Some Software

1. Secondary phenotypes for case-control genetic association studies: download the Fortran code here.

Reference: Xing, C., Dupuis, J., Cupples, L. A. Meigs, J. B., Lin, X., and Allen, A. S. Inverse-probability weighted estimating equations for analyzing secondary phenotypes in case-control genetic association studies.

2. Nonparametric Bayes Ensemble Learning (NBEL) algorithm for predicting protein-protein interactions: download the MATLAB code here to implement the NBEL algorithm.

Reference: Xing, C. and Dunson, D. B. Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. PLoS Comput Biol. 2011; 7(7):e1002110. PMID: 21829334.

3. Free Energy package to calculate the free energy between a short sequence and a DNA sequence by finding the optimal secondary structure between them: download the package here.

References:

• Xing, C.*, Bitzer, D. L., and Alexander, W. E., Vouk, M. A., and Stomp A-M. Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation. Nucleic Acids Res. 2009; 37(2):591-601.
• Xing, C., Bitzer D. L., Alexander, W. E., Stomp, A. M., Vouk, M. A. Free energy analysis on the coding region of the individual genes of Saccharomyces cerevisiae. Conf Proc IEEE Eng Med Biol Soc. 2006; 4225-4228.
• Xing, C., Mishra, M., Vu, S. K., Alexander, W. E., Bitzer, D. L., and Vouk, M. A. Free energy based analysis of the coding region of Saccharomyces cerevisiae. Technology for Life: North Carolina Symposium on Biotechnology and Bioinformatics. 2004; 25-27.