The Systems Biology Seminar Series brings to NIST leading
scientists working in the borderlands of physical science, information
science, and biology. It ordinarily meets on those Fridays for which
no NIST Colloquium is scheduled.
10:30 a.m.
Room C301 Radiation Physics Building
For further information, contact Charles W. Clark, x3709 |
November 17, 2006
Slides from presentation
(3.3 MB pdf) |
Discovery of principles of nature from mathematical modeling
of DNA microarray data
Orly Alter
Department of Biomedical Engineering, Institute for Cellular and Molecular
Biology and Institute for Computational Engineering and Sciences,
University of Texas at Austin
Abstract - DNA microarrays make
it possible to record the complete genomic signals
that guide the progression of cellular processes. Future predictive power,
discovery and control in biology and medicine will come from the
mathematical modeling of these data, which hold the key to fundamental
understanding of life on the molecular level, as well as answers to
questions regarding diagnosis, treatment and drug development. I will
describe the first data-driven models that were created from these
large-scale data through generalizations of matrix and tensor computations
that have proven successful in describing the physical world. In these
models, the mathematical variables and operations might represent
biological reality: The variables, patterns uncovered in the data, might
correlate with activities of cellular elements, such as regulators or
transcription factors, that drive the measured signals. The operations,
such as data classification and reconstruction in subspaces of selected
patterns, might simulate experimental observation of the correlations and
possibly also causal coordination of these activities. I will illustrate
these models in comparative and integrative analyses of mRNA expression
and proteins' DNA-binding data from yeast and human cell cultures. In
these analyses, the ability of the models to predict previously unknown
biological and physical principles is demonstrated with a prediction of
a novel mechanism of regulation that correlates DNA replication
initiation with RNA transcription. The predicted mechanism is in
agreement with current biological understanding, and is supported
by recent experimental results. These models may become the foundation
of a future in which biological systems are modeled as physical systems
are today. |
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February 2, 2007 |
Community Structure in Complex Networks
Michelle Girvan
Institute for Physical Science and Technology, University of Maryland
Abstract - Many systems take the form of
networks: examples include the Internet, the World-Wide Web, distribution
networks, neural networks, biochemical networks, food webs, and social
networks. Drawing on techniques from statistical physics and dynamical
systems, researchers have begun to take a complex systems approach to
understanding these networks, as they cannot be well-described by
completely structured or completely random representations. Much of
this work has been focused on identifying a few statistical features
that seem common to many networks: the small-world property, power-
law degree distributions, and network transitivity. In this talk, I
will focus on another property that is found in many networks, the
property of community structure, in which network nodes are joined
together in tightly knit groups, between which there are only looser
connections. I will discuss a set a novel algorithms developed to
find and evaluate this kind of network structure and show that they
they are highly effective at discovering community structure in
computer-generated and real-world networked data. Deconstructing
networks in this manner can shed light on the sometimes dauntingly
complex structure of networked systems. |
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February 16, 2007 |
Ultrafast Protein Folding
William Eaton
Chief, Laboratory of Chemical Physics, NIDDK, National Institutes of Health,
Bethesda, MD
Abstract -
The introduction of laser-triggering methods and advances in
computational capabilities are rapidly narrowing the historical gap
between experimental protein folding kinetics and the time-scale
accessible to atomistic molecular dynamics trajectories. It is now
possible to rigorously test the validity of the mechanisms extracted
from the analysis of multiple trajectories with experimental data from
ultrafast folding proteins. Advances are also being made in the
development of simple analytical models, which are surprisingly
successful in calculating experimental properties of specific proteins.
In this seminar I will discuss the connections between the equilibrium
and kinetic data on the ultrafast-folding 35-residue subdomain from the
villin headpiece and both atomistic simulations and a simple
statisticalmechanical model. |
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March 2, 2007 |
Sequence-Resolved Detection of Pausing by Single RNA
Polymerase Molecules
Arthur LaPorta
Department of Physics, and Institute for Physical Science and Technology,
University of Maryland, College Park, MD
Abstract - We apply an ultrastable
optical-trapping assay to follow the motion of
individual molecules of RNA polymerase (RNAP) transcribing templates
engineered with repeated sequences carrying imbedded, sequence-specific
pause sites of known regulatory function. Both the known and ubiquitous
pauses appeared at reproducible locations, identified with base-pair
accuracy. Ubiquitous pauses were associated with DNA sequences that show
similarities to regulatory pause sequences. Data obtained for the
lifetimes and efficiencies of pauses support a model where the
transition to pausing branches off of the normal elongation pathway and
is mediated by a common elemental state, which corresponds to the
ubiquitous pause. This result complements single-molecule studies,which
showed that bacterial RNAP pauses frequently during transcriptional
elongation; our results clarify the relationship of these 'ubiquitous'
pauses to the underlying DNA sequence. |
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March 8, 2007 |
What is Namomedicine?
James Baker, Jr.
Director, Nanotechnology Institute for Medicine and the Biological Sciences,
University of Michigan
Note: NIST Colloquium, in Red Auditorium,
Thursday, March 8
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April 20, 2007 |
Tissue Engineering: Tracking Large Numbers of Cells
Takeo Kande
The Robotics Institute, Carnegie Mellon University
Note: NIST Colloquium, in Red Auditorium
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Online: October 2006 -
Last update: February 13, 2007
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