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Year 2001 Awards
Division of Biological Infrastructure
Postdoctoral Research Fellowships in Biological Informatics
||Research Area/Training Plan
||NSF Award #|
|Title of Research and Training Plan|
||University of Illinois,
of biological molecules: obtaining unique information on their structure
and function from STM images
|Novel methods and
tools for computer simulations of scanning tunneling microscopy (STM)
images of biological molecules are being developed. These methods are
being used for obtaining unique information about structure, dynamics,
and function of proteins, lipids, and nucleic acids from their STM images.
The methods will also facilitate tailoring STM experiments.
||University of Tennessee
|Modeling the effects of
hurricane and fire disturbances on the population dynamics of south Florida
|Fires and hurricanes are frequent
disturbances affecting community structure and dynamics of pine forests
in the southeastern US. This research is developing spatially explicit,
individual-based models of pine population dynamics, parameterized from
empirical data that include hurricane and fire disturbances. The models
are to be used to predict how pine populations will respond to hypothetical
disturbance regimes associated with global change.
||Univ California, San Diego
|From genome to gene expression:
mapping and understanding genetic networks in Dictyostelium development
|Upon starvation, Dictyostelium
amoeba communicate, sort, and adhere to each other to form ``tissues''.
This transformation, resulting in a resistant spore, utilizes all the
mechanisms crucial for normal development of multicellular organisms.
Promoters, repressors, and the architecture of genetic networks involved
in development in Dictyostelium are being explored using both genomic
and gene expression data and mathematical modeling.
||Harvard Medical School
|How neural activity instructs
the system-wide modifications in brain structure that occur during development
of the visual system
|Spontaneously generated "retinal
waves" are required for early visual system development. This research
uses a combined theoretical and experimental approach to determine (1)
how physiologically relevant neural input causes appropriate modifications
at individual retinogeniculate synapses, and (2) how these retinal-wave-driven
modifications result in system-wide competition that drives retinogeniculate
||University of California, Davis
|Dynamic species interactions,
uncertainty, and the maintenance of ecosystem robustness
|The interplay between community
complexity and stability is the source of one of the classic debates in
ecology. Heterogeneous spatial and temporal species distributions and
trophic interactions, though central to the debate, have been studied
little. To address these issues this research develops new computational
methods to parameterize, simulate, and analyze a multi-species, multi-patch
||University of Texas, Austin
|Phylogenetic analysis using
ribosomal RNA structure
|Ribosomal RNA genes are widely
used in phylogenetics and have shaped current views of the history of
life. Traditional DNA sequence-based phylogenetic methods, however, fail
to reliably place highly divergent sequences. This research develops probabilistic
models for phylogenetics that are based on rRNA structure.
|William A. Frankino
||University of Leiden
||Evol & Ecol Physiology
|The role of epigenetic signaling
in the evolution of trait allometries: integrating development with morphometrics
|This series of studies is determining
the proximate mechanisms by which morphological trait allometries evolve
in insects, specifically the wings and bodies of butterflies. Changes
in the shapes of, and allometries among, morphological traits are being
produced by artificial selection. The response to selection is being quantified
using statistical and morphometric methods developed by the Fellow.
||Lawrence Berkeley National
|Development of alternative
clustering methods for genomic expression analysis and characterization
of coregulated genes in yeast
|This project is developing
fuzzy k-means clustering for analysis of genomic expression data, with
the goal of identifying coregulated yeast genes that are not identified
by traditional methods. After identifying sets of coregulated genes, multiple
algorithms will be applied to identify sequence motifs that contribute
to the regulation of expression.
|Jessica L. Green
University of California, Davis
|Estimating global microbial
diversity: a bioinformatics approach
|Scaling law, probability, and
combinatorial theory are being used to quantify biodiversity patterns
across a wide range of spatial scales and at different levels of phylogenetic
resolution. Using computer intensive spatial statistical analyses and
simulation modeling, hypotheses are being tested with a microbial genetic
database two orders of magnitude larger than any previously reported (~73,000
16S rDNA clones collected over ~ 1 m2 to ~10,000 km2 in Australia, analyzed
by RFLP and other sophisticated genetic techniques).
|Using local symmetry to
improve protein structure prediction
|Finding minima of a potential
energy function is a crucial part of many approaches to protein structure
prediction. The goal of this research is to exploit a geometric relationship
among the minimizing structures of a specific potential to efficiently
find distinct minima. Transformations are being automated that take one
minimizing structure to (or near) a different minimizing structure. Analogous
relationships among homologues and the interplay of such transformations
and domain classification systems are also being studied.
|How dinosaur locomotion
evolved: using 3D computer models to test biomechanical hypotheses
|This research constructs realistic
3D computer models to visualize the physics of hindlimb muscle function
in an alligator, chicken, and three extinct theropod dinosaurs. These
models permit the testing of hypotheses like "Could Tyrannosaurus
run?" and "How did the bipedal stance of birds evolve?"
with new analytical rigor.
||Oregon State University
||Evol & Ecol Physiology
|A new approach to modeling
the evolution of sexual isolation
|This project explores the evolutionary
dynamics of sexual isolation in salamanders and Drosophila. Theoretical
models are being used to simulate evolution of sexual isolation given
a phylogeny. Simulated data matrices will be compared to empirical data,
providing the first tests of the roles of inheritance, drift, selection,
and reinforcement in the evolution of sexual isolation across clades.
|Inferring the nature of
quantitative genetic variation: methods for integrating single and multi-locus
|The goal of this project is
to extend quantitative genetic theory to the study of individual genes,
and then to use that theory to develop methods for analyzing sequence
polymorphism data from quantitative trait loci (QTL). This theoretical
framework allows the testing of hypotheses about the nature of genetic
||Northwestern U Medical School
|Modeling Muscle Force Generation
during Posture and Locomotion
|This project involves developing
models of muscle force generation. The hypothesis being tested is that,
during functional conditions, whole muscle models can be constructed by
summing responses of constituent motor units. Specific aims are to test
this hypothesis experimentally and to use nonlinear system identification
to generate a database of single motor unit models.
||Univeristy of Pennsylvania
|Development of strategies
for designing novel catalytic enzymes
|This work includes an informational
approach followed by experimental application of the results. The informatics
portion includes parameterization of a whole protein energy function based
on mutant to wild-type redesigns of proteins from various structural databases.
Second, a comprehensive cataloging of specific interactions in natural
cytochromes is being conducted, noting the conformational positioning
of the reactive centers of these molecules. The strategies developed from
these sections will be applied experimentally to design a novel synthetic
cytochrome with heme binding and reactivity approaching that of its naturally
||Marine Biological Laboratory
|Determining population structure
and dynamics of Class II transposable element families in Arabidopsis
thaliana, using a coalescence-based population genetic approach
Transposons are major constituents of most eukaryotic genomes that can
dramatically alter genomic architecture, individual fitness, and species
evolution. Little is known about population dynamics and behavior of transposons.
In this research, the availability of complete genome sequence and biological
informatics capability provides a novel opportunity to evaluate their
impact and the forces that influence their movement.
|George C. Stecker
||Univ Michigan Medical School
|| Sensory Physiology
|New techniques for analyzing
the representation of auditory stimulus features by ensembles of cortical
|This project is concerned with
the analysis of stimulus-related information contained in firing patterns
of ensembles of 16 or more simultaneously-recorded neurons in auditory
cortex. Statistical pattern recognition techniques are used to characterize
relationships between the acoustic properties of sounds in space and information-bearing
features of neural responses.
|Christopher M. Summa
|Ab-initio prediction of
membrane protein structure
|Membrane proteins which play
important roles in cell function are not as well-studied as soluble proteins.
This research develops automated or semi-automated computational methods
for predicting the structures of integral membrane proteins using publicly
available data and constructs an online database of structure predications.
In doing so, it brings together information from protein folding theory,
the human genome project, and mutagenesis experiments on membrane proteins
in a unique way.
|Exploring phylogenetic trends
of gene sequence, protein form, and function to comprehend processes of
|The photosynthetic gene rbcL
and a large phylogeny are being used to link molecular selection linking
gene sequence to protein form and function. Evolutionary trends are being
used to reveal patterns of molecular selection that are otherwise invisible
and are helping to generate viable theories about gene-protein relationships.
The research is focused on developing generally applicable models of gene
and protein evolution and providing informatic tools to question processes
of molecular selection in other genes and systems.