Ewa Deelman and Ann Chervenak will be part of a new
$9 million research effort headquartered at the Keck
School of Medicine at USC
The two-year Grand Opportunity grant, funded
through the National Institutes of Mental Health, will
allow researchers to use DNA sequencing and
profiling technologies to create an atlas of when and
where thousands of genes are expressed during
key periods of development. The findings will be
freely accessible to scientists worldwide and provide
a foundation for discovering the origins of mental
disorders.
The NIH description of the project is headlined "Atlas Will Reveal When and Where Genes Turn On
in the Brain." It notes "When and where in the
brain a gene turns on holds clues to its possible role
in disease. For example, a recent study found that
forms of a gene associated with schizophrenia are
over-expressed in the fetal brain, adding to
evidence implicating this critical developmental
period.
Deelman and Chervenak will support the effort of
processing and managing
high-throughput RNA sequencing data. ISI
Project Leader Deelman (left) will
employ the Pegasus Workflow Management
System and associated
technologies to support the data analysis and data
management within the
project. Workflows will automatically process data
coming off the next
generation sequencing machines and derive the
gene expression levels of
various regions of the developmental human brain
Workflow tasks will
include domain computations, such as sequence
alignment algorithms, as
well as simple data format translations. The
Pegasus system has already
been adopted by the researchers at the USC Epigenome Center. Ben
Berman and Peter Laird at
the Epigenome Center are the key collaborators,
leading the integration
the Pegasus system into their core genomics
workflows. Pegasus is used
today to processes RNA-Seq, ChiP-Seq, DNA re-
sequencing and DNA
methylation/histone modification data.
ISI Project Leader Chervenak will design the data
management and
data upload capabilities for the project, making USC
findings available
to the Allen Brain Institute, which will then broadly
disseminate them.
Chervenak will leverage her participation within the BIRN project to
ensure that the data disseminated by the project is
compatible with BIRN.
James A. Knowles, professor of psychiatry at the
Keck School of Medicine of USC, and Pat Levitt,
director of the Zilkha Neurogenetic Institute at the
Keck School of Medicine, will lead the project in
collaboration with researchers at Yale University
and the Allen Institute for Brain Science in Seattle,
Wash.
"This project will allow us to document which
individual genes and sets of genes are turned on
and off in different brain regions through the whole
developmental time period," said Knowles, the
principal investigator on the project. "This
information is essential for understanding normal
and abnormal brain development."
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