Related papers: A fast algorithm for detecting gene-gene interacti…
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits and diseases, and a key question is how much heritability could be explained by all variants in GWAS. One widely used approach that…
Linkage disequilibrium score regression (LDSC) has emerged as an essential tool for genetic and genomic analyses of complex traits, utilizing high-dimensional data derived from genome-wide association studies (GWAS). LDSC computes the…
Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational…
Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions.…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
Molecular phenotyping by gene expression profiling is common in contemporary cancer research and in molecular diagnostics. However, molecular profiling remains costly and resource intense to implement, and is just starting to be introduced…
Here we propose a test to detect effects of single nucleotide polymorphisms (SNPs) on a quantitative trait. Significant SNP-SNP interactions are more difficult to detect than significant SNPs, partly due to the massive amount of SNP-SNP…
In Genome-Wide Association Studies (GWAS) where multiple correlated traits have been measured on participants, a joint analysis strategy, whereby the traits are analyzed jointly, can improve statistical power over a single-trait analysis…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
The standard paradigm for the analysis of genome-wide association studies involves carrying out association tests at both typed and imputed SNPs. These methods will not be optimal for detecting the signal of association at SNPs that are not…
Recently more and more evidence suggests that rare variants with much lower minor allele frequencies play significant roles in disease etiology. Advances in next-generation sequencing technologies will lead to many more rare variants…
Genome Wide Association Studies (GWAS) and eQTL analyses have produced a large and growing number of genetic associations linked to a wide range of human phenotypes. As of 2013, there were more than 11,000 SNPs associated with a trait as…
High resolution microarrays and second-generation sequencing platforms are powerful tools to investigate genome-wide alterations in DNA copy number, methylation and gene expression associated with a disease. An integrated genomic profiling…
For complex diseases, the interactions between genetic and environmental risk factors can have important implications beyond the main effects. Many of the existing interaction analyses conduct marginal analysis and cannot accommodate the…
In genetics it is often of interest to discover single nucleotide polymorphisms (SNPs) that are directly related to a disease, rather than just being associated with it. Few methods exist, however, addressing this so-called `true sparsity…
Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousands…
In this paper we consider the problem of learning the genetic-interaction-map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double knockout (DK) data. Based on a set of well established biological…
Polygnicity refers to the phenomenon that multiple genetic variants have a non-zero effect on a complex trait. It is defined as the proportion of genetic variants that have a nonzero effect on the trait. Evaluation of polygenicity can…
Single-cell spatial transcriptomics (ST) offers a unique approach to measuring gene expression profiles and spatial cell locations simultaneously. However, most existing ST methods assume that cells in closer spatial proximity exhibit more…