SecureMA: protecting participant privacy in genetic association meta-analysis.

Xie W, Kantarcioglu M, Bush WS, Crawford D, Denny JC, Heatherly R, Malin BA,. Sharing genomic data is crucial to support scientific investigation such as genome-wide association studies. However, recent investigations suggest the privacy of the individual participants in these studies can be compromised, leading to serious concerns and consequences, such as overly restricted access […]

SecureMA: protecting participant privacy in genetic association meta-analysis.

Sharing genomic data is crucial to support scientific investigation such as genome-wide association studies. However, recent investigations suggest the privacy of the individual participants in these studies can be compromised, leading to serious concerns and consequences, such as overly restricted access to data.We introduce a novel cryptographic strategy to securely perform meta-analysis for genetic association […]

Automated quantification of pancreatic β-cell mass.

β-Cell mass is a parameter commonly measured in studies of islet biology and diabetes. However, the rigorous quantification of pancreatic β-cell mass using conventional histological methods is a time-consuming process. Rapidly evolving virtual slide technology with high-resolution slide scanners and newly developed image analysis tools has the potential to transform β-cell mass measurement. To test […]

Automated quantification of pancreatic β-cell mass.

Golson ML, Bush WS, Brissova M,. β-Cell mass is a parameter commonly measured in studies of islet biology and diabetes. However, the rigorous quantification of pancreatic β-cell mass using conventional histological methods is a time-consuming process. Rapidly evolving virtual slide technology with high-resolution slide scanners and newly developed image analysis tools has the potential to […]

Genome simulation approaches for synthesizing in silico datasets for human genomics.

Ritchie MD, Bush WS,. Simulated data is a necessary first step in the evaluation of new analytic methods because in simulated data the true effects are known. To successfully develop novel statistical and computational methods for genetic analysis, it is vital to simulate datasets consisting of single nucleotide polymorphisms (SNPs) spread throughout the genome at […]

Genome simulation approaches for synthesizing in silico datasets for human genomics.

Simulated data is a necessary first step in the evaluation of new analytic methods because in simulated data the true effects are known. To successfully develop novel statistical and computational methods for genetic analysis, it is vital to simulate datasets consisting of single nucleotide polymorphisms (SNPs) spread throughout the genome at a density similar to […]

Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus.

Often in human genetic analysis, multiple tables of single nucleotide polymorphism (SNP) statistics are shown alongside a Haploview style correlation plot. Readers are then asked to make inferences that incorporate knowledge across these multiple sets of results. To better facilitate a collective understanding of all available data, we developed a Ruby-based web application, LD-Plus, to […]

Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus.

Bush WS, Dudek SM, Ritchie MD,. Often in human genetic analysis, multiple tables of single nucleotide polymorphism (SNP) statistics are shown alongside a Haploview style correlation plot. Readers are then asked to make inferences that incorporate knowledge across these multiple sets of results. To better facilitate a collective understanding of all available data, we developed […]

Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions.

Parallel multifactor dimensionality reduction is a tool for large-scale analysis of gene-gene and gene-environment interactions. The MDR algorithm was redesigned to allow an unlimited number of study subjects, total variables and variable states, and to remove restrictions on the order of interactions being analyzed. In addition, the algorithm is markedly more efficient, with approximately 150-fold […]