Mathematical and Computational Biology Seminar*
Fall 2010 – Spring 2011
Fridays 1 – 2 pm
Monroe Hall,
Organizers: Yinglei Lai (statistics), E. Arthur Robinson, Yongwu Rong (math), Guanyu Wang, and Chen Zeng (physics)
May 6, 2011,
Friday 12 – 1pm.
Speaker: Jin Wang, Stony Brook University
(SUNY).
Title: Landscape
and Flux Framework for Networks
Place: Monroe 267, 2115 G Steet.
Abstract: We developed a global framework to robustness of
networks applied to biological oscillation by directly exploring the
probabilistic distribution in the whole protein concentration space (therefore
global) for oscillations with a stochastic approach. We uncovered two distinct
natures essential for characterizing the global probabilistic dynamics of
biological oscillations: the underlying potential landscape directly
(logarithmically) related to the steady state probability distribution and the
corresponding flux related to the speed of the protein concentration changes.
We found that the underlying potential landscape for the oscillation has a distinct
closed ring valley shape when the fluctuations are small. This global landscape
structure leads to attractions of the system to the ring valley. On the ring,
we found that the non-equilibrium flux is the driving force for oscillations.
Therefore, both structured landscape and flux are needed to guarantee a global
robust oscillation. The barrier height separating the oscillation ring and
other areas derived from the landscape topography, is shown to be correlated
with the escaping time from the limit cycle attractor, and therefore provides a
quantitative measure of the robustness for the network. The landscape becomes
shallower and the closed ring valley shape structure becomes weaker (lower
barrier height) with larger fluctuations. We observe that the period and the
amplitude of the oscillations are more dispersed and oscillations become less
coherent when the fluctuations increase. When the fluctuations become very
large, the landscape is flattened out and coherence of the oscillations is
destroyed. Robustness decreases. When the fluctuations are small, changing the
inherent parameters of the system such as chemical rates, equilibrium constants
and concentrations can lead to different robust behaviors such as
multi-stability. By exploring the sensitivity of barrier height on the
parameters of the system, we can identify critical kinetic parameters important
for robust oscillations. This provides a basis for reengineering and design.
Biography: Dr. Jin Wang
received his B.S. in Physics from
April 29, 2011, Friday 10:30 – 11:30 pm (note the unusual time)
Speaker: Rong Chen, Department of
Statistics,
Title: Self-avoiding
walks, self-avoiding loops and Sequential Monte Carlo
Place: Monroe 267, 2115 G Steet.
Abstract: Self-avoiding
walks and self-avoiding loops are simplified models of protein and RNA
geometric conformations. The size of the conformation space under certain
geometric structure is often directly related to the entropy or energy needed
to maintain such a structure. Average compactness and
volume of all possible conformations under certain energy function
are also parameters of interests. As it is extremely difficult to obtain
theoretical results for these problems and it is computationally infeasible to
enumerate all possible conformations for long chains (walks), we use
Biography: Dr. Chen is a
Professor of Statistics at the Department of Statistics and Biostatistics,
April 22, 2011, Friday 12 - 1 pm
Speaker: Fengzhu Sun, Departments of Biological Sciences and
Mathematics,
Title: Diffusion
Kernel over Networks and Their Applications in Systems Biology
Place: Monroe 267, 2115 G Steet.
Abstract: Molecular
networks including protein interactions, gene regulation, and gene
co-expression are abundant in systems biology problems. Diffusion kernel
defined by random walks over a network can be used to define similarities
between the nodes in the network. By integrating the ideas of
guilty-by-association and diffusion kernel, we show the superiority of
diffusion kernel compared to other similarity measures in several practical
problems of systems biology: a). predicting protein function, b) predicting
genes related to complex phenotypes, and c) prioritizing RNAi
hits from RNAi experiments.
Biography: Fengzhu Sun is a Professor of Molecular and Computational Biology
and head of the computational biology and bioinformatics group at USC. His
Bachelors in Mathematics is from
Professor Sun works in the area of Computational Biology and Bioinformatics,
Statistical Genetics, and Mathematical Modeling. His recent research interests
include protein interaction networks, gene expression, single nucleotide
polymorphisms (SNP), linkage disequilibrium (LD) and their applications in
predicting protein functions, gene regulation networks, and disease gene
identification. He is also interested in metagenomics,
in particular, marine genomics.
April 15, 2011, Friday 1-2 pm
Speaker: John R. Cressman ,
Department of Physics,
Title: Ionic
imbalance, energy utilization and seizure dynamics.
Place: Monroe 267, 2115 G Steet.
Abstract: I will discuss
the role of ionic imbalances in the initiation, maintenance, and termination of
seizures. Under normal conditions, a
constant flow of energy is required to maintain ionic concentrations. I will describe the network of cellular and
extracellular mechanisms responsible for maintaining normal ionic balance, and
discuss how energy limitations as well as intrinsic dynamics can lead to a
break down in ionic regulation.
Biography: Dr.
John R. Cressman is an Assistant Professor of Physics
and a member of the
February 25, 2011, Friday 12 -
1pm
Jointly with the GWU Combinatorics Seminar
Speaker: Jo Ellis-Monaghan,
Department of Mathematics, St. Michael’s University
Title: Graph
Theoretical Design Strategies for Self-assembling Nanostructures
Place: Monroe 267, 2115 G Steet.
Abstract: http://home.gwu.edu/~rong/Jo-Abs.pdf
Biography: Dr. Ellis-Monaghan has an undergraduate
degree in
studio
art (painting and ceramics) from
studied
mathematics to relax from the creative intensity of being an artist,
but
eventually realized that mathematics is itself a creative process.
Dr.
Ellis-Monaghan received her Master’s degree in mathematics from
the
at
the
intensive creative work of doing mathematics.
She grew up on an island
in
lives
on an island, and grows fruits, vegetables, and small children.
Dr.
Ellis-Monaghan’s mathematical research is in the areas of graph theory,
algebraic
combinatorics, and applied combinatorics.
She works with a variety
of
graph polynomials, constructing them and embedding them in algebraic
structures
sufficiently rich to extract new information from them. She also applies
graph
theoretical techniques to problems from statistical mechanics and computer
chip
design, and, more recently, to problems from DNA nanostructures and
biomolecular computing.
She is currently a full Professor at St. Michael’s College
in
November 18, 2010,
Thursday 4 – 5 pm (note the unusual time)
Jointly with the GWU Applied Mathematics Seminar
Speaker: Carlos Castillo-Chavez,
Title: Complexity and Epidemics: Influenza Epidemics in
Place: 1957 E Street, Room 212.
Disease dynamics are
connected to biological, environmental and social processes that take place
over multiple time scales and over various levels of social and biological
organization. In today's world, epidemic outbreaks become instant potential
health and/or economic global threats with increasing segments of the
population playing active roles on the transmission patterns of infectious
diseases like influenza. Despite the myriad of complexities associated with
disease dynamics, macroscopic epidemic patterns emerge but finding ways of
making effective use of this knowledge remains.
I will address some of these challenges in a historical context starting
with the work of physicians-theoreticians like Bernoulli, Ross, Kermack and McKendrick. The
lecture will be tied in to the epidemiology of influenza with examples from the
2009 H1N1 pandemic that originated in
Biography:
Carlos Castillo-Chavez is a
Regents Professor, and Joaquin Bustoz Jr. Professor
of Mathematical Biology at
His research interests as a
mathematical epidemiologist relate to the mechanisms underlying spread of
disease, and their containment (prevention of spread) and elimination. A 2006
editorial at
He has won awards by the
American Association for the Advancement of Science (AAAS) Mentor Award and
Fellow (2007), the Ulam Distinguished Scholar by the
Center for Nonlinear Studies at Los Alamos National Laboratory (2003), the
Society for Advancement of Chicanos and Native Americans in Science (SACNAS)
Distinguished Scientist Award (2001), the Presidential Award for Excellence in
Science, Mathematics and Engineering Mentoring (1997), and the Presidential
Faculty Fellowship Award from the National Science Foundation and the Office of
the President of the United States (1992-1997). In September 2010 President
Obama nominated Carlos Castillo-Chavez to the President’s Committee on the
National Medal of Science for the period 2010-2012.
November 5, 2010, Friday 12
- 1 pm (note the new time)
Speaker: Lior Pachter, Departments of Mathematics, Molecular
& Cell Biology and Electrical Engineering & Computer Science.
UC-Berkeley.
Title: Mathematical challenges in designing and analyzing
next-gene sequencing assays for functional genomics
Place: Monroe Hall,
Abstract:
The term "next-gen
sequencing" refers to a variety of technological
developments that have
heralded a new era of cheap and fast
high-throughput and
massively parallel sequencing. The new sequencing
technologies have been
developed in response to a push for cheap human
genome sequencing, but
remarkably they are turning out to be far more
relevant for functional
genomics applications. A spate of recent
papers show how to engineer
"sequence census" methods for making
molecular measurements using
next-gen sequencing technologies. We will
review some of these
methods, and describe the accompanying
mathematical inverse problems
that must be solved.
Biography:
Lior Pachter was born in
His research interests span the mathematical and biological sciences, and
he has authored over 90 research articles in the areas of algorithms, combinatorics, comparative genomics, algebraic statistics,
molecular biology and evolution. His honors include a National Science
Foundation CAREER award, a Sloan Research
Fellowship, the Miller
Professorship, and a Federal
Laboratory Consortium award for the development of widely used sequence
alignment software.
October 29, 2010.
No talk is scheduled due to
the GWU Colonial Math Competition
_________________________________________________________________________________
Speaker: Tanya Kostova, National Science Foundation.
Title: Two Examples of Dynamical Systems in
Place
Abstract: Biological systems constantly evolve and are
best represented by using dynamical systems models. I will present two examples
of applications of dynamical systems in epidemiology and virus evolution. The
first model is a discrete dynamical system describing an epidemic evolving in a
network of hosts and the second is a nonlinear system of ordinary differential
equations. The concept of dynamic equilibrium and its stability is central for
the understanding of the biological system. I will discuss the dependences of
the dynamics of the two models on their parameters and their biological
implications in each case.
Biography: Tanya Kostova received her PhD from
October 15, 2010, Friday
1 -2 pm
Title: Mathematical Models and Analysis of
Place
Abstract: Cholera, a water-borne infectious disease,
remains a
significant public health
burden in developing countries. The
dynamics of cholera is complicated by its multiple
transmission
pathways which involve both
direct human-to-human and indirect
environment-to-human modes.
In this talk, I will present
several mathematical models
to explore the complex dynamics of
cholera. These models are
based on systems of nonlinear
differential equations which
incorporate both human population
and environmental
components. I will present results from both
epidemic and endemic
analysis and, particularly, I will discuss
some recent findings on the
global asymptotic stability of the
endemic equilibria
of the cholera models. The analytical
predictions are validated by
numerical simulation results. In
addition, I will demonstrate
the application of this
mathematical framework by
modeling the 2008-2009 cholera
outbreak in
Biography: Dr. Wang is
currently an assistant professor of mathematics at
mathematics from
research professor at Duke
from 2005 to 2007, prior to joining
the faculty at Old Dominion.
Dr. Wang's research interests
include fluid dynamics and
mathematical biology, where he
combines mathematical
analysis and numerical simulation to gain
insights into the physical
and biological problems in his
research.
September 24, 2010,
Friday 11 – 12 noon (note the unusual time)
Speaker: Tamal
Dey, Department of Computer Science,
Title: Computing Homology Cycles with Certified Geometry
Place: Monroe 267, 2115 G Steet.
Abstract: Computation of cycles representing classes of
homology
groups
is a fundamental problem arising in applications
such
as parameterization, feature identification, topology simplifications,
and
data analysis. Variations of the classical Smith
Normal
Form algorithm and the recently developed persistence algorithm
do
compute representative cycles of a homology
basis
for a simplicial complex, but they remain
oblivious
to the input geometry. Some recent research
in
computational topology have addressed the problems
of
computing homology cycles that are optimal with
respect
to a given metric. In this talk, we concentrate
on
two such developments: (i) Computing an optimal
basis
for one dimensional homology of a simplicial complex
and
using it to approximate such a basis for a smooth
manifold
from its point data; (ii) Computing an optimal
cycle
homologous to a given cycle in a simplicial complex.
We
provide efficient algorithms with their guarantees for (i)
and
show that classical Linear Programs can solve (ii)
for
some interesting cases even though the general problem is NP-hard.
Biography: Tamal K. Dey is
professor of computer science
at
the
includes
computational geometry, computational topology and
their
applications in graphics and geometric modeling.
After
finishing his PhD from
in
1991 he spent a year in
as
a post doctoral fellow. He has held academic positions
in
Indiana University-Purdue
University
at Indianapolis, Indian Institute of Technology, Kharagpur,
a
book ``Curve and surface reconstruction: Algorithms with
mathematical
analysis" published by Cambridge University Press.
He
leads the Jyamiti group which has developed
various software including the well known Cocone
software
for
surface reconstruction and DelPSC software for
mesh
generation. Details can be found at
http://www.cse.ohio-state.edu/~tamaldey.
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The Mathematical
Application Seminar in Previous Years
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* The
Mathematical and Computational Biology Seminar is sponsored by the George Washington University Seminars program.
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