Colleagues, I have a cool project for a motivated student. You may know
that in general it is extremely hard to estimate how quickly bacteria,
especially Mycobacterium tubeculosis (Mtb, causative agent of
tuberculosis in humans) replicates. We have been testing the idea that
sequencing bacterial genomes from bacterial cultures, grown in different
conditions, may provide some information about the rates of Mtb
division. My collaborators generated novel data on Mtb grown in vitro at
different rates and sequenced genomes of the bacteria. I have developed
an R code to map reads from the sequencing data to the Mtb genome and
thus, to determine if there is an enrichment of the DNA near the origin
of replication (spoiler alert: yes, there is but only for rapidly
dividing cells). I would like to recruit a talented and motivated
student to move this project further. It will involve learning basics of
DNA sequencing data analysis, how biases in DNA sequencing data can be
mitigated, and developing mathematical models of bacterial genome
duplication (to connect sequencing data and Mtb growth kinetics).
The project will require some basic programming skills (in R or
similar), knowledge of sequencing data analysis (or willingness to learn
those), and knowledge about mathematical modeling.
If this project sounds interesting or if you have any additional
questions, please contact me at [log in to unmask]
Vitaly
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Vitaly V. Ganusov
Associate Professor
1311 Cumberland Avenue
307 Ken and Blaire Mossman Building
Department of Microbiology
Department of Mathematics
University of Tennessee
Knoxville, TN 37996-1937
USA
Phone: +1 865 974-4547
FAX: +1 865 974-4007
http://ganusovlab.utk.edu
“So long as man remains free he strives for nothing more so incessantly
and so painfully as to find something to worship.“ Feodor Dostoevsky
“It is impossible to speak in such a way that you cannot be
misunderstood.” Karl Popper
“Science may be described as the art of systematic over-simplification.”
Karl Popper
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