Mathematical Application Seminar*
Fall 2009
Tuesdays 2 – 3 pm
Monroe Hall,
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November 3, 2009, Tuesday
2 – 3pm
Speaker: Hao Chen, Department of Physics, GWU
Title: The Structure of the Solution Space of the Strong Inhibition
Model
Place: Monroe Hall, 2115 G Street, Room 267
Abstract: The central task of the system biology is to understand the
biology process. During the past decade, various models have been proposed and
studied. Among them, the strong inhibition model is very simple and successful.
In this talk we will discuss the solution structure of the model.
November 10, 2009,
Tuesday 2 – 3pm
Speaker: Guanyu Wang, Department of Physics, GWU
Title: Computational complexity in Boolean networks
Place: Monroe Hall,
Abstract: We recently developed a logic-based approach for
investigating
the structure-function relationship of biomolecular networks.
In this talk, I will briefly
review the approach and then discuss
the computational complexity in some aspects of the
algorithm.
I will show the connection
between our algorithm and the well-known
set covering problem in computer science. I will prove
that finding
a minimal network (an important concept in our
approach) is
equivalent to the minimal set covering problem, which is
NP-hard.
Some perspective from the
approach will also be addressed.
November 17, 2009,
Tuesday 2 – 3 pm
Speaker: Tim McCaffrey,
Title: The evolution of massively parallel sequencing methods: Opportunities for mathematical and statistical modeling.
Place: Monroe Hall,
Abstract: The sequencing of the human genome was
transformational for biomedical research, but provided only a single template
to overlay diverse types of experimental data. The recent technological
advances in massively parallel sequencing allows scientists to acquire new
genomes in a matter of days, not years. Future discovery will require new
mathematical and statistical techniques to process and display terabytes to
petabytes of sequence information within a highly integrated software environment.
The opportunities and challenges for transforming human health will be
discussed.
November 24, 2009,
Tuesday 2 – 3 pm
Speaker: Huzefa Rangwala, Computer Science/Bioinformatics,
Title: Interactions using Kernel-based Methods.
Place: Monroe Hall,
Abstract: Proteins have
a vast influence on the molecular machinery of life.
Stunningly complex networks of proteins perform innumerable functions
in every living cell. Knowing the three-dimensional structure of
proteins is crucial to advances in biology, as this information
provides insight into how proteins operate. For example, structural
information enables function prediction, the identification of other
interacting biomolecules (e.g., proteins, DNA and
RNA), and the
rational search for ligands that can be used to
enhance or inhibit
these interactions.
In this talk I will highlight my work involving use of sequence
information to characterize the structural and functional nature of
proteins. I will introduce the notion of pairwise
kernels to study
protein-protein interactions, and finally talk about an application
towards drug discovery.
Biography:
Huzefa Rangwala’s research
interests include bioinformatics, machine
learning, and high performance computing. His research has resulted in
the development of software packages for performing protein sequence
classification (kernel-compute), predicting local structure and
functional properties (svmPRAT, MONSTER, TOPTMH).
Recently, he has
been involved in development of methods for integrating information
from heterogeneous data, learning from unlabeled instances, and
multi-label classification within the context of chemical and
biological data. He has also started developing a prototype for
fragment assembly for high throughput short reads. He got his PhD from
the
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Previous Seminars
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* The Mathematical Application
Seminar is currently sponsored by the
George Washington University Seminars program.
It also received support the Department of Mathematics at the George
Washington University.
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