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