During brain development, cells that will form the various structures and layers of the mature brain go through waves of proliferation, migration, differentiation, and maturation to form the different cell types of the brain. Control of gene expression enables cells to make the different proteins required at different stages and across different functions, from developmental transcription factors to lineage-specific neurotransmitters. Similarly, control of gene expression enables cells to maintain homeostasis and respond to environmental stimuli. Our group investigates the complex regulatory circuitry that enables tight transcriptional control, including the primary DNA sequences, the higher order epigenetic structure of chromatin, the transcription factors and other DNA and chromatin-associated proteins, and finally the transcribed RNA and translated protein products.

Research Areas

Cis-regulatory elements and regulatory circuits in brain development


Cis-regulatory elements are DNA sequences that act as control switches to activate or repress transcription of target genes. These elements drive expression patterns that are specific to cell type, region, and developmental stage in the brain. We focus on regulatory elements called enhancers, which activate target genes via transcription factor binding, promoter looping, and transcriptional activation. The big question driving our work is can we combine information from experiments that examine transcription factor binding, epigenetic state, and gene expression to understand the regulatory circuits well enough to model cellular lineage specification and neuronal function in the brain? Such an understanding is critical to unlocking the biology of brain development and evolution as well as understanding neurodevelopmental disorders such as autism, epilepsy, and schizophrenia.

Lab projects in this area:

  • Understanding the genomic basis of lineage specification in the brain (collaboration with John Rubenstein (UCSF))
  • Using mouse models to identify mechanisms and pathology associated with disease mutations
  • Functional approaches to understanding the sequence-encoded function of enhancers


Gene regulation in rodent models of neurological disorders

Mouse and rat models have been critical to understanding neurological disorders, enabling the study of brain development and function in mammalian models. Our group examines genetic and environmental models of neurological disorders, investigating how changes in gene expression linked to pathology are regulated. Current areas of focus include autism spectrum disorders, epilepsy, schizophrenia, and traumatic brain injury. Our goal is to understand the epigenetic-mediated contribution of gene expression to these disorders, and, ultimately, to developing treatments by re-balancing expression by genetic and epigenetic modulation.

Lab projects in this area:

  • Genomic screens and mouse models to study regulatory impacts and phenotypes produced by non-coding mutations
  • Linking maternal immune activation to neurodevelopmental pathology (collaboration with Kim McAllister (UCD))
  • Using genomics to map pathology in a rat model of traumatic brain injury (collaboration with Gene Gurkoff (UCD))


Applications of genomics towards understanding human health

The findings from human genetic studies drive much of our research, and a constant goal is to strengthen the connections between clinical research, to basic science and animal models, and back to translational approaches to improve clinical care.

Current and previous funding sources

  • National Institute of General Medical Sciences
  • National Institute of Mental Health
  • Simons Foundation Autism Research Initiative
  • Dravet Syndrome Foundation
  • Brains and Behavior Foundation (NARSAD Young Investigator Award)
  • MIND Institute – Autism Research Training Program (ARTP)