相关论文: On the influence of several factors on pathway enr…

Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…

A bioinformatics platform is introduced aimed at identifying models of disease-specific pathways, as well as a set of network measures that can quantify changes in terms of global structure or single link disruptions.The approach integrates…

Many common diseases are highly polygenic, modulated by a large number genetic factors with small effects on susceptibility to disease. These small effects are difficult to map reliably in genetic association studies. To address this…

Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…

Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but…

Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…

Estimating the needs of healthcare products and inventory management are still challenging issues in hospitals nowadays. Centers are supposed to cope with tight budgets and patient satisfaction at the same time. Some issues can be tackled…

In virtual screening for drug discovery, hit enrichment curves are widely used to assess the performance of ranking algorithms with regard to their ability to identify early enrichment. Unfortunately, researchers almost never consider the…

The sequence of visits and procedures performed by the patient in the health system, also known as the patient's pathway or trajectory, can reveal important information about the clinical treatment adopted and the health service provided.…

Drawing reliable inferences from data involves many, sometimes arbitrary, decisions across phases of data collection, wrangling, and modeling. As different choices can lead to diverging conclusions, understanding how researchers make…

The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…

Factor analysis is a critical component of high dimensional biological data analysis. However, modern biological data contain two key features that irrevocably corrupt existing methods. First, these data, which include longitudinal,…

The biological roles of gene sets are used to group them into collections. These collections are often characterized by being high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation…

We present a framework consisting of three approaches that can enhance meta-analyses: 1) scoping reviews (evidence map), 2) bibliometrics, and 3) alternative impact metrics. These three "enrichment" approaches facilitate the research…

The proliferation of omics datasets in public repositories has created unprecedented opportunities for biomedical research but has also posed significant challenges for their integration, particularly due to missing genes and…

A prespecified set of genes may be enriched, to varying degrees, for genes that have altered expression levels relative to two or more states of a cell. Knowing the enrichment of gene sets defined by functional categories, such as gene…

Mediation analysis seeks to infer how much of the effect of an exposure on an outcome can be attributed to specific pathways via intermediate variables or mediators. This requires identification of so-called path-specific effects. These…

The rapid advancement and widespread adoption of machine learning-driven technologies have underscored the practical and ethical need for creating interpretable artificial intelligence systems. Feature importance, a method that assigns…

Path-specific effects are a broad class of mediated effects from an exposure to an outcome via one or more causal pathways with respect to some subset of intermediate variables. The majority of the literature concerning estimation of…