Associate Professor Chemical and Biological
Engineering School of Biomedical Engineering Molecular Cellular and
Integrative Neuroscience
Samanthe Lyons,
SBME
In 2010 I graduated from Duke
University with a B.S.E. in biomedical engineering
and a second major in biology. I've joined the
Prasad lab to pursue a Ph.D. in biomedical
engineering. In 2012 I also joined the College of
Veterinary Medicine at CSU to simultaneously pursue
a DVM degree.
In the Prasad lab I have worked on a number of
exciting projects. I used information theory to
study the effect of cross-talk on signal
transduction. I simulated synthetic plant
signaling circuits in collaboration with
experimental synthetic biologists of the Medford
lab. I studied the effects of loads on biochemical
switches. My current research is an experimental
project to understand how cell shape changes
between less invasive and more invasive cancers. I
will graduate with a DVM in May 2016 and I look
forward to combine research and clinical practice
in my future life as a vet.
Chintan Joshi,
CBE
I earned my
Bachelors of Technology in Biotechnology from
SASTRA University (India). My fascination for
biofuels led me to Professional Science Masters
(PSM) in Applied Biotechnology from Oregon State
University (Corvallis, OR). My masters final
project involved Flux Balance Analysis (FBA) and
simulating (in silico) nutrient stress responses
like starch accumulation in Chlamydomonas
reinhardtii, one of the most widely
researched unicellular alga. This project
introduced me to the huge potential of
computational biology. My current projects
involve using Flux Balance Analysis and
Metabolic Flux Analysis to understand the
metabolic tradeoff between growth and
lipid production, in cyanobacteria. I have built
a new metabolic model of the cyanobacterium, Synechocystis
PCC 6803. My short-term goal includes
realizing the full potential of Computational
Biology, and eventually, contributing towards
metabolic engineering of microorganisms
(bacteria, cyanobacteria or unicellular alga).
Being a squash
player since I was 12, I got a chance to apply
some of my knowledge of squash in racquetball, a
sport more known in United States. Apart from my
research, I love working on oil paintings,
pencil sketches, calligraphy, and writing
abstract blogs.
My long term goal is to change the world though
exploring. I want to be involved in projects that
use experimental wet lab studies in conjunction
with computation modeling to approach today's
questions. Questions of interest to me included:
How biological switches among other circuit
typologies play a role in stem cell
differentiation, cell to cell communication and
genomic based diseases. Another interest is in how
previously existing data sets can be used to
identify the underling mechanism of both normal
and pathological function. I have chosen to study
Biology because it is the study of life. Life for
me is good and I would like to make it better for
others. I have a background in computational
biology and have been apart of a large variety of
projects: (i) helping to develop algorithms for
identification of cell shape parameters; (ii)
neural networks to identify transcriptomic based
bio-markers in cancer cell lines that are useful
for predicting drug response; (iii) development of
methods for quantitative characterization of
synthetic gene circuits in plant protoplasts and
(iv) predictive modeling for plant synthetic
biology. In all the projects that I have
been involved with, we have tried to use the
leading science in the field with leading edge
computational tools to discover and explore
phenomena that make up our world.
Wenlong Xu
I got my bachelor degree in bioengineering from
Northwest A&F University in China in 2010. I
then joined CSU initially to pursue research on
biofuels as a NSF IGERT fellow. This fellowship
enables me to explore my academic interests more
broadly, and I found my heart attracted to a more
general research area, that is in simultaneously
applying both quantitative experimental and
computational tools to tackle biological
questions. I have worked on analyzing the effects
of loads on biological switches, data analysis for
plant synthetic biology, image processing tools
for the synthetic plant toggle switch and modeling
multifunctional enzymes. I am currently working on
using spontaneous fluctuations in cellular
organelles to help us understand the physical
properties of the cellular cytoplasm, and its role
in disease, using a combination of experiment and
theory.
After being attracted into in biology-related
research projects since I was a sophomore, I am
still finding myself constantly amazed and awed by
what a cell can do. Like how a cell can sense and
integrate all the information it receives and make
a reasonable decision to either stay or migrate to
somewhere else, to stay as it is or differentiate
and specialize into some other cell forms etc.
Also questions like how a cell can take the
corresponding actions after taking a decision,
i.e. how to move and how to change its own
identity. It will need integration of both
experiments and theoretical analysis to understand
these phenomena, and that is the path I am trying
to follow.
Elaheh
Alizadeh
I have been doing science in one way or another
ever since my high school. After completing high
school, I entered the Physics Department at
Alzahra University, Tehran, Iran. After my
graduation with a B.Sc. in physics, I decided to
do plasma engineering. I was accepted to do
Masters in this field in Shahid Beheshti
University. My M.Sc thesis was titled as
“Fabrication of Microfluidics Channels using
Atmospheric Pressure Plasma”. I also worked
on other projects in the field of microfluidics
during my master.
I joined Dr. Prasad’s research group as a PhD
student in summer 2013. In our group I have
developed a cell culture and imaging laboratory as
an extension of a previous solely computational
group. Now, I also manage the wet lab and I
supervise and mentor two undergraduate students. My
main project is to understand how mammalian cells,
especially cancer cells, determine their shape on
surfaces, how to measure and quantify cell shape,
understand what change in shape parameters mean, and
to develop methods to use that information to help
understand cell state from cell shape. Apart
from wet lab work for my project, I do simulations
and write code for, and work with, machine learning
neural network algorithms and multivariate data
analysis. The questions that I work on have
applications in cancer biology and I hope I can
contribute to a better understanding of cancer.
Shared Students
Joshua Mannheimer
I Graduated from CSU in 2013 with a B.S. in
Applied Physics and a Minors in Biomedical
Engineering and General Mathematics. During this
time, from 2011-2013, I worked in Dr. Prasad’s lab
doing stochastic computational modeling of thymic
selection. After undergrad I did a post-bachelors
research rotation at the University of North
Carolina Chapel Hill in association with the
Biophysical Society. At UNC I worked under Dr. Tim
Elston of the school of medicine working on CFD
models for microfluidic bioreactors. I was
accepted into the Master of Engineering Program in
2014 at CSU and worked once again with Dr. Prasad
focusing on image processing for a project
studying the relationship between metastatic
potential and cell shape. Currently, I am on track
to complete my Masters in Mechanical Engineering
May of 2016 and will continue in the PhD program
in the SBME collaboratively in the labs of Dr.
Dan Gustafson and Dr. Prasad. My
research interest includes developing
computational models and methods to guide
experimental research and personalized medicine in
Oncology and the study of cancer. Being Colorado
born and raised I have a passion for the outdoors
and you can often find me exploring CO trails from
the saddle of my mountain bike or kayaking the
great whitewater Colorado has to offer.
Undergraduate
Students
Kyle
Hartson
I am a fifth year student in CSU's dual degree
program, graduating in May 2016 with a BS in
Biomedical Engineering, a BS in Mechanical
Engineering, and a minor in Physics. My research
has focused on programming stochastic simulations
of biological processes using a program called
Netlogo, and helping to integrate these teaching
tools in classrooms across the Poudre Valley
School District. I grew up in northwest Indiana,
and came to Colorado for the beautiful
surroundings; thus, in my spare time I enjoy
activities such as hiking, fishing, golfing, and
snowboarding. Upon graduation, I hope to begin my
career as an engineer with a medical device
company.
Jordan Castle
Jordan is a Biology major who has been working in
the Prasad lab for over two years. She works with
cell culture and imaging of cancer cell lines.
Jacqueline Foss
Jacqueline Foss is studying to achieve a BS in
Mechanical Engineering and a BS in Biomedical
Engineering by May, 2019. She works as an
Undergraduate Research Assistant at Colorado State
University in both a Cell Lab as well as a
Biomaterials Lab. In her limited spare time, she
loves to cook/bake, and loves to spend time with
her friends and family whenever possible.
Previous
Group Members
Dustin
Robert Berger, M.S. SBME (2009-11) I have a love for
all things fun, a passion to ride both concrete
and snow, and a desire to learn and share my
knowledge.The
mountains of Colorado have provided me with ample
opportunities to pursue my fondness for
snowboarding while being close enough to the
Colorado State mothership to allow me the best of
educational experiences around. I am currently
researching the differentiation potential of
marrow stromal cells and the various cues, both
mechanical and chemical, which signal for these
cellular changes to occur. This work involves
several different areas of study including DNA
microarray analysis, computational modeling of
growth factor signaling pathways, and in vitro
differentiation studies of MSCs on surfaces with
diverse nanotopographies. It is my goal to help
unravel the mysteries of the stem cell’s ability
to sense its surroundings and react accordingly.
Colorado State University has provided an ideal
environment for two of the most important things
in my life, learning and enjoyment.
Postdoc Vladimir Montealegre (2010-11)
Ph.D. Physics, Univ. of South Carolina I obtained my Ph.D. in physics from the
University of South Carolina in 2008, worked on
research in the field of complex networks. My
background is interdisciplinary as I also hold an
M.B.A (2002, used the back propagation algorithm to
study the behavior of market agents in an industrial
sector) and former experience working in risk
management (2001-2004). I got my Bachelor of Science
in Physics (1999) from the Universidad de los Andes
in Colombia (South America).
My Ph.D. research used methods of generalized mutual
entropy and dynamical clustering to study the
structure of complex networks. These tools were used
to provide approaches to identify potential
vulnerabilities in networks and to depict their
dynamics. My doctoral research introduced me to the
fascinating field of computational biology in which
I have found very interesting problems which can be
approached and solved efficiently using computer
simulations, stochastic models and complex network
representations; all this well aligned with my
background and goals.