Related papers: Bipartite Community Structure of eQTLs
We introduce a quantitative measure of network bipartivity as a proportion of even to total number of closed walks in the network. Spectral graph theory is used to quantify how close to bipartite a network is and the extent to which…
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or…
Genetic association analyses often involve data from multiple potentially-heterogeneous subgroups. The expected amount of heterogeneity can vary from modest (e.g., a typical meta-analysis) to large (e.g., a strong gene--environment…
An expression quantitative trait locus (eQTL) is a chromosomal region where genetic variants are associated with the expression levels of certain genes that can be both nearby or distant. The identifications of eQTLs for different tissues,…
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or…
To date, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants among a variety of traits/diseases, shedding a light on the genetic architecture of complex diseases. Polygenicity of complex…
Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In simple cases, single polymorphic loci explain a significant fraction of the phenotype variability. However, many traits of…
Motivation: Genome-wide association studies (GWAS) have successfully identified thousands of genetic risk loci for complex traits and diseases. Most of these GWAS loci lie in regulatory regions of the genome and the gene through which each…
Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes.…
This work introduces an integrative approach based on Q-analysis with machine learning. The new approach, called Neural Hypernetwork, has been applied to a case study of pulmonary embolism diagnosis. The objective of the application of…
Quantitative descriptions of network structure in big data can provide fundamental insights into the function of interconnected complex systems. Small-world structure, commonly diagnosed by high local clustering yet short average path…
We present a new method based on Functional Data Analysis (FDA) for detecting associations between one or more scalar covariates and a longitudinal response, while correcting for other variables. Our methods exploit the temporal structure…
Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, together with other important features, such as small size, short generation time, small genome…
In genome wide association studies (GWAS), researchers are often dealing with non-normally distributed traits or a mixture of discrete-continuous traits. However, most of the current region-based methods rely on multivariate linear mixed…
Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…
Population analyses of functional connectivity have provided a rich understanding of how brain function differs across time, individual, and cognitive task. An important but challenging task in such population analyses is the identification…
We introduce a mapping between graphs and pure quantum bipartite states and show that the associated entanglement entropy conveys non-trivial information about the structure of the graph. Our primary goal is to investigate the family of…
Useful information about scientific collaboration structures and patterns can be inferred from computer databases of published papers. The genetic programming bibliography is the most complete reference of papers on GP\@. In addition to…
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…
Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding…