Related papers: Bipartite Community Structure of eQTLs
Bipartite networks are a natural representation of the interactions between entities from two different types. The organization (or topology) of such networks gives insight to understand the systems they describe as a whole. Here, we rely…
Genome-Wide Association Studies (GWAS) offer an exciting and promising new research avenue for finding genes for complex diseases. Traditional case-control and cohort studies offer many advantages for such designs. Family-based association…
Identifying mutations of SARS-CoV-2 strains associated with their phenotypic changes is critical for pandemic prediction and prevention. We compared an explainable convolutional neural network (CNN) approach and the traditional genome-wide…
The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in…
Biological and social systems consist of myriad interacting units. The interactions can be represented in the form of a graph or network. Measurements of these graphs can reveal the underlying structure of these interactions, which provides…
From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on genetic variations at the DNA base pair level, called Single-Nucleotide Polymorphisms (SNPs), collected from the Ontario Heart…
Genome-wide association studies (GWAS) have achieved great success in the genetic study of Alzheimer's disease (AD). Collaborative imaging genetics studies across different research institutions show the effectiveness of detecting genetic…
Unraveling the interplay between connectivity and spatio-temporal dynamics in neuronal networks is a key step to advance our understanding of neuronal information processing. Here we investigate how particular features of network…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
We aim to learn the functional co-response group: a group of taxa whose co-response effect (the representative characteristic of the group showing the total topological abundance of taxa) co-responds (associates well statistically) to a…
This report relates to a study group hosted by the EPSRC funded network, Integrating data-driven BIOphysical models into REspiratory MEdicine (BIOREME), and supported by SofTMech and Innovate UK, Business Connect. This report summarises the…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Statistical shape modeling (SSM) is a valuable and powerful tool to generate a detailed representation of complex anatomy that enables quantitative analysis and the comparison of shapes and their variations. SSM applies mathematics,…
Background: Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusing on intermediate…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain…
Single nucleotide polymorphisms (SNPs) are variations at specific locations in DNA. Sequence responsible for marking genes associated with diseases or tracking inherited diseases within The family. These variations in the Rb1 gene can cause…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Objective: In recent years, the functional connectivity of the human brain has been studied with graph theoretical tools. One such approach is community detection which is fundamental for uncovering the localized networks. Existing methods…