuclear proteome
    Denis C Bauer
    Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia
    Bioinformatics 27:i7-14. 2011
    ..Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed...
  12. pmc Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures
    Mikael Boden
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, St Lucia, Australia
    BMC Bioinformatics 7:68. 2006
    ..e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models...
  13. pmc Assigning roles to DNA regulatory motifs using comparative genomics
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
    Bioinformatics 26:860-6. 2010
    ..Their functional roles are defined by the genes they regulate. Uncovering these roles not only sheds light on the TF at hand but puts it into the context of the complete regulatory network...
  14. pmc Epigenetic priors for identifying active transcription factor binding sites
    Gabriel Cuellar-Partida
    Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
    Bioinformatics 28:56-62. 2012
    ..Using epigenetic data such as histone modification and DNase I, accessibility data has been shown to improve motif-based in silico methods for predicting such binding, but this approach has not yet been fully explored...
  15. ncbi request reprint Searching for statistically significant regulatory modules
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Bioinformatics 19:ii16-25. 2003
    ..True binding sites may be identified by their tendency to occur in clusters, sometimes known as regulatory modules...
  16. pmc STREAM: Static Thermodynamic REgulAtory Model of transcription
    Denis C Bauer
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 24:2544-5. 2008
    ..g. different tissues, knockout/additional TFs or mutated/missing TFBSs)...
  17. ncbi request reprint Prediction of protein B-factor profiles
    Zheng Yuan
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, Australia
    Proteins 58:905-12. 2005
    ..flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods...
  18. pmc Assessing phylogenetic motif models for predicting transcription factor binding sites
    John Hawkins
    Institute for Molecular Bioscience, University of Queensland, QLD, Australia
    Bioinformatics 25:i339-47. 2009
    ..However, these phylogenetic motif models (PMMs) have never been rigorously benchmarked in order to determine whether they lead to better prediction of TFBSs than obtained using simple position weight matrix scanning...
  19. pmc Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci
    Fabian A Buske
    Division of Genomics and Computational Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Bioinformatics 29:1895-7. 2013
    ..We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genomic architecture into account...
  20. doi request reprint DLocalMotif: a discriminative approach for discovering local motifs in protein sequences
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Australia
    Bioinformatics 29:39-46. 2013
    ..Using negatives, i.e. sequences known to not contain a local motif, can further increase the specificity of their discovery...
  21. pmc Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
    Robert C McLeay
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    BMC Bioinformatics 11:165. 2010
    ..In this paper, we explore ways to make MEA applicable in more settings, and evaluate the efficacy of a number of MEA approaches...
  22. pmc Inferring transcription factor complexes from ChIP-seq data
    Tom Whitington
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Nucleic Acids Res 39:e98. 2011
    ..SpaMo can assist researchers in extracting maximum information relating to binding mechanisms from their TF ChIP-seq data. SpaMo is available for download and interactive use as part of the MEME Suite (http://meme.nbcr.net)...
  23. doi request reprint Discovering sequence motifs
    Timothy L Bailey
    ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
    Methods Mol Biol 452:231-51. 2008
    ..A discussion of some limitations of motif discovery concludes the chapter...
  24. pmc Associating transcription factor-binding site motifs with target GO terms and target genes
    Mikael Boden
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Nucleic Acids Res 36:4108-17. 2008
    ..Results on human reference sets are similarly encouraging. Validation of our target gene prediction method shows that its accuracy exceeds that of simple motif scanning...
  25. pmc Tissue-specific prediction of directly regulated genes
    Robert C McLeay
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Bioinformatics 27:2354-60. 2011
    ....
  26. pmc Optimizing static thermodynamic models of transcriptional regulation
    Denis C Bauer
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 25:1640-6. 2009
    ..However, the parameter fitting process is computationally very expensive and this limits the number of alternative types of model that can be explored...
  27. pmc GONOME: measuring correlations between GO terms and genomic positions
    Stefan M Stanley
    Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
    BMC Bioinformatics 7:94. 2006
    ..However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions...
  28. pmc High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
    Tom Whitington
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:14-25. 2009
    ....
  29. pmc Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster
    Denis C Bauer
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
    BMC Bioinformatics 11:366. 2010
    ..However, all of the models to date assume a transcription factor (TF) to have either activating or repressing function towards all the genes it is regulating...
  30. doi request reprint Discovering novel sequence motifs with MEME
    Timothy L Bailey
    University of Queensland, Brisbane, Australia
    Curr Protoc Bioinformatics . 2002
    ..MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. MEME's hypertext (HTML) output also contains buttons that allow for the convenient use of the motifs in other searches...
  31. pmc Studying the functional conservation of cis-regulatory modules and their transcriptional output
    Denis C Bauer
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072 Australia
    BMC Bioinformatics 9:220. 2008
    ....
  32. doi request reprint A Bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies
    Mikael Boden
    Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
    J Comput Biol 17:617-30. 2010
    ..Supplementary Material is available online at www.liebertonline.com...
  33. ncbi request reprint Identifying sequence regions undergoing conformational change via predicted continuum secondary structure
    Mikael Boden
    School of Information Technology and Electrical Engineering, QLD 4072, The University of Queensland Australia
    Bioinformatics 22:1809-14. 2006
    ....
  34. pmc Cyclic peptides arising by evolutionary parallelism via asparaginyl-endopeptidase-mediated biosynthesis
    Joshua S Mylne
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Plant Cell 24:2765-78. 2012
    ..We believe this is evolutionary evidence that, in addition to its known roles in proteolysis, AEP is especially suited to performing protein cyclization...
  35. doi request reprint NFIA controls telencephalic progenitor cell differentiation through repression of the Notch effector Hes1
    Michael Piper
    Queensland Brain Institute, The University of Queensland, Brisbane, Australia
    J Neurosci 30:9127-39. 2010
    ....
  36. pmc Potential in vivo roles of nucleic acid triple-helices
    Fabian A Buske
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
    RNA Biol 8:427-39. 2011
    ....
  37. doi request reprint A probabilistic model of nuclear import of proteins
    Ahmed M Mehdi
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
    Bioinformatics 27:1239-46. 2011
    ..Despite progress on experimentally characterizing a number of nuclear localization signals, their presence alone remains an unreliable indicator of actual translocation...
  38. pmc Discriminative motif discovery in DNA and protein sequences using the DEME algorithm
    Emma Redhead
    Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072 Australia
    BMC Bioinformatics 8:385. 2007
    ....
  39. ncbi request reprint Estimating and evaluating the statistics of gapped local-alignment scores
    Timothy L Bailey
    ACMC, Mathematics Department, The University of Queensland, Brisbane, Queensland, 4072 Australia
    J Comput Biol 9:575-93. 2002
    ..We explain this paradox and argue that statistical accuracy, not classification accuracy, should be the primary criterion in comparisons of similarity search methods that return p-values that adjust for target sequence length...
  40. pmc DREME: motif discovery in transcription factor ChIP-seq data
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 27:1653-9. 2011
    ..Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF...
  41. doi request reprint Nuclear factor one X regulates Bobby sox during development of the mouse forebrain
    Chantelle Dixon
    The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
    Cell Mol Neurobiol 33:867-73. 2013
    ..Moreover, we reveal that NFIX can repress Bbx promoter-driven expression. Collectively, these data suggest that Bbx is a downstream target of NFIX during development of the forebrain. ..
  42. pmc A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells
    Michael R Tallack
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Genome Res 20:1052-63. 2010
    ..Additionally, we suggest new mechanisms for KLF1 cooperation with other transcription factors, in particular the erythroid transcription factor GATA1, to maintain homeostasis in the erythroid compartment...
  43. pmc Pseudo-messenger RNA: phantoms of the transcriptome
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e23. 2006
    ..Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level...
  44. ncbi request reprint Discovering sequence motifs
    Timothy L Bailey
    IMB University of Queensland
    Methods Mol Biol 395:271-92. 2007
    ..A discussion of some limitations of motif discovery concludes the chapter...
  45. ncbi request reprint Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  46. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  47. pmc Discovering sequence motifs with arbitrary insertions and deletions
    Martin C Frith
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tokyo, Japan
    PLoS Comput Biol 4:e1000071. 2008
    ..It may be equally useful for arbitrarily gapped motifs in DNA and RNA, although fewer examples of such motifs are known at present. GLAM2 is public domain software, available for download at http://bioinformatics.org.au/glam2...
  48. pmc The abundance of short proteins in the mammalian proteome
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e52. 2006
    ..Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway...
  49. ncbi request reprint Splicing bypasses 3' end formation signals to allow complex gene architectures
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Gene 403:188-93. 2007
    ..This bypassing mechanism permits nested and interleaved gene architectures, as well as fusion transcripts that combine exons from adjacent genes...