Sample-based Models of Biomolecular
Structure and Dynamics as Microscopes over the Healthy and the
Diseased Cell
Thursday, November 9th, 2017 at
11:00am
HUB, Room 1 & 2
Dr. Amarda Shehu
Department of Computer Science
George Mason University
In 1952, Sir Alan Turing published
“The chemical basis of morphogenesis,” where he introduced the
ingredients of a model-driven investigation into how matter
changes form. Decades of scientific enquiry have demonstrated just
how fundamental form and changes to form are to function and
function modulation, whether in understanding and predicting phase
transitions in statistical physics, the evolution and dynamics of
complex networks in network science, or structural rearrangements
of biological molecules regulating cellular processes in a growing
cell or a beating heart.
A primary objective of my research
is the design of novel algorithmics for elucidating biomolecular
structures and their rearrangements as fundamental to
understanding (dys)function, cellular processes, our own biology,
disease, and disease treatments. My research advocates for a
paradigm shift to address the algorithmic impasse in physics-based
simulation. Inspiration comes from a combination of biology and
science and engineering fields that model dynamic systems. My
research group has proposed and matured sample-based models that
are allowing us to conduct in-silico biology at scales previously
impossible. These models build increasingly-detailed
representations of biomolecular energy landscapes and equilibrium
structural dynamics. They are now instigating our design of novel
spatial data mining techniques to harness information embedded in
biomolecular landscapes. As I will demonstrate, computing and
mining landscapes is allowing us to discover and categorize
mechanisms via which pathogenic mutations alter protein dynamics
and function in human disorders. This research is bringing closer
the dawn of machines learning how mutations alter biological
activities.
As application-driven basic
research, my work has also made important contributions to many
domains in computer science. I will show selected advancements in
stochastic optimization under the umbrella of evolutionary
computation, in robot motion planning, the interplay between the
two, and the integration of machine-learned models for effective
state space exploration and state-to-state navigation problems
posed by complex, modular, intrinsically-dynamic systems operating
in the presence of constraints.
Biography: Dr. Amarda Shehu is an Associate
Professor in the Department of Computer Science at George Mason
University and is also affiliated with the School of Systems
Biology and the Department of Bioengineering. Shehu received her
B.S. with a dual degree in Computer Science and Mathematics from
Clarkson University in Potsdam, NY in 2002 and her Ph.D. in
Computer Science from Rice University in Houston, TX in 2008,
where she was an NIH fellow of the Nanobiology Training Program of
the Gulf Coast Consortia. Shehu’s research is supported by various
NSF programs, including Intelligent Information Systems, Computing
Core Foundations, and Software Infrastructure. Shehu is also the
recipient of an NSF CAREER Award, two Jeffress Memorial Trust
Awards, and a Virginia Youth Tobacco Program Award. Shehu is an
Associate Editor of IEEE/ACM Transactions in Computational Biology
and Bioinformatics. She has served as program committee chair and
general chair of the premiere IEEE and ACM bioinformatics
conferences and is a frequent editor of special journal
collections and issues in PLoS Computational Biology, IEEE/ACM
Transactions in Computational Biology and Bioinformatics, BMC
Structural Biology, and Journal of Computational Biology. Shehu is
also the recipient of the 2014 Mason Emerging
Researcher/Scholar/Creator Award and the 2013 Mason OSCAR
Undergraduate Mentor Excellence Award.
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Stephen G. Nash
Senior Associate Dean
Volgenau School of Engineering
George Mason University
Nguyen Engineering Building, Room 2500
Mailstop 5C8
Fairfax, VA 22030
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Phone: (703) 993-1505
Fax: (703) 993-1633
https://volgenau.gmu.edu/profile/view/10248