1. Samanthe M. Lyons,
Elaheh Alizadeh, Joshua Mannheimer,
Katherine Schuamberg, Jordan Castle, Bryce
Schroder, Philip Turk, Douglas Thamm,
Ashok Prasad, Changes in Cell Shape Are
Correlated with Metastatic Potential in
Murine and Human Osteosarcomas, Biology
Open 2016 5: 289-299; doi:
10.1242/bio.013409
2. Katherine A. Schaumberg, Mauricio S.
Antunes, Tessema K. Kassaw, Wenlong Xu,
Christopher S. Zalewski, June I. Medford,
Ashok Prasad, Quantitative
characterization of genetic parts and
circuits for plant synthetic biology, Nature Methods, v13, 94-100
2016, doi: 10.1038/nmeth.3659
Published online on November 16, 2015
5. S. M. Lyons, W. Xu, J. Medford, Ashok
Prasad (2014) Loads Bias Genetic and
Signaling Switches in Synthetic and
Natural Systems. PLoS
Comput Biol 10(3): e1003533 (2014).
doi:10.1371/journal.pcbi.1003533
7. Dustin Robert Berger, Ketul Popat,
Ashok Prasad, PCL Nanopillars Vs
Nanofibers: A Contrast in Progenitor Cell
Morphology, Proliferation, and Fate
Determination, Advanced Engineering
Materials, 14(6), B351-B356, 2012 http://onlinelibrary.wiley.com/doi/10.1002/adem.201180086/abstract
8. S. M. Lyons, Ashok Prasad, Cross-talk
and information transfer in mammalian and
bacterial signaling, PLoS
ONE 7(4): e34488. (2012)
doi:10.1371/journal.pone.0034488
11. A. W. C. Lau, Ashok Prasad and Z.
Dogic: Condensation of isolated
semi-flexible filaments driven by
depletion interactions, European Physical
Letters 87, 48006 (2009)
My research group works in a number of different areas at
the intersection of the physical sciences and mathematics
with biology. The main philosophical motivation is the
belief that nontrivial biologically important phenomena
arise as emergent properties from constituent parts. Part of
the reason why we work on many different projects is the
realization of the need for integrative explanations. Of
course part of the reason is also that I find so many things
interesting and worthy of study!
Reading information from the shapes of cells (theory
and experiment)
Mammalian cells have
shapes that appear to be correlated with their function and
their phenotype. We are trying to understand how cell shape
is determined and what its relation is with cell properties.
In a couple of recent papers and in ongoing work we have
shown that there are subtle changes in cell shape that are
correlated with increasing cancer invasiveness. We run a wet
lab in which we do the experiments and we use image
processing, machine learning and statistical data analysis
to make inferences about cell shape changes.
Physical properties and nonequilibrium dynamics of the
cellular cytoskeleton (theory and experiment)
Live cell imaging yields movies that are rich with movement.
Organelles move around displaying both random walks and
directed motion. The cell as a whole extends protrusions and
the cytoskeleton breathes. Can we learn something about the
underlying cytoskeletal mechanics by looking at internal
cellular movement? We take movies of mitochondria and the
whole cell, analyze the motion and try to interpret what we
see. This is a very new project, but something that we are
very excited about.
Development of synthetic gene circuits, especially in
plants
Synthetic biology is an interdisciplinary field centrally
concerned with the construction of synthetic control
circuits in organisms. Ultimately it will help us create new
technologies that could, depending upon how our species uses
them, have major beneficial impacts. One of the reasons I am
interested in synthetic biology is that it allows us to test
our knowledge of how genetic circuits operate using
predictive quantitative modeling and experiments.
We are currently working on developing methods to
quantitatively test synthetic plant parts as well as
developing the first synthetic switches in plants.
Collaborator: June
Medford, CSU Biology department.
Theoretical analysis of signal transduction and gene
transcription.
There are literally hundreds of questions that can be probed
by mathematical modeling of the relevant networks. The broad
themes I am most interested in relate to questions related
with biological complexity in gene networks and signal
transduction. I am also interested in how biology encodes
switches and how decisions are made by cells, as well as
parallels and differences between cellular computation and
computation performed by the brain. I am also interested in
more specific biological questions such as understanding the
structure of switches in T cell activation, in the cell
cycle and in cancer.
Network analysis and gene expression data analysis to
understand and help combat cancer.
This is a very new project in which we are currently using
gene expression data to predict cancer disease outcome using
machine learning and multivariate data analysis techniques.
Collaborator: Dan
Gustafson and Dawn
Duval.
Modeling cyanobacterial metabolism for metabolic
engineering
We are interested in the broad question of whether
metabolism follows an optimization protocol. In the short
term we use genome scale metabolic models to help metabolic
engineers design methods for using cyanobacteria as chemical
factories to produce, for example, biofuels.
We have currently built the most up to date and accurate
model of Synechocystis metabolism so far, and are developing
methods for dynamic analysis of day-night metabolism in
cyanobacteria. Collaborator: Christie
Peebles
