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Bioinformatics Experience at Zacharewski Laboratory
My work at the Zacharewski lab involves both wet lab and in
silico work. In the lab, I have worked on expanding our mouse
array using the National Institute of Aging's 15K mouse clone
set under the direction of Darrell
Boverhof. This includes determining which clones would be
valuable additions to the array, cherrypicking them, growing
them up, PCR amplification, and subsequent purification of the
PCR product for spotting on the array. I also worked on some
quality control measures for microarray spotting, such as determining
the optimal spotting solution to be used on a new type of slide.
My work in silico deals with what I love best - bioinformatics!
Under Lyle Burgoon's guidance,
I have worked on the development and maintenance of dbZach,
our in-house toxicogenomic database which runs on Oracle 9i.
I have also written several Perl scripts as ad hocs for members
of the lab which retrieve information from dbZach and NCBI websites.
The last portion of my bioinformatics work is the development
of Java interfaces, which provide a very user-friendly means
of mining the valuable data within dbZach.
The first interface I developed was the Gene Annotation Tool,
which allows the user to receive gene annotation information
(such as UniGene cluster, official gene names, etc.) for a list
of clones. It also generates a histogram of Gene Ontology number
frequencies, which lets the user visualize which functions are
common within the list of clones they submitted. This is useful
if the list of clones is a cluster found to have similar expression
patterns in a microarray experiment; the similar expression
patterns can possibly be linked to a common function.
Another one of my interfaces is the Real-Time PCR Interface,
which allows the user to: 1) input primers for a Real-Time PCR
experiment into dbZach, 2) query existing primers, 3) input
experimental data into dbZach, 4) retrieve past experimental
data.
Finally, I will work on developing a Pathway Subsystem within
dbZach, which will maintain data on biological pathways, including
toxins/chemicals which interact with a pathway, target-effector
relationships, and subcellular locations of these interactions.
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