Matthew T. Weirauch, PhD

Assistant Professor, UC Department of Pediatrics

Phone: 513-803-9078


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Transcription factors; transcriptional regulation; functional genomics; genome analysis; network-based algorithms; bioinformatics

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The staggering diversity of life on our planet stems from the elegant system encoded in our genomes.   A major finding of the genomic era is that a substantial proportion of the wide range of biological form and function is likely explained by differences in gene regulation (the processes governing how and when genes are utilized), as opposed to differences in the genes themselves.  An important component of gene regulation is the binding of transcription factors (TFs) to genomic DNA.  A typical metazoan genome contains thousands of TFs, and knowledge of their sequence binding preferences is crucial to our understanding of the “regulatory code” governing health and disease. 

Two major obstacles stand in our way before we can even begin to accurately model gene regulation.  First, we must gain a thorough knowledge of the sequence binding preferences of TFs.  Of an estimated 165,000 TFs present in the approximately 300 sequenced eukaryotic organisms, sequence preferences are currently known for only ~2,000 (~1%).  In collaboration with Tim Hughes at the University of Toronto, I have developed a joint experimental and computational approach to determine or predict binding preferences for > 55,000 eukaryotic TFs (>30%), representing an order of magnitude improvement over our current knowledge.  Second, there is an ongoing controversy surrounding the optimal way to represent TF binding preferences, and how to accurately model them to predict binding to genomic sequences.  To address this issue, I have recently led the largest evaluation of computational TF binding models to date, involving 20 methods developed by researchers from around the world.  Together, these two studies will provide the groundwork for the future development of models of gene regulation in both normal and disease states.

Education and Training

Postdoctoral Fellow: University of Toronto (Donnelly Center for Cellular and Biomolecular Research), Toronto, Ontario, Canada.

PhD: Bioinformatics, University of California Santa Cruz, Santa Cruz, California.

BSc: Computer Science, Pennsylvania State University, University Park, PA.


View PubMed Publications


Lupus Association with Signal Transducer and Activator of Transcription 4. Investigator. US Department of Veterans Affairs. 2012.