Related papers: Bipartite Community Structure of eQTLs
Signed networks are such social networks having both positive and negative links. A lot of theories and algorithms have been developed to model such networks (e.g., balance theory). However, previous work mainly focuses on the unipartite…
Introduction: The HAS conducted a study in 2018 using the French National Health Data System (SNDS) on the care pathway of patients with epilepsy. This study used 2 algorithms to identify patients with epilepsy, based on hospitalization for…
Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine…
Motivated by empirical arguments that are well-known from the genome-wide association studies (GWAS) literature, we study the statistical properties of linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of LMMs to…
Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to, among other reasons, the high-dimensional multivariate nature of gene-expression traits. Next to the expression heterogeneity produced by…
It has been observed that mutualistic bipartite networks have a nested structure of interactions. In addition, the degree distributions associated with the two guilds involved in such networks (e.g. plants & pollinators or plants & seed…
Small-World Networks (SWNs) represent a fundamental model for the comprehension of many complex man-made and biological networks. In the central nervous system, SWN models have been shown to fit well both anatomical and functional maps at…
Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to a deeper understanding of microbial pathogenesis. We have considered all complete SARS-CoV-2 genomes…
Genome-wide association studies (GWASs) have been extensively adopted to depict the underlying genetic architecture of complex diseases. Motivated by GWASs' limitations in identifying small effect loci to understand complex traits'…
In bipartite networks, community structures are restricted to being disassortative, in that nodes of one type are grouped according to common patterns of connection with nodes of the other type. This makes the stochastic block model (SBM),…
Community detection in citation networks offers a powerful approach to understanding knowledge flow and identifying core research areas within academic disciplines. This study focuses on knowledge source discovery in statistics by analyzing…
Determining the functional structure of biological networks is a central goal of systems biology. One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to…
Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct…
The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However,…
Node role explainability in complex networks is very difficult, yet is crucial in different application domains such as social science, neurosciences or computer science. Many efforts have been made on the quantification of hubs revealing…
Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…
In modern scientific studies, it is often imperative to determine whether a set of phenotypes is affected by a single factor. If such an influence is identified, it becomes essential to discern whether this effect is contingent upon…
Since the emergence of genome-wide association studies (GWASs), estimation of the narrow sense heritability explained by common single-nucleotide polymorphisms (SNPs) via linear mixed model approaches became widely used. As in most GWASs,…
Several approaches have been recently proposed for community search in bipartite graphs. These methods have shown promising results in identifying communities in real-world bipartite networks, such as social and biological networks. Given a…
Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the…