John Vries

John K. Vries, MD
Associate Professor

M.D., University of California San Francisco

Phone: (412) 383-9146

Research Summary

Asymmetry in the distribution of attributes along biological sequences generates signals with characteristic frequency and phase spectra. Asymmetry in the distribution of contacts in 3-dimensional models also generates signals with characteristic spectra. In some cases, these spectra are correlated. My research attempts to predict tertiary structure from these correlations. The long term goal is go develop an alignment-independent method for protein classification. The methodologies employed include n-gram analysis, Fourier analysis, eigenfunction decomposition and all poles spectral density estimation. In related research, correlations between the periodicity of pairwise relationships in molecular dynamics simulations and the results of Gaussian network analysis are compared.

Recent Publications

Lui VW, Peyser ND, Ng PK, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway LA, Mills GB, Johnson DE, Grandis JR (2014) Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer Proc Natl Acad Sci U S A 111(3):1114-1119.

Vries JK, Liu X. (2008) “Subfamily specific conservation profiles for proteins based on n-gram patterns” BMC Bioinformatics 9, 72. [JIF: 3.493]

Vries, J.K., Liu, X., and Bahar, I. (2007) “Relationship between n-gram patterns and secondary structure” Proteins-Structure Function and Bioinformatics 68, 830-838. [JIF: 3.73]