Timothy Bailey, Ph.D.|
Senior Research Fellow
Institute for Molecular Bioscience
Affiliate Senior Research Fellow
School of Chemistry and Molecular Bioscience
University of Queensland, Australia
The advent of affordable high-throughput sequencing has resulted in tremendous advances in
our understanding of transcriptional regulation. This talk will focus on the types of questions
that we can now ask using ChIP-seq, and on some of the most useful algorithms and approaches for answering them. We will illustrate these using our recently
published analysis of the role of transcription factor Klf1 in the development of red blood
cells. We will discuss identifying the targeted genes, targeted genomic regions, biological
roles, DNA-binding affinity, co-factors and protein-complex partners of the ChIP-ed transcription
factor. To aid in accomplishing this last task, we will describe SpaMo, an algorithm we recently developed for identifying
transcription factor complexes from ChIP-seq data.
Timothy Bailey is a Senior Research Fellow at the Institute for
Molecular Biosciences at the University of Queensland. His group develops computational
approaches for studying the mechanisms gene expression. Current projects include the
analysis ChIP data, utilization of epigenetic data for predicting regulation, and
exploring the role of DNA-RNA triplex formation in regulation. This work funded by the
Australian Research Council's Centre of Excellence in Bioinformatics, and by the NIH.
Dr Bailey is known for developing the MEME motif discovery algorithm, as well as
for his roles in creating a number of widely-used motif-based sequence analysis
tools (MAST, Meta-MEME, MCAST, GOMO, and Tomtom), all of which are integrated into the MEME Suite of tools (meme.nbcr.net).
Dr Bailey received his Bachelors degree from Stanford University (Mathematical Sciences, 1977)
and his PhD from UCSD (Computer Science, 1995). He worked in industry for more than a decade in computer graphics before beginning
his career in computational biology.