List of Software

  1. OmicShare
  2. Linkage Disequilibrium (LD) Mapping
  3. Genome-wide Association Studies
  1. OmicShare [top]
    2. OmicShare is a collaborative work environment that enables scientists to easily store, manage and share all types of instrumental and analytical data files for project management in biomedical research.  It facilitates research collaboration and reduces the risk of data loss.  OmicShare has a user friendly interface accessed through an Internet browser.  Data files are uploaded to the system underlying a robust database (The database can be any one of the relational databases, such as Oracle, MySQL, PostgreSQL, etc.) by selecting, coping, or simple drag-and-drop files.  OmicShare allows users to upload/download multiple subfolders and files by a simple click.  Folders or files can be granted different permissions to other collaborators by the data supplier or system administrator.  OmicShare allows users to share files with collaborators quickly, easily, and professionally.   Users can securely and quickly navigate to the projects in which they are involved to communicate with other collaborators inside and outside their organizations, upload/download single or multiple data file(s) by one click, as well as download analyses.  Click here to evalute the software.
  2. Linkage Disequilibrium (LD) Mapping [top]
    3. Identifying multiple loci LD patterns are important for population genetic research and gene-disease association mapping.  A new statistical method is developed to measure the complexity of higher order LD structures among multiple single nucleotide polymorphisms (SNPs) on a dense map.  Derived from a multiple order Markov Chain model, this approach uses the order of Markov Chain as a quantity to estimate the order of LD and summarize general LD structures along the chromosomes.  Based on the method, complicated LD structures can be decomposed into multiple constraints, with each interpreted as functions of conventional LD parameters.  The tool is able to scan the available HapMap whole-genome data and ENCODE data very effectively to get the higher order LD patterns.
  3. Genome-wide Association Studies [top]
    4. Whole-genome association studies of major determinants for host control of HIV-1: A tool is developed for analyzing single-marker genotype trend tests of quality control (QC) - passed SNPs, using linear regression and generalized linear models.  Analyses incorporating HLA (Human Leukocyte Antigen) typing was carried out on 1,400 patients with available 4-digit HLA Class I allelic determination.  It assesses significance with a Bonferroni correction.  Eight independently acting SNPs were identified by the analyses.