Mathematical Application Seminar*
Spring 2009
Tuesdays 11 – 12 noon
Monroe Hall,
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February 10, 2009,
Tuesday 11 – 12 noon
Speaker: Yongwu Rong, GWU
Title: Computational Complexity of a Boolean Network Model
Place: Monroe Hall,
Abstract:
This
talk is related to my talk last semester on a biological Boolean network model
- the strong inhibition model, due to Guanyu Wang, Rahul Simha, and Chen Zeng. Under this model, the reverse engineering problem,
which asks for the interaction between units in the network given information
on its dynamics (often expressed as a biological dynamic trajectory), is
naturally related to the Satisfiability problem in
logic. A natural problem was to understand its computational complexity.
We show that the decision
problem for the reverse engineering problem can be solved in polynomial time.
That is, given information on dynamics, there is a polynomial time algorithm
that determines either (1)
there is no network which
yields the given dynamics or (2) there is such a network. In the case of
(2), the algorithm provides a specific network solution. This algorithm is now
being implemented by Rahul Simha
on computer.
Consequences on the solutions
space, such as the maximal or minimal network solutions will be discussed.
March 10, 2009, Tuesday
11 – 12 noon
Speaker: David Joyner, US Naval Academy
Title: An invitation to Sage
Place: Monroe Hall,
Abstract:
A general introduction to
Sage
Comments from Robbie
Robinson (host of talk):
From the Sage website:
http://www.sagemath.org/ "Sage a free open-source mathematics software
system licensed under the GPL. It combines the power of many existing
open-source packages into a common Python-based interface." Sage seeks to
a free alternative to Maple, Matlab and Mathematica. Come and see how to use it in your own
research and teaching.
This talk may be interesting to people attending this seminar:
Mathematics Colloquium
Date: March 23, 2009
Time: 4:00-5:00
Room:
Speaker: John Harer, Departments of Mathematics and Computer Science,
Title: Topological Data
Analysis, Using Persistence to Find Large Scale Structure in Point Clouds
For further detail, check http://www.gwu.edu/~math/events/colloquia.html
March 24, 2009, Tuesday 11
– 12 noon
Speaker: Alissa Resch, NIH/NLM/NCBI.
Title: Evolution of alternative and constitutive regions of mammalian 5’UTRs
Place: Monroe Hall,
Abstract:
The 5’-untranslated regions
(5’UTRs) of eukaryotic genes are known to harbor regulatory elements that play
important roles in translational efficiency.
Experimental evidence shows that the occurrence of initiation codons (uAUGs) and open reading
frames (uORFs) upstream of the authentic start codon can affect translation of mRNA into protein,
frequently resulting in translational repression. Mammalian 5’UTRs are also targeted by
alternative splicing and alternative transcription initiation mechanisms, which
can lead to changes in translational efficiency between alternative isoforms, via the rearrangement of regulatory elements
within the 5’UTR.
We performed a genome-wide
comparative study of 5’UTR sequences in primates and rodents with the goal of
understanding how alternative events (alternative splicing and alternative transcription
initiation) impact the regulation of translation in mammals. We compared the abundance, conservation and
evolution of putative translational control elements within alternative and
constitutive regions of 5’UTR. Our
computational analysis revealed that putative regulatory elements are
significantly more abundant in alternative versus constitutive regions of
5’UTR, and that elements located in both regions are conserved compared to
background levels. Alternative regions
of 5’UTR evolve faster and are subject to a weaker purifying selection than
constitutive portions, in both human-macaque and mouse-rat comparisons. However, even in alternative regions, uORFs evolve under a stronger selection than the rest of
the sequence, indicating that some uORFs may be
conserved regulatory elements. These
findings are consistent with the hypothesis that alternative events in the
5’UTRs of mammalian genes are likely to contribute to the regulation of
translation.
This work is in
collaboration with Eugene Koonin, Svetlana Shabalina, Igor Rogozin and
Aleksey Ogurtsov from NCBI, NLM, NIH.
April 2, 2009, Thursday 4
– 5 pm (jointly with Applied Math Seminar)
Speaker: Qiang Du,
Title: Diffuse interface modeling of some interface problems
involving elastic energy contributions
Place: Monroe Hall,
Abstract:
We report some recent works
on the diffuse interface modeling and simulation of some interface problems in
materials science and biology. We present particular examples on the study of
deformation of biomimetic vesicle membranes and
homogeneous nucleation in anisotropic elastic solids. In both cases, elastic
energy contributions are taken into account. We consider various theoretical
and computational issues related to diffuse interface models and present some
simulations results.
April 7, 2009, Tuesday 11
– 12 noon
Speaker: A.Saeid Yasamin, SAMSI.
Title: A Generalization of
Place: Monroe Hall,
Abstract:
In this talk we consider testing hypotheses for a
statistical model, where the observation space and the parameter space are both
a symmetric cone. In particular, we derive the joint density of the eigenvalues of the generalized Wishart
distribution, and propose a test statistic analog to that of classical
multivariate statistics for testing homoscedasticity
of covariance parameter. This test extends
April 14, 2009. Tuesday, 11:00 – 12:00 noon*
Speaker:
Title:
Parameter estimation for Boolean network models
Place: Monroe Hall,
*This talk is co-sponsored
with the GW Institute for Biomolecular Networks.
Abstract:
Algebraic models, in
particular Boolean networks, have been used extensively in recent years in
systems biology. They are useful in situations where little information is
available about the kinetics of molecular processes. One of the shortcomings of
algebraic models is the lack of the types of tools used to build continuous
models, in particular parameter estimation. This talk will describe a software
package that makes available data discretization,
parameter estimation, and simulation capabilities.
April 21, 2009. Tuesday, 11:00 – 12:00 noon*
Speaker:
Damian Wojtowicz, NIH/NLM/NCBI
Title: A
discrete model of gene families’ evolution
Place: Monroe Hall,
Abstract:
I will present a simple
discrete probabilistic model of genome evolution, called DLCI model. The model
is based on four fundamental evolutionary events: gene duplication, loss,
accumulated change and innovation. The focus of the analysis is on the size
distribution of gene families. It has been shown that the equilibrium of gene
family sizes follow a logarithmic distribution. I will also consider a disjoint
union of DLCI models and present some empirical results for bacterial genomes.
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Future speakers
More speakers, dates TBA
Robbie Robinson, GWU.
James Yorke,
UMD. Possibly Fall 09.
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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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