Before coming to UC Davis, I studied and worked at the University of Utah. During my undergraduate
career, I worked in Jean-Marc Lalouel's lab investigating genes associated with salt-sensitive hypertension
in C57BL/6 mice. While studying hypertension, I was able to delve in to the (what was then new) world of
computational microarray analysis, which really started me on the path to where I am today. After receiving
my B.Sc. in Biology, I was fortunate to work with Dr. Victoria Lawson studying mitochondrial fusion and
function in Charcot-Marie-Tooth neuropathy type 2A in patient fibroblasts.
I am currently a PhD Candidate in the Korf lab, where I am able to combine two passions. Genetics and
Computers. I'm currently to developing a flexible hidden Markov model framework called StochHMM.
StochHMM allows us to rapidly create and apply HMM models to make important predictions, while allowing
us to integrate varied data sources in our predictions. I've been blessed to be able to use StochHMM in
a couple past and ongoing collaborations. At the moment, I'm working feverishly to get StochHMM released
to the public, where I can then facilitate others in developing HMMs to further their own research.
Outside of the lab: Before moving to Davis, you could find me up in the mountains climbing and
biking every day after work. I enjoy spending time with my family, providing technical support for my
wife's law firm, and playing around with Arduinos.
Oh, if time were limitless ... In general, I am interested in developing and applying machine
learning tools to mine "omics" data. While interested in many facets of genetics and bioinformatics,
lack of time has currently limited me to the following:
Ginno, PA, Lott, P., Christensen, HC, Korf, I., and Chedin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Molecular Cell. 2012 Mar 30;45(6):814-25. Epub 2012 Mar 1
Schroeder, DI, Lott, P., Korf, I., and LaSalle JM. Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res. 2011 Oct;21(10):1583-91. Epub 2011 Jul 22.
Wang YZ, Yamagami T, Gan Q, Wang Y, Zhao T, Hamad S, Lott P, Schnittke N, Schwob JE, Zhou CJ. Canonical Wnt signaling promotes the proliferation and neurogenesis of peripheral olfactory stem cells during postnatal development and adult regeneration. J Cell Sci. 2011 May 1;124(Pt 9):1553-63. Epub 2011 Apr 12.
Gociman B, Rohrwasser A, Hillas E, Cheng T, Hunter G, Hunter J, Lott P, Monson S, Ying J, Lalouel JM. Response to genetic manipulations of liver angiotensinogen in the physiological range. J Hum Genet. 2008;53(9):775-88. Epub 2008 Jul 4.
Rohrwasser A, Lott P, Weiss RB, Lalouel JM. From genetics to mechanism of disease liability. Adv Genet. 2008;60:701-26. Review.
Amiott EA, Lott P, Soto J, Kang PB, McCaffery JM, DiMauro S, Abel ED, Flanigan KM, Lawson VH, Shaw JM. Mitochondrial fusion and function in Charcot-Marie-Tooth type 2A patient fibroblasts with mitofusin 2 mutations. Exp Neurol. 2008 May;211(1):115-27. Epub 2008 Jan 26.
Gociman B, Rohrwasser A, Lantelme P, Cheng T, Hunter G, Monson S, Hunter J, Hillas E, Lott P, Ishigami T, Lalouel JM. Expression of angiotensinogen in proximal tubule as a function of glomerular filtration rate. Kidney Int. 2004 Jun;65(6):2153-60.
About Korf Lab
Korflab in the news
Jan 28, 2013:A Haldane's Sieve Blog Post
by Keith Bradnam that discusses the Assemblathon 2 pre-print
Nov 12, 2012:a feature on Danielle Lemay
by the Calfifornia Dairy Research Foundation