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.
A focus of my work is 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 "CLIP-seq" and related protocols. Motif analysis is also useful for understanding the function and evolution of proteins.
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, which is used by thousands of biologists each month and has been cited over 12,000 times.
- January 2016 - Present. Professor, Department of Pharmacology, University of Nevada, Reno.
- January 2012 - December 2015. Associate Professor, Principal Research Fellow, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia.
- December 2009 - December 2015. Affiliate Senior Research Fellow, School of Chemistry and Molecular Biosciences, University of Queensland.
- February 2003 - December 2011. Senior Research Fellow, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia.
- March 1, 2002 - December 31, 2004. Senior Lecturer, Advanced Computational Modelling Center, University of Queensland, Brisbane, Qld, Australia.
- October 1, 2000 - May 1, 2001. Researcher, Center for Genome Research, Karolinska Institute, Stockholm, Sweden.
- July 1, 1998 - October 1, 2000. Assistant Research Scientist, Center for Advanced Computational Science and Engineering, University of California at San Diego.
- Spring, 1996. Lecturer in computer science at UCSD. (Concurrent with post-doctoral research position at the San Diego Supercomputer Center.)
- July 1995-June 30, 1998. Post-doctoral researcher at San Diego Supercomputer Center.