Timothy L. Bailey Senior Research Fellow Institute for Molecular Bioscience Affiliate Senior Research Fellow School of Chemistry and Molecular Bioscience University of Queensland Brisbane, Queensland 4072 Australia

Courier address: Institute for Molecular Bioscience Queensland Bioscience Precinct (Bldg 80) The University of Queensland 306 Carmody Road St Lucia, QLD 4067 Australia

Check out my IMB Group Leader Page

RESEARCH

My research seeks to understand all stages of gene expression and to construct computational models of how gene expression is regulated. To accomplish this goal, we develop and employ computational approaches for analyzing genomic, RNA and protein data. These approaches are based on statistical analysis, pattern recognition and mathematical modeling techniques, areas in which we have long experience.

Recently we have developed methods for finding the DNA-binding patterns (motifs) of transcription factor proteins utilizing high-throughput sequencing of chromatin immunoprecipitation data (ChIP-seq). Many of these analysis methods are directly applicable to the study of RNA-binding motifs as well through the analysis of RNA data from the related "CLIP-seq" protocol.

I have also developed non-linear models that integrate predictions of binding by transcription factors to estimate the level of transcription of genes. Currently, we are extending these approaches to use large-scale data on the state of the genome (chromatin state), as well as the presence of RNA stability motifs, to improve the models of gene expression.

Making the algorithms and models we develop easily accessible to biologists is a major goal. We try to provide web-based interfaces, and much of my work is included in the popular MEME Suite of sequence analysis tools. Check them out.

I'm always looking for promising Honours and PhD students, so please contact me [t.bailey AT uq.edu.au] if you are interested in pursuing a degree in Bioinformatics or Computational Biology as part of my research group at The University of Queensland in beautiful Brisbane, Australia.

Publications

Supplementary data/software for publications

Links

• The MEME Suite of Motif-Based Sequence Analysis Tools
  • [Usage Report]
  • [Current Load]
• STREAM: modeling, visualizing, and predicting the regulation of the transcription rate of a target gene
• DEME: Discovering discriminative motifs in DNA and protein sequences
• Protein Continuum Secondary Structure Predictor
• Predicting Good Recombination Sites in Protein sequences
• GONOME: Finding Associations between Genomic Positions and Genome Ontology (GO) Terms

Teaching

• BIOL3014 -- Advanced Bioinformatics (Winter 2010)
• BIOL3014 -- Advanced Bioinformatics (Winter 2009)
• BIOL3014 -- Advanced Bioinformatics (Winter 2008)
• BIOL3014 -- Advanced Bioinformatics (Winter 2005)

My Students

• Robert Mcleay, PhD student
• Fabian Buske, PhD student
• Ahmed Mehdi, PhD student
• Lei Sun, visiting PhD student

Former Students

• Gabriel Cuellar Partida, undergraduate intern
• Tom Whitington, PhD
• Denis Bauer, PhD
• Emma Redhead, Honours Student
• Rolv Seehuus, Visiting PhD student (Norwegian University of Science and Technology)

Some of my coworkers and collaborators:

• John Hawkins, Former Post Doc
• Bill Noble
• Mikael Bodén
• Martin Frith
• Charles Elkan
• Michael Gribskov
• Kevin Burrage
• Mark Ragan

Other

• MEME and MAST Figure
• MetaMEME Figure
• EPS from Powerpoint
• gnuplot tricks

Contact me