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

Interests

• My research is about discovering knowledge from data using techniques from machine learning, data mining and statistics.
• My focus is on applications in computational biology and genomics where the need for fast and reliable ways to make sense of the flood of data from modern, high-throughput biological experiments is extremely acute.
• I developed and support two highly-utilized tools for biological sequence analysis: MEME (for motif discovery) and MAST (for scanning sequences with motifs).
• Other tools I have helped develop include Meta-MEME and MCAST for motif-based sequence modeling, various tools for predicting protein properties, structure and family membership, and GONOME, a tool for finding associations between genomic positions and gene annotation classes.
• Hallmarks of my research are making software tools available to users via free web interfaces, and developing statistical methods for insuring the reliability of predictions made by the algorithms.
• Current projects include developing static models of the transcriptional output of genes; studying the function of small RNA in human cells; exploring the regulation of genes involved in the development of red blood cells; predicting the targets of transcription factors using methods combining models DNA of evolution with models of DNA binding.

Publications

Available positions in my research group

• November 3, 2009: Postdoctoral Position available in "Integrative genomics approaches to transcriptional regulation".

Links

• IMB Group Leader Home Page
• MEME: biological sequence motif discovery tool
• MAST: Motif Alignment and Search Tool
• Meta-MEME: Motif-based hidden Markov modeling of biological sequences
• STREAM: modeling, visualizing, and predicting the regulation of the transcription rate of a target gene
• DEME: Discovering discriminative motifs in DNA and protein sequences
• GLAM2: Discovering GAPPED 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
• FPS: Family Pairwise Search Protein Family Classification

Teaching

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

My Students

• Denis Bauer, PhD student
• Tom Whitington, PhD student
• Robert Mcleay, PhD student
• Fabian Buske, PhD student

Former Students

• 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/MAST Usage Stats
• MEME/MAST/MetaMEME Usage Report [postscript] [PDF]
• MEME and MAST Figure
• MetaMEME Figure
• EPS from Powerpoint
• gnuplot tricks

Contact me