About Korf Lab

Contact

plott@ucdavis.edu

Paul Lott

Genetics Graduate Student

Biography

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.

Research Interests

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:

  • StochHMM - flexible hidden Markov model framework in C++ (code.google.com/p/stochhmm)
  • Mod3 - Metagenomics gene finder
  • Sickle - Informed gene predictions
  • SkewR - R-Loop prediction in Human genome (Paul Ginno, Frederic Chedin Lab, UC Davis)
  • Methylation Domains Prediction (Diane Schroeder, Janine LaSalle Lab, UC Davis)
  • Trellis - HMM to integrate diverse data sources
  • More coming soon!!!

Publications

  • 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

Korf Lab in the news

Dec 10, 2013: A short piece in the UC Davis Alumni Magazine that discusses the new Genomics undergraduate major that Ian Korf co-developed.


Nov 26, 2013: Ian Korf writes a News & Views piece for Nature Methods about two new comparisons of programs that work with RNA-seq data


Nov 1, 2013: Keith B. and Kristen are both featured in a piece on Inquiring Minds as part of the new One UC Davis campaign.


Nov 1, 2013: Kristen made a list of the Top 10 moments of the IMGC symposium for the SPLASH! newsletter


Oct 1, 2013: The new paper by Lemay et al., was featured in This Week in PLOS by Genome Web.


Sep 24, 2013: An article on genome assembly by My Science Work includes an interview with Keith Bradnam about Assemblathon 2 & 3.


Aug 12, 2013: Biome Magazine includes a piece that features Ian Korf discussing a novel platform for bioinformatics education (with Daniel Barker)


Aug 8, 2013: Biome, the online magazine for BioMed Central, features an extensive Q&A with Keith Bradnam about the Assemblathon 2 paper.


Jul 22, 2013: The News blog at Nature.com writes about the Assemblathon 2 paper.

More news

Contact Us

For questions or comments about the website, please e-mail:

korflab AT ucdavis DOT edu

Contact information for specific members of our lab can be found on their personal pages.