"Science is a lot like an onion: you discover truth with each new layer, and you cry throughout the whole process."
I'm a PhD student in the Biological Sciences department at CarnegieMellon University, studying proteomics. I enjoy solving complex problems that have practical implications, and have found CMU to be a great fit.
Complex problem #1 (undergrad, 2005-2007): predict the spread of an invasive species
I came to the University of
Washington intending to study Computer Science. When my scholarship ended, I worked as a programmer
for the medical library and later, a sysadmin to pay for tuition. I
gradually became more interested in biology than algorithms and instead pursued ecology and physiology. My thesis
project in ecology predicted the spread of nutria
(Myocastor coypus,
common names coypu and nutria), an invasive species then-recently sighted in Seattle.
I developed some web-based tools to collect public sightings, developed a simple model
to predict spread using vegetation cover, and generated a range map in GIS. The UW administration took us seriously enough to factor
our results in their pest control plans. This work was funded by the Wildlife Society, and
was covered by the Seattle Post-Intelligencer and the
Daily, the UW student newspaper. I also worked for the US Forest
Service on the Colville
National Forest as a Wildlife Biologist trainee for two summers.
Complex problem #2 (post-bac, 2007-2009): infer molecular biology from high-throughput data
The statistical and programming skills I gained at UW brought me first an
internship, then a job at the Institute for Systems Biology.
The lab I worked in had a huge amount of gene and protein expression data for
Halobacterium, an extremophilic archaeon. For the proteomic data
I developed some tools that identified proteotypic peptides (protein fragments that are likely to be detected). For the gene expression data
I worked on an algorithm that found physiologically-relevant co-expression patterns. For more details on these projects, see Publications below.
I also have a secondary interest in public health and along the way got involved with research on cancer among Native American populations at the Center for Clinical and Epidemiological Research.
Complex problem #3 (doctoral work, 2009- ): proteomics
Stay tuned...
Publications
- Kaur A, Van PT, Busch C, Robinson C, Pan M, Pang WL, Reiss D, DiRuggiero J, and Baliga NS. Coordination of frontline defense mechanisms under severe oxidative stress. Molecular Systems Biology. 6:393 2010 [PubMed: 20664639]
- Koide T, Reiss DJ, Bare CJ, Pang WL, Facciotti, MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo F-Y, Deutsch E, Peterson A, Martin D, and Baliga NS. Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular Systems Biology. 5:285 2009 [PubMed: 19536208]
- Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti M, Deutsch E, Reiss D, Mallick P, and Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics. Journal of Proteome Research. 7(9):3755-3764 2008 [PubMed: 18652504]
- Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, and Baliga NS. Anatomy of microbial cell state transitions in response to oxygen. Genome Research. 17(10):1399-413. 2007 [PubMed: 17785531]
