A new framework for the selection of tag SNPs by multimarker haplotypes
Journal of Biomedical Informatics
International Journal of Computational Intelligence in Bioinformatics and Systems Biology
IEEE Transactions on Information Technology in Biomedicine - Special section on computational intelligence in medical systems
A Novel Method to Select Informative SNPs and Their Application in Genetic Association Studies
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multiple ant colony algorithm method for selecting tag SNPs
Journal of Biomedical Informatics
A hybrid Lagrangean heuristic with GRASP and path-relinking for set k-covering
Computers and Operations Research
Hi-index | 3.84 |
Motivation: Recent studies have shown that a small subset of Single Nucleotide Polymorphisms (SNPs) (called tag SNPs) is sufficient to capture the haplotype patterns in a high linkage disequilibrium region. To find the minimum set of tag SNPs, exact algorithms for finding the optimal solution could take exponential time. On the other hand, approximation algorithms are more efficient but may fail to find the optimal solution. Results: We propose a hybrid method that combines the ideas of the branch-and-bound method and the greedy algorithm. This method explores larger solution space to obtain a better solution than a traditional greedy algorithm. It also allows the user to adjust the efficiency of the program and quality of solutions. This algorithm has been implemented and tested on a variety of simulated and biological data. The experimental results indicate that our program can find better solutions than previous methods. This approach is quite general since it can be used to adapt other greedy algorithms to solve their corresponding problems. Availability: The program is available upon request. Contact: kmchao@csie.ntu.edu.tw